diff --git a/.badgery.yaml b/.badgery.yaml new file mode 100644 index 0000000..99bcdc1 --- /dev/null +++ b/.badgery.yaml @@ -0,0 +1,72 @@ +default_branch: master +develop_branch: develop + +cards: + - group: Tests + type: gh_action + title: Code/package tests (GitHub) + file: test.yml + enabled: true + - group: Tests + type: gh_action + title: Tutorial tests (GitHub) + file: tutorial-tests.yml + enabled: true + + - group: Tests + type: gh_action + title: Package tests (PyPI) + file: pypi-test.yml + enabled: true + + - group: Code Quality + type: codefactor + title: Code quality (CodeFactor) + enabled: true + + - group: Code Quality + type: radon_mi + title: Maintainability index (radon) + report: reports/{branch}/maintainability-index.json + enabled: true + + - group: Code Quality + type: radon_cc + title: Cyclomatic complexity (radon) + report: reports/{branch}/cyclomatic-complexity.json + enabled: true + + - group: Size + type: radon_loc + title: Source/Logical lines of code (radon) + report: reports/{branch}/raw-metrics.json + enabled: true + + - group: Size + type: radon_ff + title: Functions/Files count (radon) + report: reports/{branch}/cyclomatic-complexity.json + enabled: true + + - group: Coverage + type: codecov + title: Unit test coverage (Codecov) + flag: unittests + enabled: true + + - group: Coverage + type: interrogate + title: Docstring coverage (interrogate) + report: reports/{branch}/coverage-docstring.txt + enabled: true + - group: Build & Release + type: gh_action + title: Publishing (PyPI) + workflow: pypi-publish.yml + enabled: true + + - group: Build & Release + type: gh_action + title: Docs build/deployment + workflow: docs.yml + enabled: true diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 0000000..40872be --- /dev/null +++ b/.codecov.yml @@ -0,0 +1,27 @@ +# Codecov configuration +# https://docs.codecov.com/docs/codecov-yaml + +github_checks: + annotations: true + +comment: + layout: 'reach, diff, flags, files' + behavior: default + require_changes: false + require_base: false + require_head: true + +coverage: + status: + project: + default: + target: 80% + threshold: 0% + # require project coverage, don't allow wiggle room. + informational: false + patch: + default: + target: 80% + threshold: 5% + # Make patch coverage informational (won't block PR) + informational: true diff --git a/.copier-answers.yml b/.copier-answers.yml index 01349b0..92b8e27 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,11 +1,27 @@ -# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY -_commit: e4625c1 -_src_path: gh:/EasyScience/EasyProjectTemplate -description: Python package for bragg-edge analysis -max_python: '3.12' -min_python: '3.9' -orgname: EasyScience -packagename: easyimaging -prettyname: Easyimaging -projectname: EasyImaging -year: 2024 +# WARNING: Do not edit this file manually. +# Any changes will be overwritten by Copier. +_commit: v0.11.4 +_src_path: gh:easyscience/templates +app_docs_url: https://easyscience.github.io/imaging-app +app_doi: 10.5281/zenodo.18163581 +app_package_name: easyimaging_app +app_python: '3.13' +app_repo_name: imaging-app +home_page_url: https://easyscience.github.io/imaging +home_repo_name: imaging +lib_docs_url: https://easyscience.github.io/imaging-lib +lib_doi: 10.5281/zenodo.18163581 +lib_package_name: easyimaging +lib_python_max: '3.13' +lib_python_min: '3.11' +lib_repo_name: imaging-lib +project_contact_email: support@easyscience.org +project_copyright_years: 2024-2026 +project_extended_description: A software for performing Bragg-edge calculations based + on a crystalliographic model and refining its parameters against experimental + data +project_name: EasyImaging +project_short_description: Neutron imaging data analysis +project_shortcut: EI +project_type: both +template_type: lib diff --git a/.github/actions/download-artifact/action.yml b/.github/actions/download-artifact/action.yml new file mode 100644 index 0000000..d1fff1a --- /dev/null +++ b/.github/actions/download-artifact/action.yml @@ -0,0 +1,50 @@ +name: 'Download artifact' +description: 'Wrapper for actions/download-artifact' +inputs: + name: + description: 'Name of the artifact to download' + required: true + + path: + description: 'Destination path' + required: false + default: '.' + + pattern: + description: 'Glob pattern to match artifact names (optional)' + required: false + default: '' + + merge-multiple: + description: 'Merge multiple artifacts into the same directory' + required: false + default: 'false' + + github-token: + description: 'GitHub token for cross-repo download (optional)' + required: false + default: '' + + repository: + description: 'owner/repo for cross-repo download (optional)' + required: false + default: '' + + run-id: + description: 'Workflow run ID for cross-run download (optional)' + required: false + default: '' + +runs: + using: 'composite' + steps: + - name: Download artifact + uses: actions/download-artifact@v8 + with: + name: ${{ inputs.name }} + path: ${{ inputs.path }} + pattern: ${{ inputs.pattern }} + merge-multiple: ${{ inputs.merge-multiple }} + github-token: ${{ inputs.github-token }} + repository: ${{ inputs.repository }} + run-id: ${{ inputs.run-id }} diff --git a/.github/actions/github-script/action.yml b/.github/actions/github-script/action.yml new file mode 100644 index 0000000..50de89b --- /dev/null +++ b/.github/actions/github-script/action.yml @@ -0,0 +1,19 @@ +name: 'GitHub Script' +description: 'Wrapper for actions/github-script' +inputs: + script: + description: 'JavaScript to run' + required: true + + github-token: + description: 'GitHub token (defaults to github.token)' + required: false + default: ${{ github.token }} + +runs: + using: 'composite' + steps: + - uses: actions/github-script@v9 + with: + script: ${{ inputs.script }} + github-token: ${{ inputs.github-token }} diff --git a/.github/actions/setup-easyscience-bot/action.yml b/.github/actions/setup-easyscience-bot/action.yml new file mode 100644 index 0000000..e51eb01 --- /dev/null +++ b/.github/actions/setup-easyscience-bot/action.yml @@ -0,0 +1,40 @@ +name: 'Setup EasyScience bot for pushing' +description: 'Create GitHub App token and configure git identity + origin remote' +inputs: + app-id: + description: 'GitHub App ID' + required: true + private-key: + description: 'GitHub App private key (PEM)' + required: true + repositories: + description: 'Additional repositories to grant access to (newline-separated)' + required: false + default: '' + +outputs: + token: + description: 'Installation access token' + value: ${{ steps.app-token.outputs.token }} + +runs: + using: 'composite' + steps: + - name: Create GitHub App installation token + id: app-token + uses: actions/create-github-app-token@v3 + with: + client-id: ${{ inputs.app-id }} + private-key: ${{ inputs.private-key }} + repositories: ${{ inputs.repositories }} + + - name: Configure git for pushing + shell: bash + run: | + git config user.name "easyscience[bot]" + git config user.email "${{ inputs.app-id }}+easyscience[bot]@users.noreply.github.com" + + - name: Configure origin remote to use the bot token + shell: bash + run: | + git remote set-url origin https://x-access-token:${{ steps.app-token.outputs.token }}@github.com/${{ github.repository }}.git diff --git a/.github/actions/setup-pixi/action.yml b/.github/actions/setup-pixi/action.yml index 8c68f51..dc3232c 100644 --- a/.github/actions/setup-pixi/action.yml +++ b/.github/actions/setup-pixi/action.yml @@ -1,16 +1,24 @@ name: 'Setup Pixi Environment' -description: 'Sets up pixi with common configuration' +description: 'Wrapper for prefix-dev/setup-pixi' inputs: environments: description: 'Pixi environments to setup' required: false - default: 'dev' + default: 'default' activate-environment: description: 'Environment to activate' required: false - default: 'dev' + default: 'default' run-install: - description: 'Whether to run install' + description: 'Whether to run pixi install' + required: false + default: 'true' + locked: + description: 'Whether to run pixi install --locked' + required: false + default: 'false' + frozen: + description: 'Whether to run pixi install --frozen' required: false default: 'true' cache: @@ -25,10 +33,12 @@ inputs: runs: using: 'composite' steps: - - uses: prefix-dev/setup-pixi@v0.9.0 + - uses: prefix-dev/setup-pixi@v0.9.5 with: environments: ${{ inputs.environments }} activate-environment: ${{ inputs.activate-environment }} run-install: ${{ inputs.run-install }} + locked: ${{ inputs.locked }} + frozen: ${{ inputs.frozen }} cache: ${{ inputs.cache }} - post-cleanup: ${{ inputs.post-cleanup }} \ No newline at end of file + post-cleanup: ${{ inputs.post-cleanup }} diff --git a/.github/actions/upload-artifact/action.yml b/.github/actions/upload-artifact/action.yml new file mode 100644 index 0000000..fe8e468 --- /dev/null +++ b/.github/actions/upload-artifact/action.yml @@ -0,0 +1,49 @@ +name: 'Upload artifact' +description: 'Wrapper for actions/upload-artifact' +inputs: + name: + description: 'Artifact name' + required: true + + path: + description: 'File(s)/dir(s)/glob(s) to upload (newline-separated)' + required: true + + include-hidden-files: + description: 'Include hidden files' + required: false + default: 'true' + + if-no-files-found: + description: 'warn | error | ignore' + required: false + default: 'error' + + compression-level: + description: '0-9 (0 = no compression)' + required: false + default: '0' + + retention-days: + description: 'Retention in days (optional)' + required: false + default: '' + + overwrite: + description: 'Overwrite an existing artifact with the same name' + required: false + default: 'false' + +runs: + using: 'composite' + steps: + - name: Upload artifact + uses: actions/upload-artifact@v7 + with: + name: ${{ inputs.name }} + path: ${{ inputs.path }} + include-hidden-files: ${{ inputs.include-hidden-files }} + if-no-files-found: ${{ inputs.if-no-files-found }} + compression-level: ${{ inputs.compression-level }} + retention-days: ${{ inputs.retention-days }} + overwrite: ${{ inputs.overwrite }} diff --git a/.github/actions/upload-codecov/action.yml b/.github/actions/upload-codecov/action.yml new file mode 100644 index 0000000..0cb15d1 --- /dev/null +++ b/.github/actions/upload-codecov/action.yml @@ -0,0 +1,42 @@ +name: 'Upload coverage to Codecov' +description: 'Wrapper for codecov/codecov-action' + +inputs: + name: + description: 'Codecov upload name' + required: true + + flags: + description: 'Codecov flags' + required: false + default: '' + + files: + description: 'Coverage report files' + required: true + + fail_ci_if_error: + description: 'Fail CI if upload fails' + required: false + default: 'true' + + verbose: + description: 'Enable verbose output' + required: false + default: 'true' + + token: + description: 'Codecov token' + required: true + +runs: + using: composite + steps: + - uses: codecov/codecov-action@v6 + with: + name: ${{ inputs.name }} + flags: ${{ inputs.flags }} + files: ${{ inputs.files }} + fail_ci_if_error: ${{ inputs.fail_ci_if_error }} + verbose: ${{ inputs.verbose }} + token: ${{ inputs.token }} diff --git a/.github/configs/pages-deployment.json b/.github/configs/pages-deployment.json new file mode 100644 index 0000000..c0d3fbe --- /dev/null +++ b/.github/configs/pages-deployment.json @@ -0,0 +1,6 @@ +{ + "source": { + "branch": "gh-pages", + "path": "/" + } +} diff --git a/.github/configs/rulesets-develop.json b/.github/configs/rulesets-develop.json new file mode 100644 index 0000000..04489e5 --- /dev/null +++ b/.github/configs/rulesets-develop.json @@ -0,0 +1,37 @@ +{ + "name": "develop branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["refs/heads/develop"], + "exclude": [] + } + }, + "bypass_actors": [ + { + "actor_id": 2476259, + "actor_type": "Integration", + "bypass_mode": "always" + } + ], + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + }, + { + "type": "pull_request", + "parameters": { + "allowed_merge_methods": ["squash"], + "dismiss_stale_reviews_on_push": false, + "require_code_owner_review": false, + "require_last_push_approval": false, + "required_approving_review_count": 0, + "required_review_thread_resolution": false + } + } + ] +} diff --git a/.github/configs/rulesets-gh-pages.json b/.github/configs/rulesets-gh-pages.json new file mode 100644 index 0000000..ebf3892 --- /dev/null +++ b/.github/configs/rulesets-gh-pages.json @@ -0,0 +1,19 @@ +{ + "name": "gh-pages branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["refs/heads/gh-pages"], + "exclude": [] + } + }, + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + } + ] +} diff --git a/.github/configs/rulesets-master.json b/.github/configs/rulesets-master.json new file mode 100644 index 0000000..f658a5c --- /dev/null +++ b/.github/configs/rulesets-master.json @@ -0,0 +1,30 @@ +{ + "name": "master branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["~DEFAULT_BRANCH"], + "exclude": [] + } + }, + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + }, + { + "type": "pull_request", + "parameters": { + "allowed_merge_methods": ["merge"], + "dismiss_stale_reviews_on_push": false, + "require_code_owner_review": false, + "require_last_push_approval": false, + "required_approving_review_count": 0, + "required_review_thread_resolution": false + } + } + ] +} diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index a95ea8f..16c5c0d 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -2,30 +2,30 @@ name-template: v$NEXT_PATCH_VERSION 🌈 tag-template: v$NEXT_PATCH_VERSION categories: -- title: 🚀 Features - labels: - - feature - - enhancement -- title: 🐛 Bug Fixes - labels: - - fix - - bugfix - - bug -- title: 🧰 Maintenance - labels: - - chore - - documentation + - title: 🚀 Features + labels: + - feature + - enhancement + - title: 🐛 Bug Fixes + labels: + - fix + - bugfix + - bug + - title: 🧰 Maintenance + labels: + - chore + - documentation change-template: '- $TITLE @$AUTHOR (#$NUMBER)' version-resolver: major: labels: - - major + - major minor: labels: - - minor + - minor patch: labels: - - patch + - patch default: patch template: | ## Changes diff --git a/.github/scripts/backmerge-conflict-issue.js b/.github/scripts/backmerge-conflict-issue.js new file mode 100644 index 0000000..f6bd98b --- /dev/null +++ b/.github/scripts/backmerge-conflict-issue.js @@ -0,0 +1,69 @@ +module.exports = async ({ github, context, core }) => { + // Repo context + const owner = context.repo.owner + const repo = context.repo.repo + + // Link to the exact workflow run that detected the conflict + const runUrl = `${context.serverUrl}/${owner}/${repo}/actions/runs/${context.runId}` + + // We use a *stable title* so we can find/reuse the same "conflict tracker" issue + // instead of creating a new issue on every failed run. + const title = 'Backmerge conflict: master → develop' + + // Comment/issue body includes the run URL so maintainers can jump straight to logs. + const body = [ + 'Automatic backmerge failed due to merge conflicts.', + '', + `Workflow run: ${runUrl}`, + '', + 'Manual resolution required.', + ].join('\n') + + // Label applied to the tracker issue (assumed to already exist in the repo). + const label = '[bot] backmerge' + + // Search issues by title across *open and closed* issues. + // Why: if the conflict was resolved previously and the issue was closed, + // we prefer to reopen it and append a new comment instead of creating duplicates. + const q = `repo:${owner}/${repo} is:issue in:title "${title}"` + const search = await github.rest.search.issuesAndPullRequests({ + q, + per_page: 10, + }) + + // Pick the first exact-title match (search can return partial matches). + const existing = search.data.items.find((i) => i.title === title) + + if (existing) { + // If a tracker issue exists, reuse it: + // - reopen it if needed + // - add a comment with the new run URL + if (existing.state === 'closed') { + await github.rest.issues.update({ + owner, + repo, + issue_number: existing.number, + state: 'open', + }) + } + + await github.rest.issues.createComment({ + owner, + repo, + issue_number: existing.number, + body, + }) + + core.notice(`Conflict issue updated: #${existing.number}`) + return + } + + // No tracker issue exists yet -> create the first one. + await github.rest.issues.create({ + owner, + repo, + title, + body, + labels: [label], + }) +} diff --git a/.github/scripts/publish-dashboard.sh b/.github/scripts/publish-dashboard.sh new file mode 100644 index 0000000..dcbd0b3 --- /dev/null +++ b/.github/scripts/publish-dashboard.sh @@ -0,0 +1,77 @@ +#!/usr/bin/env bash + +set -euo pipefail + +remote_repository="${DASHBOARD_REMOTE_REPOSITORY:?}" +publish_branch="${DASHBOARD_PUBLISH_BRANCH:-master}" +source_dir="${DASHBOARD_SOURCE_DIR:?}" +token="${DASHBOARD_TOKEN:?}" +git_user_name="${DASHBOARD_GIT_USER_NAME:-easyscience[bot]}" +git_user_email="${DASHBOARD_GIT_USER_EMAIL:?}" +commit_message="${DASHBOARD_COMMIT_MESSAGE:?}" +max_attempts="${DASHBOARD_PUSH_ATTEMPTS:-3}" +delay_seconds="${DASHBOARD_PUSH_DELAY_SECONDS:-15}" + +workspace_dir="$(mktemp -d)" +repo_dir="${workspace_dir}/dashboard" +remote_url="https://x-access-token:${token}@github.com/${remote_repository}.git" + +cleanup() { + rm -rf "${workspace_dir}" +} + +prepare_worktree() { + if [[ ! -d "${repo_dir}/.git" ]]; then + git clone --branch "${publish_branch}" --depth 1 "${remote_url}" "${repo_dir}" + else + git -C "${repo_dir}" fetch origin "${publish_branch}" + git -C "${repo_dir}" checkout "${publish_branch}" + git -C "${repo_dir}" reset --hard "origin/${publish_branch}" + git -C "${repo_dir}" clean -fd + fi + + git -C "${repo_dir}" config user.name "${git_user_name}" + git -C "${repo_dir}" config user.email "${git_user_email}" +} + +sync_publish_dir() { + cp -R "${source_dir}/." "${repo_dir}/" + git -C "${repo_dir}" add . + + if git -C "${repo_dir}" diff --cached --quiet; then + return 1 + fi + + git -C "${repo_dir}" commit -m "${commit_message}" +} + +trap cleanup EXIT + +prepare_worktree + +if ! sync_publish_dir; then + echo "No dashboard changes to publish." + exit 0 +fi + +for ((attempt = 1; attempt <= max_attempts; attempt += 1)); do + if git -C "${repo_dir}" push origin "HEAD:${publish_branch}"; then + echo "Dashboard published on attempt ${attempt}." + exit 0 + fi + + if ((attempt == max_attempts)); then + echo "Dashboard publish failed after ${max_attempts} attempts." >&2 + exit 1 + fi + + echo "Dashboard push attempt ${attempt} failed. Retrying in ${delay_seconds}s." >&2 + sleep "${delay_seconds}" + + prepare_worktree + + if ! sync_publish_dir; then + echo "Dashboard changes already exist in the target repository." + exit 0 + fi +done \ No newline at end of file diff --git a/.github/workflows/backmerge.yml b/.github/workflows/backmerge.yml new file mode 100644 index 0000000..36ce6f5 --- /dev/null +++ b/.github/workflows/backmerge.yml @@ -0,0 +1,109 @@ +# This workflow automatically merges `master` into `develop` whenever a +# new version release with a tag is published. It can also be triggered +# manually via workflow_dispatch for cases where an automatic backmerge +# is needed outside of the standard release process. +# If a merge conflict occurs, the workflow creates an issue to notify +# maintainers for manual resolution. + +name: Backmerge (master → develop) + +on: + release: + types: [published, prereleased] + workflow_dispatch: + +permissions: + contents: write + issues: write + +concurrency: + group: backmerge-master-into-develop + cancel-in-progress: false + +jobs: + backmerge: + runs-on: ubuntu-latest + timeout-minutes: 10 + + steps: + - name: Checkout repository (for local actions) + uses: actions/checkout@v6 + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + repositories: ${{ github.event.repository.name }} + + - name: Checkout repository (with bot token) + uses: actions/checkout@v6 + with: + fetch-depth: 0 + token: ${{ steps.bot.outputs.token }} + + - name: Configure git identity + run: | + git config user.name "easyscience[bot]" + git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com" + + - name: Set merge message + run: | + if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then + MESSAGE="Backmerge: master into develop (manual) [skip ci]" + else + TAG="${{ github.event.release.tag_name }}" + MESSAGE="Backmerge: master (${TAG}) into develop [skip ci]" + fi + + echo "MESSAGE=$MESSAGE" >> "$GITHUB_ENV" + echo "message=$MESSAGE" >> "$GITHUB_OUTPUT" + echo "📝 Merge message: $MESSAGE" | tee -a "$GITHUB_STEP_SUMMARY" + + - name: Prepare branches + run: | + git fetch origin master develop + git checkout -B develop origin/develop + + - name: Check if develop is already up-to-date + id: up_to_date + run: | + if git merge-base --is-ancestor origin/master develop; then + echo "value=true" >> "$GITHUB_OUTPUT" + echo "ℹ️ Develop is already up-to-date with master" | tee -a "$GITHUB_STEP_SUMMARY" + else + echo "value=false" >> "$GITHUB_OUTPUT" + fi + + - name: Try merge master into develop + id: merge + if: steps.up_to_date.outputs.value == 'false' + continue-on-error: true + run: | + if ! git merge origin/master --no-ff -m "${MESSAGE}"; then + echo "conflict=true" >> "$GITHUB_OUTPUT" + echo "❌ Backmerge conflict detected." | tee -a "$GITHUB_STEP_SUMMARY" + git status --porcelain || true + exit 0 + fi + + echo "conflict=false" >> "$GITHUB_OUTPUT" + echo "✅ Merge commit created." | tee -a "$GITHUB_STEP_SUMMARY" + + - name: Push to develop (if merge succeeded) + if: + steps.up_to_date.outputs.value == 'false' && steps.merge.outputs.conflict == + 'false' + run: | + git push origin develop + echo "🚀 Backmerge successful: master → develop" | tee -a "$GITHUB_STEP_SUMMARY" + + - name: Create issue (if merge failed with conflicts) + if: steps.merge.outputs.conflict == 'true' + uses: ./.github/actions/github-script + with: + github-token: ${{ steps.bot.outputs.token }} + script: | + const run = require('./.github/scripts/backmerge-conflict-issue.js') + await run({ github, context, core }) diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml new file mode 100644 index 0000000..21c72b3 --- /dev/null +++ b/.github/workflows/cleanup.yml @@ -0,0 +1,84 @@ +# This workflow will delete old workflow runs based on the input +# parameters. +# https://github.com/Mattraks/delete-workflow-runs + +name: Old workflow runs cleanup + +on: + # Run monthly, at 00:00 on the 1st day of month. + schedule: + - cron: '0 0 1 * *' + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + inputs: + days: + description: 'Number of days.' + required: true + default: '30' + minimum_runs: + description: 'The minimum runs to keep for each workflow.' + required: true + default: '6' + delete_workflow_pattern: + description: + 'The name or filename of the workflow. if not set then it will target all + workflows.' + required: false + delete_workflow_by_state_pattern: + description: + 'Remove workflow by state: active, deleted, disabled_fork, + disabled_inactivity, disabled_manually' + required: true + default: 'All' + type: choice + options: + - 'All' + - active + - deleted + - disabled_inactivity + - disabled_manually + delete_run_by_conclusion_pattern: + description: + 'Remove workflow by conclusion: action_required, cancelled, failure, skipped, + success' + required: true + default: 'All' + type: choice + options: + - 'All' + - action_required + - cancelled + - failure + - skipped + - success + dry_run: + description: 'Only log actions, do not perform any delete operations (dry run).' + required: false + default: 'false' + type: choice + options: + - 'false' + - 'true' + +jobs: + del-runs: + runs-on: ubuntu-latest + + permissions: + actions: write + + steps: + - name: Delete workflow runs + uses: Mattraks/delete-workflow-runs@v2 + with: + token: ${{ github.token }} + repository: ${{ github.repository }} + retain_days: ${{ github.event.inputs.days }} + keep_minimum_runs: ${{ github.event.inputs.minimum_runs }} + delete_workflow_pattern: ${{ github.event.inputs.delete_workflow_pattern }} + delete_workflow_by_state_pattern: + ${{ github.event.inputs.delete_workflow_by_state_pattern }} + delete_run_by_conclusion_pattern: + ${{ github.event.inputs.delete_run_by_conclusion_pattern }} + dry_run: ${{ github.event.inputs.dry_run }} diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml deleted file mode 100644 index 42eee5b..0000000 --- a/.github/workflows/codeql-analysis.yml +++ /dev/null @@ -1,71 +0,0 @@ -# CodeQL is the code analysis engine developed by GitHub to automate security checks. -# -# For more information see: https://docs.github.com/en/code-security/code-scanning/introduction-to-code-scanning/about-code-scanning-with-codeql - - -name: "CodeQL" - -on: - push: - branches: [ master, pre-release, develop ] - pull_request: - # The branches below must be a subset of the branches above - branches: [ master ] - schedule: - - cron: '0 16 * * 5' - -jobs: - analyze: - name: Analyze - runs-on: ubuntu-latest - - strategy: - fail-fast: false - matrix: - # Override automatic language detection by changing the below list - # Supported options are ['csharp', 'cpp', 'go', 'java', 'javascript', 'python'] - language: ['python'] - # Learn more... - # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection - - steps: - - name: Checkout repository - uses: actions/checkout@v4 - with: - # We must fetch at least the immediate parents so that if this is - # a pull request then we can checkout the head. - fetch-depth: 2 - - # If this run was triggered by a pull request event, then checkout - # the head of the pull request instead of the merge commit. - - run: git checkout HEAD^2 - if: ${{ github.event_name == 'pull_request' }} - - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v3 - with: - languages: ${{ matrix.language }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. - # queries: ./path/to/local/query, your-org/your-repo/queries@master - - # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). - # If this step fails, then you should remove it and run the build manually (see below) - - name: Autobuild - uses: github/codeql-action/autobuild@v3 - - # ℹ️ Command-line programs to run using the OS shell. - # 📚 https://git.io/JvXDl - - # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines - # and modify them (or add more) to build your code if your project - # uses a compiled language - - #- run: | - # make bootstrap - # make release - - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 \ No newline at end of file diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml new file mode 100644 index 0000000..5208a33 --- /dev/null +++ b/.github/workflows/coverage.yml @@ -0,0 +1,70 @@ +name: Coverage checks + +on: + # Trigger the workflow on push to develop + push: + branches: + - develop + # Trigger the workflow on pull request + pull_request: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Need permissions to trigger the dashboard build workflow +permissions: + actions: write + contents: read + +# Allow only one concurrent workflow per PR or branch ref. +# Cancel in-progress runs only for pull requests, but let branch push runs finish. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: ${{ github.event_name == 'pull_request' }} + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + +jobs: + # Job 1: Run docstring coverage + docstring-coverage: + runs-on: ubuntu-latest + + steps: + - name: Check-out repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run docstring coverage + run: pixi run docstring-coverage + + # Job 2: Run unit tests with coverage and upload to Codecov + unit-tests-coverage: + runs-on: ubuntu-latest + + steps: + - name: Check-out repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run unit tests with coverage + run: pixi run unit-tests-coverage --cov-report=xml:coverage-unit.xml + + - name: Upload unit tests coverage to Codecov + if: ${{ !cancelled() }} + uses: ./.github/actions/upload-codecov + with: + name: unit-tests-job + flags: unittests + files: ./coverage-unit.xml + token: ${{ secrets.CODECOV_TOKEN }} + + # Job 4: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.github/workflows/dashboard.yml b/.github/workflows/dashboard.yml new file mode 100644 index 0000000..573e308 --- /dev/null +++ b/.github/workflows/dashboard.yml @@ -0,0 +1,115 @@ +name: Dashboard build and publish + +on: + workflow_dispatch: + workflow_call: + +permissions: + contents: read + +concurrency: + group: dashboard-publish-${{ github.repository }} + cancel-in-progress: false + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + DEVELOP_BRANCH: develop + REPO_OWNER: ${{ github.repository_owner }} + REPO_NAME: ${{ github.event.repository.name }} + +jobs: + dashboard: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + with: + fetch-depth: 0 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + # Install badgery into the active Pixi environment without modifying + # pixi.toml/pixi.lock. Using `pixi add` here re-solves the whole project + # and rebuilds the local editable package, which can cause intermittent + # Linux CI failures (`Text file busy`, os error 26). + - name: Install badgery + shell: bash + run: pixi run python -m pip install git+https://github.com/enhantica/badgery + + - name: Run docstring coverage and code complexity/maintainability checks + run: | + for BRANCH in $DEFAULT_BRANCH $DEVELOP_BRANCH $CI_BRANCH; do + echo + echo "🔹🔸🔹🔸🔹 Processing branch $BRANCH 🔹🔸🔹🔸🔹" + if [ -d "../$BRANCH" ]; then + echo "Branch $BRANCH already processed, skipping" + continue + fi + + git worktree add ../$BRANCH origin/$BRANCH + mkdir -p reports/$BRANCH + + echo "Docstring coverage for branch $BRANCH" + pixi run interrogate -c pyproject.toml --fail-under=0 ../$BRANCH/src > reports/$BRANCH/coverage-docstring.txt + + echo "Cyclomatic complexity for branch $BRANCH" + pixi run radon cc -s -j ../$BRANCH/src > reports/$BRANCH/cyclomatic-complexity.json + + echo "Maintainability index for branch $BRANCH" + pixi run radon mi -j ../$BRANCH/src > reports/$BRANCH/maintainability-index.json + + echo "Raw metrics for branch $BRANCH" + pixi run radon raw -s -j ../$BRANCH/src > reports/$BRANCH/raw-metrics.json + done + + - name: Generate dashboard HTML + run: > + pixi run python -m badgery --config .badgery.yaml --repo ${{ github.repository + }} --branch ${{ env.CI_BRANCH }} --output index.html + + - name: Prepare publish directory + run: | + mkdir -p _dashboard_publish/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }} + cp index.html _dashboard_publish/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }} + + # Create GitHub App token for pushing to external dashboard repo. + # The 'repositories' parameter is required to grant access to repos + # other than the one where the workflow is running. + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + repositories: | + ${{ github.event.repository.name }} + dashboard + + # Push to external dashboard repository with retry logic. + # Retry is needed to handle transient GitHub API/authentication issues + # that occasionally cause 403 errors when multiple workflows push concurrently. + # Uses personal_token (not github_token) as GITHUB_TOKEN cannot access external repos. + - name: + Push to ${{ env.REPO_OWNER }}/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH + }} + shell: bash + env: + DASHBOARD_COMMIT_MESSAGE: ${{ env.CI_BRANCH }} + DASHBOARD_GIT_USER_EMAIL: + ${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com + DASHBOARD_PUSH_ATTEMPTS: '3' + DASHBOARD_PUSH_DELAY_SECONDS: '15' + DASHBOARD_PUBLISH_BRANCH: master + DASHBOARD_REMOTE_REPOSITORY: ${{ env.REPO_OWNER }}/dashboard + DASHBOARD_SOURCE_DIR: ./_dashboard_publish + DASHBOARD_TOKEN: ${{ steps.bot.outputs.token }} + run: bash ./.github/scripts/publish-dashboard.sh + + - name: Add dashboard link to summary + run: | + URL="https://${{ env.REPO_OWNER }}.github.io/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }}" + echo "Dashboard link: [$URL]($URL)" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..6b6db79 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,188 @@ +# This workflow builds and deploys documentation for the project. +# +# Overview: +# - Converts tutorial Python scripts to Jupyter notebooks and executes them. +# - Builds the documentation site using MkDocs with the Material theme. +# - Uploads the built site as an artifact for local inspection. +# - Deploys versioned documentation to the gh-pages branch using Mike: +# - For release tags (v*): deploys to a versioned folder (e.g., /0.9.1/) and updates /latest/. +# - For branches: deploys to /dev/. +# +# The action summary page will contain a link to the built artifact for downloading +# and inspecting, as well as a link to the deployed documentation site. + +name: Docs build and deployment + +on: + # Trigger the workflow on push + push: + # Selected branches + branches: [develop] # master and main are already verified in PR + # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3' + tags: ['v*'] + # Trigger the workflow on pull request + pull_request: + # Selected branches + branches: [master, main, develop] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# - Non-tagged pushes and pull requests all use `docs-dev` group, so +# they cancel each other. +# - Tagged pushes use their own group like docs-v1.2.3, so they do not +# cancel non-tagged runs, and non-tagged runs do not cancel them. +concurrency: + group: >- + ${{ startsWith(github.ref, 'refs/tags/v') + && format('docs-{0}', github.ref_name) + || 'docs-dev' }} + cancel-in-progress: true + +# Set the environment variables to be used in all jobs defined in this workflow +env: + # CI_BRANCH - the branch name (used in mkdocs.yml) + # For PRs: github.head_ref is the source branch + # For pushes: github.ref_name is the branch + # For tags: github.ref_name is the tag name + # GITHUB_REPOSITORY - the repository name (used in mkdocs.yml) + # NOTEBOOKS_DIR - the directory containing the Jupyter notebooks (used in mkdocs.yml) + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + DEVELOP_BRANCH: develop + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }} + GITHUB_REPOSITORY: ${{ github.repository }} + NOTEBOOKS_DIR: tutorials + +jobs: + # Single job that builds and deploys documentation. + # Uses macOS runner for consistent Plotly chart rendering. + build-deploy-docs: + runs-on: ubuntu-latest # macos-latest + + permissions: + contents: write # Required for pushing to the gh-pages branch + + steps: + # Setting DOCS_VERSION to be used in mkdocs.yml, and then in the + # main.html template. It defines the versioned docs subfolder name + # in the gh-pages branch. If it's a release tag, use the version + # number without the 'v' prefix, otherwise use 'dev'. + # Setting RELEASE_VERSION to be used in mkdocs.yml to show + # the latest release version in the index.md file. If it's a + # release tag, use the tag name, otherwise use the branch name + # for development builds. + - name: Set extra env variables + shell: bash + run: | + if [[ "${IS_RELEASE_TAG}" == "true" ]]; then + RELEASE_VERSION="${GITHUB_REF_NAME}" + DOCS_VERSION="${RELEASE_VERSION#v}" + else + RELEASE_VERSION="${CI_BRANCH}" + DOCS_VERSION="dev" + fi + echo "RELEASE_VERSION=${RELEASE_VERSION}" >> "$GITHUB_ENV" + echo "DOCS_VERSION=${DOCS_VERSION}" >> "$GITHUB_ENV" + + # Check out the repository source code. + # Note: The gh-pages branch is fetched separately later for mike deployment. + - name: Checkout repository + uses: actions/checkout@v6 + + # Activate dark mode to create documentation with Plotly charts in dark mode + # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher + # Something similar to mkdocs_plotly_plugin https://haoda-li.github.io/mkdocs-plotly-plugin/, + # but for generating documentation from notepads + #- name: Activate dark mode + # run: | + # brew install dark-mode + # dark-mode status + # dark-mode on + # dark-mode status + + # Set up the pixi package manager and install dependencies from pixi.toml. + # Uses frozen lockfile to ensure reproducible builds. + - name: Set up pixi + uses: ./.github/actions/setup-pixi + # Pre-import the main package to exclude info messages from the docs + # E.g., Matplotlib may print messages to stdout/stderr when first + # imported. This step allows to avoid "Matplotlib is building the font + # cache" messages during notebook execution. + - name: Pre-build site step + run: pixi run python -c "import easyimaging" + + # Prepare the Jupyter notebooks for documentation (strip output, etc.). + - name: Prepare notebooks + run: pixi run notebook-prepare + + # Execute all Jupyter notebooks to generate output cells (plots, tables, etc.). + # Uses multiple cores for parallel execution to speed up the process. + - name: Run notebooks + # if: false # Temporarily disabled to speed up the docs build + run: pixi run notebook-exec + + # Build the static files for the documentation site for local inspection + # Input: docs/ directory containing the Markdown files + # Output: site/ directory containing the generated HTML files + - name: Build site for local check + run: pixi run docs-build-local + + # Upload the static files from the site/ directory to be used for + # local check + - name: Upload built site as artifact + uses: ./.github/actions/upload-artifact + with: + name: site-local_easyimaging-lib-${{ env.RELEASE_VERSION }} + path: docs/site/ + + # Create GitHub App token for pushing to gh-pages as easyscience[bot]. + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + # Configure git identity and remote URL so mike pushes as easyscience[bot]. + - name: Configure git for pushing + run: | + set -euo pipefail + git config user.name "easyscience[bot]" + git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com" + git remote set-url origin "https://x-access-token:${{ steps.bot.outputs.token }}@github.com/${{ github.repository }}.git" + + # Fetch the gh-pages branch to ensure mike has the latest remote state. + # This is required because the checkout step only fetches the source branch, + # not the gh-pages branch that mike needs to update. + - name: Fetch gh-pages branch + run: | + git fetch origin gh-pages:gh-pages 2>/dev/null || true + + # Deploy versioned documentation using mike (MkDocs plugin for versioning). + # - For release tags (v*): deploys to versioned folder (e.g., /0.9.1/) and aliases to /latest/. + # - For branches: deploys to /dev/. + # The "${RELEASE_VERSION#v}" syntax strips the 'v' prefix (v0.9.1 -> 0.9.1). + # Also sets 'latest' as the default version for the version selector. + - name: Rebuild and deploy docs with mike + run: | + # Exit on error (-e), undefined vars (-u), and pipeline failures (pipefail) + set -euo pipefail + + REPO_NAME="${{ github.event.repository.name }}" + BASE_URL="https://easyscience.github.io/${REPO_NAME}" + + # Deploy the release version and update the "latest" alias + if [[ "${IS_RELEASE_TAG}" == "true" ]]; then + pixi run docs-deploy-pre "${RELEASE_VERSION#v}" latest + pixi run docs-set-default-pre latest + DEPLOYMENT_URL="${BASE_URL}/latest" + + # Deploy/update the "dev" alias (or whatever your convention is) + else + pixi run docs-deploy-pre dev + DEPLOYMENT_URL="${BASE_URL}/dev" + + fi + + # Add links to the action summary page for easy access + echo "🔗 deployment url [${DEPLOYMENT_URL}](${DEPLOYMENT_URL})" >> "${GITHUB_STEP_SUMMARY}" diff --git a/.github/workflows/documentation-build.yml b/.github/workflows/documentation-build.yml deleted file mode 100644 index b238f74..0000000 --- a/.github/workflows/documentation-build.yml +++ /dev/null @@ -1,48 +0,0 @@ -# This pipeline -# - builds developer documentation -# - pushes documentation to gh-pages branch of the same repository -# -# Deployment is handled by pages-build-deployment bot -# -# For more information see: https://docs.github.com/en/pages/getting-started-with-github-pages - -name: Build Documentation and Push to gh-pages Branch - -# Controls when the workflow will run -on: - # Triggers the workflow on tag creation - push: - tags: - - 'v*' - - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - -# A workflow run is made up of one or more jobs that can run sequentially or in parallel -jobs: - # This workflow contains a single job called "build" - build_documentation: - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v5 - with: - fetch-depth: 0 # otherwise, you will failed to push refs to dest repo - - - name: Setup Pixi - uses: ./.github/actions/setup-pixi - - - name: Build documentation - run: pixi run docs-build - - - name: Build and Commit - uses: sphinx-notes/pages@master - with: - install_requirements: true - documentation_path: docs/src - - - name: Push changes - uses: ad-m/github-push-action@master - continue-on-error: true - with: - branch: gh-pages \ No newline at end of file diff --git a/.github/workflows/issues-labels.yml b/.github/workflows/issues-labels.yml new file mode 100644 index 0000000..4fbf4fa --- /dev/null +++ b/.github/workflows/issues-labels.yml @@ -0,0 +1,40 @@ +# Verifies if the current issue has at least one `[scope]` label and one +# `[priority]` label. If either is missing, the workflow adds a reminder label. + +name: Issue labels check + +on: + issues: + types: [opened, labeled, unlabeled] + +permissions: + issues: write + +jobs: + check-labels: + runs-on: ubuntu-latest + + concurrency: + group: issue-labels-${{ github.event.issue.number }} + cancel-in-progress: true + + steps: + - name: Ensure [scope] label + uses: Rindrics/expect-label-prefix@v1.2.1 + with: + repository_full_name: ${{ github.repository }} + token: ${{ github.token }} + label_prefix: '[scope]' + label_separator: ' ' + add_label: 'true' + default_label: '[scope] ⚠️ label needed' + + - name: Ensure [priority] label + uses: Rindrics/expect-label-prefix@v1.2.1 + with: + repository_full_name: ${{ github.repository }} + token: ${{ github.token }} + label_prefix: '[priority]' + label_separator: ' ' + add_label: 'true' + default_label: '[priority] ⚠️ label needed' diff --git a/.github/workflows/lint-format.yml b/.github/workflows/lint-format.yml new file mode 100644 index 0000000..16dd95c --- /dev/null +++ b/.github/workflows/lint-format.yml @@ -0,0 +1,124 @@ +# The workflow checks +# - the validity of pyproject.toml, +# - the presence and correctness of SPDX license headers, +# - linting and formatting of Python code, +# - linting and formatting of docstrings in Python code, +# - formatting of non-Python files (like markdown and toml). +# - linting of Python code in Jupyter notebooks (for library template). +# +# A summary of the checks is added to the GitHub Actions summary. + +name: Lint and format checks + +on: + # Trigger the workflow on push + push: + branches-ignore: [master, main] # Already verified in PR + # Do not run this workflow on creating a new tag starting with + # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) + tags-ignore: ['v*'] + # Trigger the workflow on pull request + pull_request: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +permissions: + contents: read + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + +jobs: + lint-format: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run post-install developer steps + run: pixi run post-install + + - name: Check validity of pyproject.toml + id: pyproject + continue-on-error: true + shell: bash + run: pixi run pyproject-check + + - name: Check SPDX license headers + id: license_headers + continue-on-error: true + shell: bash + run: pixi run license-check + + - name: Check linting of Python code + id: py_lint + continue-on-error: true + shell: bash + run: pixi run py-lint-check + + - name: Check formatting of Python code + id: py_format + continue-on-error: true + shell: bash + run: pixi run py-format-check + + - name: Check linting of docstrings in Python code + id: docstring_lint + continue-on-error: true + shell: bash + run: pixi run docstring-lint-check + + - name: Check formatting of non-Python files (md, toml, etc.) + id: nonpy_format + continue-on-error: true + shell: bash + run: pixi run nonpy-format-check + + - name: Check linting of Python code in Jupyter notebooks (ipynb) + id: notebook_lint + continue-on-error: true + shell: bash + run: pixi run notebook-lint-check + + # Add summary + - name: Add quality checks summary + if: always() + shell: bash + run: | + { + echo "## 🧪 Checks Summary" + echo "" + echo "| Check | Status |" + echo "|-------|--------|" + echo "| pyproject.toml | ${{ steps.pyproject.outcome == 'success' && '✅' || '❌' }} |" + echo "| license headers | ${{ steps.license_headers.outcome == 'success' && '✅' || '❌' }} |" + echo "| py lint | ${{ steps.py_lint.outcome == 'success' && '✅' || '❌' }} |" + echo "| py format | ${{ steps.py_format.outcome == 'success' && '✅' || '❌' }} |" + echo "| docstring lint | ${{ steps.docstring_lint.outcome == 'success' && '✅' || '❌' }} |" + echo "| nonpy format | ${{ steps.nonpy_format.outcome == 'success' && '✅' || '❌' }} |" + echo "| notebooks lint | ${{ steps.notebook_lint.outcome == 'success' && '✅' || '❌' }} |" + } >> "$GITHUB_STEP_SUMMARY" + + # Fail job if any check failed + - name: Fail job if any check failed + if: | + steps.pyproject.outcome == 'failure' + || steps.license_headers.outcome == 'failure' + || steps.py_lint.outcome == 'failure' + || steps.py_format.outcome == 'failure' + || steps.docstring_lint.outcome == 'failure' + || steps.nonpy_format.outcome == 'failure' + || steps.notebook_lint.outcome == 'failure' + shell: bash + run: exit 1 diff --git a/.github/workflows/nightly-check.yml b/.github/workflows/nightly-check.yml deleted file mode 100644 index 133ba4d..0000000 --- a/.github/workflows/nightly-check.yml +++ /dev/null @@ -1,24 +0,0 @@ -# Nightly Check - install dependencies and run tests after pixi update-lock -name: Nightly Check -on: - schedule: - - cron: '0 0 * * *' # Runs every day at midnight UTC - workflow_dispatch: - -jobs: - nightly-check: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v5 - - - name: Setup Pixi - uses: ./.github/actions/setup-pixi - - - name: Update lock file - run: pixi run update-lock - - - name: Build package - run: pixi run build - - - name: Run tox tests - run: pixi run tox diff --git a/.github/workflows/ossar-analysis.yml b/.github/workflows/ossar-analysis.yml deleted file mode 100644 index 1b941b7..0000000 --- a/.github/workflows/ossar-analysis.yml +++ /dev/null @@ -1,51 +0,0 @@ -# This workflow integrates a collection of open source static analysis tools -# with GitHub code scanning. -# -# For more information see: https://github.com/github/ossar-action - - -name: OSSAR - -on: - pull_request: - -jobs: - OSSAR-Scan: - # OSSAR runs on windows-latest. - # ubuntu-latest and macos-latest support coming soon - runs-on: windows-latest - - steps: - # Checkout your code repository to scan - - name: Checkout repository - uses: actions/checkout@v4 - with: - # We must fetch at least the immediate parents so that if this is - # a pull request then we can checkout the head. - fetch-depth: 2 - - # If this run was triggered by a pull request event, then checkout - # the head of the pull request instead of the merge commit. - - run: git checkout HEAD^2 - if: ${{ github.event_name == 'pull_request' }} - - # Ensure a compatible version of dotnet is installed. - # The [Microsoft Security Code Analysis CLI](https://aka.ms/mscadocs) is built with dotnet v3.1.201. - # A version greater than or equal to v3.1.201 of dotnet must be installed on the agent in order to run this action. - # Remote agents already have a compatible version of dotnet installed and this step may be skipped. - # For local agents, ensure dotnet version 3.1.201 or later is installed by including this action: - # - name: Install .NET - # uses: actions/setup-dotnet@v1 - # with: - # dotnet-version: '3.1.x' - - # Run open source static analysis tools - - name: Run OSSAR - uses: github/ossar-action@v2.0.0 - id: ossar - - # Upload results to the Security tab - - name: Upload OSSAR results - uses: github/codeql-action/upload-sarif@v3 - with: - sarif_file: ${{ steps.ossar.outputs.sarifFile }} \ No newline at end of file diff --git a/.github/workflows/pr-labels.yml b/.github/workflows/pr-labels.yml new file mode 100644 index 0000000..fcb8a78 --- /dev/null +++ b/.github/workflows/pr-labels.yml @@ -0,0 +1,45 @@ +# Verifies if a pull request has at least one label from a set of valid +# labels before it can be merged. +# +# The label validation is delegated to `mheap/github-action-required-labels`, +# which checks the current PR labels via the GitHub API and can add or update a +# PR comment when the required label set is missing. + +name: PR labels check + +on: + pull_request_target: + types: [opened, labeled, unlabeled, synchronize] + +permissions: + issues: write + pull-requests: write + +jobs: + check-labels: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - uses: mheap/github-action-required-labels@v5 + with: + token: ${{ steps.bot.outputs.token }} + add_comment: true + mode: minimum + count: 1 + labels: | + [bot] release + [scope] bug + [scope] documentation + [scope] enhancement + [scope] maintenance + [scope] significant diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml new file mode 100644 index 0000000..cd47c82 --- /dev/null +++ b/.github/workflows/pypi-publish.yml @@ -0,0 +1,46 @@ +# Builds a Python package and publish it to PyPI when a new tag is +# created. + +name: PyPI publishing + +on: + # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3' + push: + tags: ['v*'] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +jobs: + pypi-publish: + runs-on: ubuntu-latest + + permissions: + contents: read + id-token: write # IMPORTANT: this permission is mandatory for trusted publishing + + steps: + - name: Check-out repository + uses: actions/checkout@v6 + with: + fetch-depth: 0 # full history with tags to get the version number by versioningit + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + # Build the Python package (to dist/ folder) + - name: Create Python package + run: pixi run default-build + + # Publish the package to PyPI (from dist/ folder) + # Instead of publishing with personal access token, we use + # GitHub Actions OIDC to get a short-lived token from PyPI. + # New publisher must be previously configured in PyPI at + # https://pypi.org/manage/project/easyimaging/settings/publishing/ + # Use the following data: + # Owner: easyscience + # Repository name: imaging-lib + # Workflow name: pypi-publish.yml + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + packages-dir: 'dist' diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml new file mode 100644 index 0000000..0ea822e --- /dev/null +++ b/.github/workflows/pypi-test.yml @@ -0,0 +1,80 @@ +name: PyPI package tests + +on: + # Run daily, at 00:00. + schedule: + - cron: '0 0 * * *' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +permissions: + contents: read + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + +jobs: + # Job 1: Test installation from PyPI on multiple OS + pypi-package-tests: + strategy: + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + with: + environments: '' + activate-environment: '' + run-install: false + frozen: false + + - name: Init pixi project + run: pixi init easyimaging + + - name: Set the minimum system requirements + working-directory: easyimaging + run: pixi project system-requirements add macos 14.0 + + - name: Add Python 3.13 from Conda + working-directory: easyimaging + run: pixi add "python=3.13" + + - name: Add other Conda dependencies + working-directory: easyimaging + run: pixi add gsl + + - name: Add easyimaging (with dev dependencies) from PyPI + working-directory: easyimaging + run: pixi add --pypi "easyimaging[dev]" + + - name: Run unit tests to verify the installation + working-directory: easyimaging + run: pixi run python -m pytest ../tests/unit/ --color=yes -v + + # - name: Run functional tests to verify the installation + # working-directory: easyimaging + # run: pixi run python -m pytest ../tests/functional/ --color=yes -v + + - name: Run integration tests to verify the installation + working-directory: easyimaging + run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto + + # Job 2: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: pypi-package-tests # depend on previous job + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml deleted file mode 100644 index 3fc3cfb..0000000 --- a/.github/workflows/python-ci.yml +++ /dev/null @@ -1,95 +0,0 @@ -# This workflow will for a variety of Python versions -# - install the code base -# - lint the code base -# - test the code base -# - upload the test coverage to codecov -# -# It will also -# - build the package -# - check the package -# -# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries - -name: CI using Pixi - -on: [push, pull_request] - -jobs: - Code_Consistency: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v5 - - name: Setup Pixi - uses: ./.github/actions/setup-pixi - - name: Run linting - run: pixi run lint - - - name: Suggestion to fix lint issues - if: ${{ failure() }} - run: | - echo "::notice::In project root run 'pixi run lint-fix' and commit changes to fix issues." - exit 1 - - - name: Run formatting - run: pixi run format-check - - - name: Suggestion to fix format issues - if: ${{ failure() }} - run: | - echo "::notice::In project root run 'pixi run format' and commit changes to fix issues." - exit 1 - - Code_Testing: - strategy: - max-parallel: 4 - matrix: - python-version: ['3.11', '3.12', '3.13'] - os: [ubuntu-latest, macos-latest, macos-15-intel, windows-latest] - - runs-on: ${{ matrix.os }} - if: "!contains(github.event.head_commit.message, '[ci skip]')" - - steps: - - uses: actions/checkout@v5 - - - name: Setup Pixi - uses: prefix-dev/setup-pixi@v0.9.0 - with: - run-install: false - cache: false - post-cleanup: false - - - name: Set Python version - run: pixi add python=${{ matrix.python-version }} - - - - name: Install dependencies and run tests - run: pixi run -e dev test - - - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v5 - with: - name: unit-tests-job - flags: unittests - files: ./coverage-unit.xml - fail_ci_if_error: true - verbose: true - token: ${{ secrets.CODECOV_TOKEN }} - slug: EasyScience/imaging-lib - - Package_Testing: - - runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, '[ci skip]')" - - steps: - - uses: actions/checkout@v5 - - - name: Setup Pixi - uses: ./.github/actions/setup-pixi - - - name: Build package - run: pixi run build - - - name: Run tox tests - run: pixi run tox \ No newline at end of file diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml deleted file mode 100644 index 1b4b1b8..0000000 --- a/.github/workflows/python-package.yml +++ /dev/null @@ -1,43 +0,0 @@ -# This workflow will for a variety of Python versions -# - build a python package -# - run tests on the produced package -# - upload the package as an artifact -# -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Create Python Package - -on: - push: - branches: [ master, pre-release ] - pull_request: - branches: [ master, pre-release ] - -jobs: - build: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ['3.11', '3.12', '3.13'] - if: "!contains(github.event.head_commit.message, '[ci skip]')" - - steps: - - uses: actions/checkout@v5 - - - name: Setup Pixi - uses: ./.github/actions/setup-pixi - - - name: Set Python version - run: pixi add python=${{ matrix.python-version }} - - - name: Build package - run: pixi run build - - - name: Run tests with tox - run: pixi run tox - - - uses: actions/upload-artifact@v4 - with: - name: EasyImaging - Python ${{ matrix.python-version }} - path: ${{ github.workspace }}/dist/* - overwrite: true \ No newline at end of file diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml deleted file mode 100644 index d3775cb..0000000 --- a/.github/workflows/python-publish.yml +++ /dev/null @@ -1,40 +0,0 @@ -# This workflow will -# - build distribution package, pure python wheel -# - publish produced distribution package to PyPI -# -# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries - - -name: Publish Python Package - -# Controls when the workflow will run -on: - # Triggers the workflow on tag creation - push: - tags: - - 'v*' - - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - -jobs: - deploy: - - runs-on: ubuntu-latest - permissions: - id-token: write - contents: read - - steps: - - uses: actions/checkout@v5 - - - name: Setup Pixi - uses: ./.github/actions/setup-pixi - - - name: Build package - run: pixi run build - - - name: Publish distribution 📦 to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - password: ${{ secrets.PYPI_TOKEN_ES }} \ No newline at end of file diff --git a/.github/workflows/release-drafter-verify-pr-labels.yml b/.github/workflows/release-drafter-verify-pr-labels.yml deleted file mode 100644 index b024955..0000000 --- a/.github/workflows/release-drafter-verify-pr-labels.yml +++ /dev/null @@ -1,26 +0,0 @@ -# This workflow will -# - verify that a PR has a known label before it can be merged. -# -# A PR is enforced to have one of the labels listed in the valid-labels input. -# -# For more information see: https://github.com/marketplace/actions/release-drafter - - -name: Verify PR labels -on: - pull_request_target: - types: [opened, labeled, unlabeled, synchronize] - -jobs: - check_pr_labels: - runs-on: ubuntu-latest - name: Verify that the PR has a valid label - steps: - - name: Verify PR label action - uses: jesusvasquez333/verify-pr-label-action@v1.4.0 - id: verify-pr-label - with: - github-token: ${{ secrets.GITHUB_TOKEN }} - valid-labels: chore, fix, bugfix, bug, enhancement, feature, dependencies, documentation - pull-request-number: ${{ github.event.pull_request.number }} - disable-reviews: false diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml deleted file mode 100644 index beb4813..0000000 --- a/.github/workflows/release-drafter.yml +++ /dev/null @@ -1,23 +0,0 @@ -# This workflow will -# - draft a new release the next time a release is tagged. -# -# Uses the release-drafter.yml configuration file in the .github directory. -# -# For more information see: https://github.com/marketplace/actions/release-drafter - - -name: Release Drafter - -on: - push: - tags: - - 'v*' - -jobs: - update_release_draft: - runs-on: ubuntu-latest - steps: - # Drafts your next Release notes as Pull Requests are merged into "master" - - uses: release-drafter/release-drafter@v6 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml new file mode 100644 index 0000000..1f32bd4 --- /dev/null +++ b/.github/workflows/release-notes.yml @@ -0,0 +1,71 @@ +# Drafts your next Release notes as pull requests are merged into +# default branch + +name: Release draft update + +on: + # Runs on pushes targeting the default branch (updates the real draft release) + push: + branches: [master, main] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +jobs: + draft-release-notes: + permissions: + # write permission is required to create a github release + contents: write + + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + with: + fetch-depth: 0 # full history with tags to get the version number + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Drafts the next release notes + id: draft + uses: enhantica/drafterino@v2 + with: + config: | + title: 'easyimaging $COMPUTED_VERSION' + tag: 'v$COMPUTED_VERSION' + note-template: '- $PR_TITLE (#$PR_NUMBER)' + + default-bump: post + + major-bump-labels: ['[scope] significant'] + minor-bump-labels: ['[scope] enhancement'] + patch-bump-labels: ['[scope] bug', '[scope] maintenance'] + post-bump-labels: ['[scope] documentation'] + + release-notes: + - title: 'Added' + labels: ['[scope] significant', '[scope] enhancement'] + - title: 'Fixed' + labels: ['[scope] bug'] + - title: 'Changed' + labels: ['[scope] maintenance', '[scope] documentation'] + env: + GITHUB_TOKEN: ${{ steps.bot.outputs.token }} + + - name: Create GitHub draft release + uses: softprops/action-gh-release@v3 + with: + draft: true + tag_name: ${{ steps.draft.outputs.tag_name }} + name: ${{ steps.draft.outputs.release_name }} + body: ${{ steps.draft.outputs.release_notes }} + env: + GITHUB_TOKEN: ${{ steps.bot.outputs.token }} diff --git a/.github/workflows/release-pr.yml b/.github/workflows/release-pr.yml new file mode 100644 index 0000000..3fa073b --- /dev/null +++ b/.github/workflows/release-pr.yml @@ -0,0 +1,55 @@ +# This workflow creates an automated release PR from a source branch into the default branch. +# +# Usage: +# - Triggered manually via workflow_dispatch. +# - Creates a PR titled "Release: merge into ". +# - Adds the label "[bot] release" so it is excluded from changelogs. +# - The PR body makes clear that this is automation only (no review needed). + +name: 'Release PR (develop → master)' + +on: + workflow_dispatch: + inputs: + source_branch: + description: 'Source branch to create PR from' + required: false + default: 'develop' + type: string + +permissions: + contents: read + pull-requests: write + +env: + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + SOURCE_BRANCH: ${{ inputs.source_branch || 'develop' }} + +jobs: + create-pull-request: + runs-on: ubuntu-latest + steps: + - name: Checkout ${{ env.SOURCE_BRANCH }} branch + uses: actions/checkout@v6 + with: + ref: ${{ env.SOURCE_BRANCH }} + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Create PR from ${{ env.SOURCE_BRANCH }} to ${{ env.DEFAULT_BRANCH }} + env: + GH_TOKEN: ${{ steps.bot.outputs.token }} + run: | + gh pr create \ + --base ${{ env.DEFAULT_BRANCH }} \ + --head ${{ env.SOURCE_BRANCH }} \ + --title "🎉 Release: merge ${{ env.SOURCE_BRANCH }} into ${{ env.DEFAULT_BRANCH }}" \ + --label "[bot] release" \ + --body "This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from \`${{ env.SOURCE_BRANCH }}\` into \`${{ env.DEFAULT_BRANCH }}\`. + + ⚠️ It is labeled \`[bot] release\` and is excluded from release notes and version bump logic." diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml new file mode 100644 index 0000000..0f43db3 --- /dev/null +++ b/.github/workflows/security.yml @@ -0,0 +1,93 @@ +# Code scanning (CodeQL) for vulnerabilities and insecure coding patterns. +# +# What this workflow does +# - Runs GitHub CodeQL analysis and uploads results to your repository's Security tab. +# - Triggers on PRs (so findings appear as PR checks) and on pushes to `develop`. +# - Runs on a weekly schedule. +# +# Where to find results on GitHub +# - Repository → Security → Code scanning alerts +# (You can filter by tool = CodeQL and by branch.) +# +# Where to configure on GitHub +# - Repository → Settings → Advanced Security +# Enable "GitHub Advanced Security" (if available) and configure CodeQL there. +# - Repository → Security → Code scanning alerts +# This page shows findings produced by this workflow. +# +# Notes about the scheduled run +# - Scheduled workflows are triggered from the repository's *default branch*. +# If your default branch is `master` but you want the scheduled scan to analyze +# `develop`, this workflow checks out `develop` explicitly for scheduled runs. +# +# References +# - CodeQL Action: https://github.com/github/codeql-action +# - Advanced setup docs: https://docs.github.com/en/code-security/code-scanning + +name: Security scans with CodeQL + +on: + # Run on pull requests so results show up as PR checks and code + # scanning alerts. + pull_request: + branches: [master, main, develop] + + # Run on pushes (e.g., after merging PRs). + push: + branches: [master, main, develop] + + # Run weekly. (Cron is in UTC.) + schedule: + - cron: '0 3 * * 1' + +permissions: + contents: read + security-events: write + +jobs: + codeql: + name: Code scanning + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + # Keep this list tight to avoid noise and speed up runs. + language: [python, actions] + + steps: + # Scheduled workflows run from the default branch. + # We explicitly analyze `develop` on the schedule to keep the scan + # focused on the active dev branch. + - name: Checkout repository (scheduled → develop) + if: ${{ github.event_name == 'schedule' }} + uses: actions/checkout@v6 + with: + ref: develop + + - name: Checkout repository + if: ${{ github.event_name != 'schedule' }} + uses: actions/checkout@v6 + + - name: Initialize CodeQL + uses: github/codeql-action/init@v4 + with: + languages: ${{ matrix.language }} + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v4 + + print-link: + name: Print results link + runs-on: ubuntu-latest + + needs: codeql + permissions: {} # no special perms needed just to print links + + steps: + - name: Add Code Scanning link to job summary + run: | + echo "## 🔎 CodeQL Results" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "View Code Scanning alerts here:" >> $GITHUB_STEP_SUMMARY + echo "${{ github.server_url }}/${{ github.repository }}/security/code-scanning" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/test-trigger.yml b/.github/workflows/test-trigger.yml new file mode 100644 index 0000000..440bae3 --- /dev/null +++ b/.github/workflows/test-trigger.yml @@ -0,0 +1,40 @@ +name: Scheduled code tests trigger + +on: + # Run daily, at 00:00. + schedule: + - cron: '0 0 * * *' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +permissions: + contents: read + +jobs: + code-tests-trigger: + runs-on: ubuntu-latest + + steps: + - name: Checkout develop branch + uses: actions/checkout@v6 + with: + ref: develop + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Dispatch code tests workflow + uses: ./.github/actions/github-script + with: + github-token: ${{ steps.bot.outputs.token }} + script: | + await github.rest.actions.createWorkflowDispatch({ + owner: context.repo.owner, + repo: context.repo.repo, + workflow_id: "test.yml", + ref: "develop" + }); diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..ff7e4e9 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,302 @@ +# This is the main workflow for testing the code before and after +# packaging it. +# The workflow is divided into three jobs: +# 1. env-prepare: +# - Prepare the environment for testing +# 2. source-test: +# - Test the code base against the latest code in the repository +# - Create the Python package +# - Upload the Python package for the next job +# 3. package-test: +# - Download the Python package (including extra files) from the previous job +# - Install the downloaded Python package +# - Test the code base against the installed package +# 4. dashboard-build-trigger: +# - Trigger the dashboard build workflow to update the code quality +# metrics on the dashboard + +name: Code and package tests + +on: + # Trigger the workflow on push + push: + branches-ignore: [master, main] # Already verified in PR + # But do not run this workflow on creating a new tag starting with + # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) + tags-ignore: ['v*'] + # Trigger the workflow on pull request + pull_request: + branches: ['**'] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Need permissions to trigger the dashboard build workflow +permissions: + actions: write + contents: read + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + PY_VERSIONS: '3.11 3.13' + PIXI_ENVS: 'py-311-env py-313-env' + +jobs: + # Job 1: Set up environment variables + env-prepare: + runs-on: [ubuntu-latest] + + outputs: + pytest-marks: ${{ steps.set-mark.outputs.pytest_marks }} + + steps: + # Determine if integration tests should be run fully or only the fast ones + # (to save time on branches other than master and develop) + - name: Set mark for integration tests + id: set-mark + run: | + if [[ "${{ env.CI_BRANCH }}" == "master" || "${{ env.CI_BRANCH }}" == "develop" ]]; then + echo "pytest_marks=" >> $GITHUB_OUTPUT + else + echo "pytest_marks=-m fast" >> $GITHUB_OUTPUT + fi + + # Job 2: Test code + source-test: + needs: env-prepare # depend on previous job + + strategy: + fail-fast: false + matrix: + os: [ubuntu-24.04, macos-15, windows-2022] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + with: + environments: ${{ env.PIXI_ENVS }} + + - name: Run unit tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + echo "Running tests in environment: $env" + pixi run --environment $env unit-tests + done + + # - name: Run functional tests + # shell: bash + # run: | + # set -euo pipefail + + # for py_ver in $PY_VERSIONS; do + # echo + # echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + # env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + # echo "Running tests in environment: $env" + # pixi run --environment $env functional-tests + # done + + - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }} + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + echo "Running tests in environment: $env" + pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }} + done + + # Delete all local tags when not on a tagged commit to force versioningit + # to fall back to the configured default-tag, which is '999.0.0' in our case. + # This is needed for testing the package in the next job, as its version + # must be higher than the PyPI version for pip to prefer the local version. + - name: Force using versioningit default tag (non tagged release) + if: startsWith(github.ref , 'refs/tags/v') != true + run: git tag --delete $(git tag) + + - name: Build package wheels for all Python versions + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env + + echo "Building wheel in environment: $env" + pixi run --environment $env dist-build + + echo "Moving built wheel to dist/py$py_ver/" + pixi run mkdir -p dist/py$py_ver + pixi run mv dist/*.whl dist/py$py_ver/ + done + + - name: Remove Python cache files before uploading + shell: bash + run: pixi run clean-pycache + + # More than one file/dir need to be specified in 'path', to preserve the + # structure of the dist/ directory, not only its contents. + - name: Upload package (incl. extras) for next job + uses: ./.github/actions/upload-artifact + with: + name: easyimaging_${{ matrix.os }}_${{ runner.arch }} + path: dist/ + + # Job 3: Test the package + package-test: + needs: source-test # depend on previous job + + strategy: + fail-fast: false + matrix: + os: [ubuntu-24.04, macos-15, windows-2022] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Download package (incl. extras) from previous job + uses: ./.github/actions/download-artifact + with: + # name and path should be taken from the upload step of the previous job + name: easyimaging_${{ matrix.os }}_${{ runner.arch }} + path: dist/ + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + with: + environments: '' + activate-environment: '' + run-install: false + frozen: false + + - name: Install easyimaging from the built wheel + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Initializing pixi project" + pixi init easyimaging_py$py_ver + cd easyimaging_py$py_ver + + echo "Adding Python $py_ver" + pixi add "python=$py_ver" + + echo "Setting macOS 14.0 as minimum required" + pixi project system-requirements add macos 14.0 + + echo "Looking for wheel in ../dist/py$py_ver/" + ls -l "../dist/py$py_ver/" + + whl_path=(../dist/"py$py_ver"/*.whl) + if [[ ! -f "${whl_path[0]}" ]]; then + echo "❌ No wheel found in ../dist/py$py_ver/" + exit 1 + fi + + whl_abs_path="$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")" + + echo "Adding easyimaging from: $whl_abs_path" + pixi add --pypi "easyimaging[dev] @ ${whl_abs_path}" + + echo "Exiting pixi project directory" + cd .. + done + + - name: Run unit tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Entering pixi project directory easyimaging_py$py_ver" + cd easyimaging_py$py_ver + + echo "Running tests" + pixi run python -m pytest ../tests/unit/ --color=yes -v + + echo "Exiting pixi project directory" + cd .. + done + + # - name: Run functional tests + # shell: bash + # run: | + # set -euo pipefail + + # for py_ver in $PY_VERSIONS; do + # echo + # echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + # echo "Entering pixi project directory easyimaging_py$py_ver" + # cd easyimaging_py$py_ver + + # echo "Running tests" + # pixi run python -m pytest ../tests/functional/ --color=yes -v + + # echo "Exiting pixi project directory" + # cd .. + # done + + - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }} + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Entering pixi project directory easyimaging_py$py_ver" + cd easyimaging_py$py_ver + + echo "Running tests" + pixi run python -m pytest ../tests/integration/ --color=yes -n auto -v ${{ needs.env-prepare.outputs.pytest-marks }} + + echo "Exiting pixi project directory" + cd .. + done + + # Job 4: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: package-test # depend on previous job + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.github/workflows/tutorial-tests-trigger.yml b/.github/workflows/tutorial-tests-trigger.yml new file mode 100644 index 0000000..4b160d8 --- /dev/null +++ b/.github/workflows/tutorial-tests-trigger.yml @@ -0,0 +1,40 @@ +name: Scheduled tutorial tests trigger + +on: + # Run daily, at 00:00. + schedule: + - cron: '0 0 * * *' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +permissions: + contents: read + +jobs: + tutorial-tests-trigger: + runs-on: ubuntu-latest + + steps: + - name: Checkout develop branch + uses: actions/checkout@v6 + with: + ref: develop + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Dispatch tutorial tests workflow + uses: ./.github/actions/github-script + with: + github-token: ${{ steps.bot.outputs.token }} + script: | + await github.rest.actions.createWorkflowDispatch({ + owner: context.repo.owner, + repo: context.repo.repo, + workflow_id: "tutorial-tests.yml", + ref: "develop" + }); diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml new file mode 100644 index 0000000..a4fc940 --- /dev/null +++ b/.github/workflows/tutorial-tests.yml @@ -0,0 +1,60 @@ +name: Tutorial tests + +on: + # Trigger the workflow on push + push: + # Selected branches + branches: [develop] # master and main are already verified in PR + # Trigger the workflow on pull request + pull_request: + branches: ['**'] + # Trigger the workflow on workflow_call (to be called from other workflows) + # Needed, as standard schedule triggers the master branch only, but we want + # to run this workflow on develop branch. + workflow_call: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +permissions: + contents: read + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + +jobs: + # Job 1: Test tutorials as scripts and notebooks on multiple OS + tutorial-tests: + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, macos-latest, windows-latest] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Prepare notebooks + shell: bash + run: pixi run notebook-prepare + + - name: Test tutorials as notebooks + shell: bash + run: pixi run notebook-tests + + # Job 2: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: tutorial-tests # depend on previous job + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.github/workflows/verify_issue_labels.yml b/.github/workflows/verify_issue_labels.yml deleted file mode 100644 index 69ec3a1..0000000 --- a/.github/workflows/verify_issue_labels.yml +++ /dev/null @@ -1,31 +0,0 @@ -# This workflow will verify that all issues have at -# least one of the [scope] labels and one of the [priority] labels - -name: Verify issue labels -on: - issues: - types: [opened, labeled, unlabeled] - -jobs: - check_issue_labels: - runs-on: ubuntu-latest - permissions: - issues: write - steps: - - name: Require [scope] label - uses: trstringer/require-label-prefix@v1 - with: - secret: ${{ github.TOKEN }} - prefix: "[scope]" - addLabel: true - defaultLabel: "[scope] ⚠️ label needed" - - - name: Require [priority] label - if: always() - uses: trstringer/require-label-prefix@v1 - with: - secret: ${{ github.TOKEN }} - prefix: "[priority]" - addLabel: true - defaultLabel: "[priority] ⚠️ label needed" - diff --git a/.github/workflows/verify_pr_labels.yml b/.github/workflows/verify_pr_labels.yml deleted file mode 100644 index e7eb0f5..0000000 --- a/.github/workflows/verify_pr_labels.yml +++ /dev/null @@ -1,23 +0,0 @@ -# This workflow will verify that all PRs have at -# least one of the [scope] labels before they can be merged. - -name: Verify PR labels -on: - pull_request_target: - types: [opened, labeled, unlabeled, synchronize] - -jobs: - check_pr_label: - runs-on: ubuntu-latest - permissions: - pull-requests: write - name: Verify that the PR has a valid label - steps: - - name: Verify PR label action - uses: jesusvasquez333/verify-pr-label-action@v1.4.0 - id: verify-pr-label - with: - github-token: ${{ github.TOKEN }} - valid-labels: '[scope] bug, [scope] enhancement, [scope] documentation, [scope] significant, [scope] maintenance' - pull-request-number: ${{ github.event.pull_request.number }} - disable-reviews: false diff --git a/.gitignore b/.gitignore index 772dbfe..5034033 100644 --- a/.gitignore +++ b/.gitignore @@ -1,48 +1,49 @@ -# QtCreator -*.autosave - -# QtCreator Qml -*.qmlproject.user -*.qmlproject.user.* - -# QtCreator Python -*.pyproject.user -*.pyproject.user.* - -# QtCreator CMake -CMakeLists.txt.user* - # Python -__pycache__ -.venv +__pycache__/ +.venv/ .coverage .pyc -# Poetry -dist -poetry.lock -*.egg-info +# Pixi +.pixi/ # PyInstaller -build +dist/ +build/ *.spec -# Jupyter +# MkDocs +docs/site/ + +# Jupyter Notebooks .ipynb_checkpoints +# Node +node_modules/ + +# QtCreator +*.autosave +*.qmlproject.user +*.qmlproject.user.* +*.pyproject.user +*.pyproject.user.* +CMakeLists.txt.user* + +# PyCharm +.idea/ + +# VS Code +.vscode/ + # macOS .DS_Store *.app *.dmg -# Docs -docs/_build - -# VSCode -.vscode - -# Pixi -.pixi/ +# Misc +.cache/ +*.log +*.zip # Large files *.hdf @@ -50,11 +51,4 @@ docs/_build *sample.tiff *open_beam.tiff ProofOfConcept/sample_data/*.tiff -ProofOfConcept/sample_data/* - -# Misc -..* -*.log -*.zip -.ci/ -.idea/ +ProofOfConcept/sample_data/* \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..9a3855f --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,61 @@ +repos: + - repo: local + hooks: + # ------------- + # Manual checks + # ------------- + - id: pixi-pyproject-check + name: pixi run pyproject-check + entry: pixi run pyproject-check + language: system + pass_filenames: false + stages: [manual] + + - id: license-headers-check + name: pixi run license-check + entry: pixi run license-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-py-lint-check + name: pixi run py-lint-check + entry: pixi run py-lint-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-py-format-check + name: pixi run py-format-check + entry: pixi run py-format-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-docstring-lint-check + name: pixi run docstring-lint-check + entry: pixi run docstring-lint-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-nonpy-format-check + name: pixi run nonpy-format-check + entry: pixi run nonpy-format-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-notebook-lint-check + name: pixi run notebook-lint-check + entry: pixi run notebook-lint-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-unit-tests + name: pixi run unit-tests + entry: pixi run unit-tests + language: system + pass_filenames: false + stages: [manual] diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 0000000..ec19b5e --- /dev/null +++ b/.prettierignore @@ -0,0 +1,35 @@ +# Git +.git/ + +# Copier +.copier-answers*.yml + +# Pixi +.pixi +pixi.lock + +# MkDocs +docs/overrides/ +docs/site/ +docs/docs/assets/ + +# Python +.pytest_cache/ + +# MyPy +.mypy_cache/ + +# Ruff +.ruff_cache/ + +# Node +node_modules + +# Tox +.tox + +# Misc +.benchmarks +.cache +deps/ +tmp/ diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..49a61c0 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,448 @@ +# Contributing to EasyImaging + +Thank you for your interest in contributing to **EasyImaging**! + +This guide explains how you can: + +- Report issues +- Contribute code +- Improve documentation +- Suggest enhancements +- Interact with the EasyScience community + +Whether you are an experienced developer or contributing for the first +time, this document walks you through the entire process step by step. + +Please make sure you follow the EasyScience organization-wide +[Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md). + +--- + +## Table of Contents + +- [How to Interact With This Project](#how-to-interact-with-this-project) +- [1. Understanding the Development Model](#1-understanding-the-development-model) +- [2. Getting the Code](#2-getting-the-code) +- [3. Setting Up the Development Environment](#3-setting-up-the-development-environment) +- [4. Creating a Branch](#4-creating-a-branch) +- [5. Implementing Your Changes](#5-implementing-your-changes) +- [6. Code Quality Checks](#6-code-quality-checks) +- [7. Opening a Pull Request](#7-opening-a-pull-request) +- [8. Continuous Integration (CI)](#8-continuous-integration-ci) +- [9. Code Review](#9-code-review) +- [10. Documentation Contributions](#10-documentation-contributions) +- [11. Reporting Issues](#11-reporting-issues) +- [12. Security Issues](#12-security-issues) +- [13. Releases](#13-releases) + +--- + +## How to Interact With This Project + +If you are not planning to contribute code, you may want to: + +- 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues) +- 🛡 Report a security issue — see [Security Issues](#12-security-issues) +- 💬 Ask a question or start a discussion at + [Project Discussions](https://github.com/easyscience/imaging-lib/discussions) + +If you plan to contribute code or documentation, continue below. + +--- + +## 1. Understanding the Development Model + +Before you start coding, it is important to understand how development +works in this project. + +### Branching Strategy + +We use the following branches: + +- `master` — stable releases only +- `develop` — active development branch +- Short-lived branches — feature or fix branches created for a single + contribution and deleted after merge + +> [!IMPORTANT] +> +> All normal contributions must target the `develop` branch. +> +> - Do **not** open Pull Requests against `master` +> - Always create your branch from `develop` +> - Always target `develop` when opening a Pull Request + +See ADR easyscience/.github#12 for more details on the branching +strategy. + +--- + +## 2. Getting the Code + +### 2.1. If You Are an External Contributor + +If you are not a core maintainer of this repository, follow these steps. + +1. Open the repository page: `https://github.com/easyscience/imaging-lib` + +2. Click the **Fork** button (top-right corner). This creates your own + copy of the repository. + +3. Clone your fork locally: + + ```bash + git clone https://github.com//imaging-lib.git + cd imaging-lib + ``` + +4. Add the original repository as `upstream`: + + ```bash + git remote add upstream https://github.com/easyscience/imaging-lib.git + ``` + +5. Switch to the `develop` branch and update it: + + ```bash + git fetch upstream + git checkout develop + git pull upstream develop + ``` + +If you have contributed before, make sure your local `develop` branch is +up to date before starting new work. You can update it with: + +```bash +git fetch upstream +git pull upstream develop +``` + +This ensures you are working on the latest version of the project. + +### 2.2. If You Are a Core Team Member + +Core team members can create branches directly in this repository and +therefore do not need to fork it, but the rest of the workflow remains +the same. + +--- + +## 3. Setting Up the Development Environment + +You need: + +- Git +- Pixi + +EasyScience projects use **Pixi** to manage the development environment. + +To install Pixi, follow the official instructions: +https://pixi.prefix.dev/latest/installation/ + +You do **not** need to manually install Python. Pixi automatically: + +- Creates the correct Python environment +- Installs all required dependencies +- Installs development tools (linters, formatters, test tools) + +Set up the environment: + +```bash +pixi install +pixi run post-install # Install additional tooling +``` + +After this step, your development environment is ready. + +See ADR easyscience/.github#63 for more details about using Pixi for +development. + +--- + +## 4. Creating a Branch + +Never work directly on `develop`. + +Create a new branch: + +```bash +git checkout -b my-change develop +``` + +> [!IMPORTANT] +> +> Use a clear and descriptive name, for example: +> +> - `improve-solver-speed` +> - `fix-boundary-condition` +> - `add-tutorial-example` + +Clear branch names make reviews and history easier to understand. + +--- + +## 5. Implementing Your Changes + +While developing, make small, logical commits with clear messages. + +Example: + +```bash +git add . +git commit -m "Improve performance of time integrator for large systems" +``` + +--- + +## 6. Code Quality Checks + +> [!IMPORTANT] +> +> When adding new functionality or making changes, make sure to add or +> update the following as needed: +> +> - 📘 docstrings +> - 🧪 unit tests + +Before opening a Pull Request, always run: + +```bash +pixi run check +``` + +This command: + +- Validates the pyproject.toml file +- Checks for licence headers in code files +- Identifies linting and formatting issues in Python code +- Checks docstring linting and formatting issues in Python code +- Detects formatting issues in non-Python files (MD, YAML, TOML etc.) +- Checks linting issues in Jupyter notebooks (if applicable) +- Runs unit tests + +A successful run should look like this: + +```bash +pixi run pyproject-check.......................Passed +pixi run license-check.........................Passed +pixi run py-lint-check.........................Passed +pixi run py-format-check.......................Passed +pixi run docstring-lint-check..................Passed +pixi run nonpy-format-check....................Passed +pixi run notebook-lint-check...................Passed +pixi run unit-tests............................Passed +``` + +If something fails, read the error message carefully and fix the issue. + +You can run individual checks, for example, to run only unit tests: + +```bash +pixi run unit-tests +``` + +or to run only Python linting checks: + +```bash +pixi run py-lint-check +``` + +To add missing license headers: + +```bash +pixi run spdx-add +``` + +Some formatting issues can be fixed automatically: + +```bash +pixi run fix +``` + +If everything is correctly formatted, you will see: + +```text +✅ All auto-formatting steps completed successfully! +``` + +This indicates that the auto-formatting pipeline completed successfully. +If you do not see this message and no error messages appear, try running +the command again. + +If errors are reported, resolve them and re-run: + +```bash +pixi run check +``` + +> [!IMPORTANT] +> +> All checks must pass before your Pull Request can be merged. + +If you are unsure how to fix an issue, ask for help in your Pull Request +discussion. + +--- + +## 7. Opening a Pull Request + +Push your branch: + +```bash +git push origin my-change +``` + +On GitHub: + +- Click **Compare & Pull Request** +- Ensure the base branch is `develop` +- Write a clear and concise title +- Add a description explaining what changed and why +- Add the required `[scope]` label + +### Pull Request Title + +> [!IMPORTANT] +> +> The PR title appears in release notes and changelogs. It should be +> concise and informative. + +Good examples: + +- Improve performance of time integrator for large systems +- Fix incorrect boundary condition handling in solver +- Add adaptive step-size control to ODE solver +- Add tutorial for custom model configuration +- Refactor solver API for improved readability + +### Required `[scope]` Label + +> [!IMPORTANT] +> +> Each Pull Request must include a `[scope]` label, which is used for +> automatically suggesting version bumps when preparing a new release. + +The available scopes are: + +| Label | Description | +| ----------------------- | ----------------------------------------------------------------------- | +| `[scope] bug` | Bug report or fix (major.minor.**PATCH**) | +| `[scope] documentation` | Documentation-only changes (major.minor.patch.**POST**) | +| `[scope] enhancement` | Adds or improves features (major.**MINOR**.patch) | +| `[scope] maintenance` | Code/tooling cleanup without feature or bug fix (major.minor.**PATCH**) | +| `[scope] significant` | Breaking or major changes (**MAJOR**.minor.patch) | + +See ADR easyscience/.github#33 for more details on the standardized +labeling scheme. + +--- + +## 8. Continuous Integration (CI) + +After opening a Pull Request: + +- Automated checks run automatically +- You will see green checkmarks or red crosses + +If checks fail: + +1. Open the failing check +2. Read the logs +3. Fix the issue locally +4. Run `pixi run check` +5. Push your changes + +The Pull Request updates automatically. + +--- + +## 9. Code Review + +All Pull Requests are reviewed by at least one core team member. + +Code review is collaborative and aims to improve quality. + +Do not take comments personally — they are meant to help. + +To update your PR: + +```bash +git add . +git commit -m "Address review comments" +git push +``` + +--- + +## 10. Documentation Contributions + +> [!IMPORTANT] +> +> If your change affects user-facing functionality, update the project +> documentation accordingly — specifically the `nav:` (navigation) +> structure in `mkdocs.yml` and the relevant documentation Markdown files +> in `docs/docs/`. +> +> ```text +> 📁 docs +> ├── 📁 docs - Markdown files for documentation +> │ └── ... +> └── 📄 mkdocs.yml - Configuration file (navigation, theme, etc.) +> ``` + +This may include: + +- API documentation +- Examples +- Tutorials +- Jupyter notebooks + +Preview documentation locally: + +```bash +pixi run docs-serve +``` + +Open the URL shown in the terminal to review your changes. + +--- + +## 11. Reporting Issues + +If you find a bug but cannot work on a fix, please consider opening an +issue. + +When reporting an issue, it helps to: + +- Search existing issues first. +- Provide clear reproduction steps. +- Include logs, screenshots, and environment details. + +Clear and detailed reports help maintainers investigate and resolve +issues more effectively. + +--- + +## 12. Security Issues + +> [!IMPORTANT] +> +> Please do **not** report security vulnerabilities publicly. + +If you discover a potential vulnerability, please contact the maintainers +privately so the issue can be investigated and addressed responsibly. + +--- + +## 13. Releases + +Once your contribution is merged into `develop`, it will eventually be +included in the next stable release. + +When enough changes have accumulated in `develop`, core team members +merge `develop` into `master` to prepare a new release. The release is +then tagged and published on GitHub and PyPI. + +--- + +Thank you for contributing to EasyImaging and the EasyScience ecosystem! diff --git a/LICENSE b/LICENSE index c1ee0cf..25f8a20 100644 --- a/LICENSE +++ b/LICENSE @@ -1,7 +1,6 @@ BSD 3-Clause License -Copyright (c) 2024, Easyscience contributors (https://github.com/EasyScience) -All rights reserved. +Copyright (c) 2024-2026 EasyScience contributors. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/README.md b/README.md index 43830ef..3721732 100644 --- a/README.md +++ b/README.md @@ -2,14 +2,54 @@ [![PyPI badge](http://img.shields.io/pypi/v/EasyImaging.svg)](https://pypi.python.org/pypi/EasyImaging) [![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](LICENSE) - +

+ + + + + + + EasyImaging + +

-## About +**EasyImaging** is a software for performing Bragg-edge calculations +based on a crystalliographic model and refining its parameters against +experimental data. -Python package for bragg-edge analysis + -## Installation +**EasyImaging** is developed both as a Python library and as a +cross-platform desktop application. -```sh -python -m pip install easyimaging -``` +Here, we focus on the Python library. For the graphical user interface +(GUI), please see the corresponding +[GUI resources](https://github.com/easyscience/imaging-app). + +License: +[BSD 3-Clause](https://github.com/easyscience/imaging-lib/blob/master/LICENSE) + +## Useful Links + +### For Users + +- 📖 [Documentation](https://easyscience.github.io/imaging-lib/latest) +- 🚀 + [Getting Started](https://easyscience.github.io/imaging-lib/latest/introduction) +- 🧪 + [Tutorials](https://easyscience.github.io/imaging-lib/latest/tutorials) +- 💬 + [Get in Touch](https://easyscience.github.io/imaging-lib/latest/introduction/#get-in-touch) +- 🧾 + [Citation](https://easyscience.github.io/imaging-lib/latest/introduction/#citation) + +### For Contributors + +- 🧑‍💻 [Source Code](https://github.com/easyscience/imaging-lib) +- 🐞 [Issue Tracker](https://github.com/easyscience/imaging-lib/issues) +- 💡 + [Discussions](https://github.com/easyscience/imaging-lib/discussions) +- 🤝 + [Contributing Guide](https://github.com/easyscience/imaging-lib/blob/master/CONTRIBUTING.md) +- 🛡 + [Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md) diff --git a/docs/docs/api-reference/index.md b/docs/docs/api-reference/index.md new file mode 100644 index 0000000..62b1c78 --- /dev/null +++ b/docs/docs/api-reference/index.md @@ -0,0 +1,8 @@ +--- +icon: material/code-braces-box +--- + +# :material-code-braces-box: API Reference + +This section contains the reference detailing the functions and modules +available in EasyImaging. diff --git a/docs/docs/assets/images/favicon.png b/docs/docs/assets/images/favicon.png new file mode 100644 index 0000000..2a9b4c4 Binary files /dev/null and b/docs/docs/assets/images/favicon.png differ diff --git a/docs/docs/assets/images/logo_dark.svg b/docs/docs/assets/images/logo_dark.svg new file mode 100644 index 0000000..0f47840 --- /dev/null +++ b/docs/docs/assets/images/logo_dark.svg @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + Logo + + Main circle + + + + + + + Text + + + + + \ No newline at end of file diff --git a/docs/docs/assets/images/logo_light.svg b/docs/docs/assets/images/logo_light.svg new file mode 100644 index 0000000..9495214 --- /dev/null +++ b/docs/docs/assets/images/logo_light.svg @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + Logo + + Main circle + + + + + + + Text + + + + + \ No newline at end of file diff --git a/docs/docs/assets/javascripts/extra.js b/docs/docs/assets/javascripts/extra.js new file mode 100644 index 0000000..9596ee0 --- /dev/null +++ b/docs/docs/assets/javascripts/extra.js @@ -0,0 +1,27 @@ +;(function () { + 'use strict' + + // Variables + const header = document.getElementsByTagName('header')[0] + + console.log(window.pageYOffset) + + // Hide-show header shadow + function toggleHeaderShadow() { + if (window.pageYOffset <= 0) { + header.classList.remove('md-header--shadow') + } else { + header.classList.add('md-header--shadow') + } + } + + // Onload + window.onload = function () { + toggleHeaderShadow() + } + + // Onscroll + window.onscroll = function () { + toggleHeaderShadow() + } +})() diff --git a/docs/docs/assets/javascripts/mathjax.js b/docs/docs/assets/javascripts/mathjax.js new file mode 100644 index 0000000..333524e --- /dev/null +++ b/docs/docs/assets/javascripts/mathjax.js @@ -0,0 +1,33 @@ +window.MathJax = { + tex: { + //inlineMath: [['\\(', '\\)']], + //displayMath: [['\\[', '\\]']], + // Add support for $...$ and \(...\) delimiters + inlineMath: [ + ['$', '$'], + ['\\(', '\\)'], + ], + // Add support for $$...$$ and \[...]\ delimiters + displayMath: [ + ['$$', '$$'], + ['\\[', '\\]'], + ], + processEscapes: true, + processEnvironments: true, + }, + options: { + //ignoreHtmlClass: ".*|", + //processHtmlClass: "arithmatex" + // Skip code blocks only + skipHtmlTags: ['script', 'noscript', 'style', 'textarea', 'pre', 'code'], + // Only ignore explicit opt-out + ignoreHtmlClass: 'no-mathjax|tex2jax_ignore', + }, +} + +document$.subscribe(() => { + MathJax.startup.output.clearCache() + MathJax.typesetClear() + MathJax.texReset() + MathJax.typesetPromise() +}) diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css new file mode 100644 index 0000000..a625be8 --- /dev/null +++ b/docs/docs/assets/stylesheets/extra.css @@ -0,0 +1,359 @@ +/*************/ +/* Variables */ +/*************/ + +:root { + --sz-link-color--lightmode: #0184c7; + --sz-hovered-link-color--lightmode: #37bdf9; + --sz-body-background-color--lightmode: #fafafa; + --sz-body-text-color--lightmode: #525252; + --sz-body-heading-color--lightmode: #434343; + --sz-code-background-color--lightmode: #ececec; + + --sz-link-color--darkmode: #37bdf9; + --sz-hovered-link-color--darkmode: #2890c0; + --sz-body-background-color--darkmode: #262626; + --sz-body-text-color--darkmode: #a3a3a3; + --sz-body-heading-color--darkmode: #e5e5e5; + --sz-code-background-color--darkmode: #212121; +} + +/****************/ +/* Color styles */ +/****************/ + +/* Default styles https://github.com/squidfunk/mkdocs-material/blob/master/src/assets/stylesheets/main/_typeset.scss */ + +/* Light mode */ + +/* Default light mode https://github.com/squidfunk/mkdocs-material/blob/master/src/assets/stylesheets/main/_colors.scss */ + +[data-md-color-scheme="default"] { + + /* Primary color shades */ + --md-primary-fg-color: var(--sz-body-background-color--lightmode); /* Navigation background */ + --md-primary-bg-color: var(--sz-body-text-color--lightmode); /* E.g., Header title and icons */ + --md-primary-bg-color--light: var(--sz-body-text-color--lightmode); /* E.g., Header search */ + + /* Accent color shades */ + --md-accent-fg-color: var(--sz-hovered-link-color--lightmode); /* E.g., Hovered `a` elements & copy icon in code */ + + /* Default color shades */ + --md-default-fg-color: var(--sz-body-text-color--lightmode); + --md-default-fg-color--light: var(--sz-body-heading-color--lightmode); /* E.g., `h1` color & TOC viewed items & `$` in code */ + --md-default-fg-color--lighter: var(--sz-body-text-color--lightmode); /* E.g., `¶` sign near `h1-h8` */ + --md-default-fg-color--lightest: var(--sz-body-text-color--lightmode); /* E.g., Copy icon in code */ + --md-default-bg-color: var(--sz-body-background-color--lightmode); + + /* Code color shades */ + --md-code-bg-color: var(--sz-code-background-color--lightmode); + + /* Typeset color shades */ + --md-typeset-color: var(--sz-body-text-color--lightmode); + + /* Typeset `a` color shades */ + --md-typeset-a-color: var(--sz-link-color--lightmode); + + /* Footer color shades */ + --md-footer-fg-color: var(--sz-body-text-color--lightmode); /* E.g., Next -> */ + --md-footer-fg-color--light: var(--sz-body-text-color--lightmode); /* E.g., © 2022 EasyDiffraction, Material for MkDocs */ + --md-footer-fg-color--lighter: var(--sz-body-text-color--lightmode); /* E.g. 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+} + +.jp-Notebook .jp-Cell { + /* Key: flex children often need min-width: 0 to prevent weird shrink */ + width: 100% !important; + max-width: 100% !important; + min-width: 0 !important; + + /* Removes jupyter cell paddings */ + padding-left: 0 !important; +} + +/* Removes jupyter cell prefixes, like In[123]: */ +.prompt, +.jp-InputPrompt, +.jp-OutputPrompt { + display: none !important; +} + +/* Removes jupyter output cell padding to align with input cell text */ +.jp-RenderedText { + padding-left: 0.85em !important; +} + +/* Extra styling the panda dataframes, on top of the style included in the code */ +table.dataframe { + float: left; + margin-left: 0.75em !important; + margin-bottom: 0.5em !important; + font-size: var(--jp-code-font-size) !important; + color: var(--md-primary-bg-color) !important; + /* Allow table cell wrapping in MkDocs-Jupyter outputs */ + /* + table-layout: auto !important; + width: auto !important; + */ +} + +/* Allow wrap for the last column */ +/* +table.dataframe td:last-child, +table.dataframe th:last-child { + white-space: normal !important; + word-break: break-word !important; +} +*/ + +/* Custom styles for the CIF files */ + +.cif { + padding-left: 1em; + padding-right: 1em; + padding-top: 1px; + padding-bottom: 1px; + background-color: var(--md-code-bg-color); + font-size: small; +} +.red { + color: var(--sz-red-color); +} +.green { + color: var(--sz-green-color); +} +.blue { + color: var(--sz-blue-color); +} +.orange { + color: var(--sz-orange-color); +} +.grey { + color: grey; +} + +/**********/ +/* Labels */ +/**********/ + +.label-cif { + padding-top: 0.5ex; + padding-bottom: 0.5ex; + padding-left: 0.9ex; + padding-right: 0.9ex; + border-radius: 1ex; + color: var(--md-default-fg-color) !important; + background-color: var(--md-code-bg-color); +} + +p .label-cif, li .label-cif { + vertical-align: 5%; + font-size: 12px; +} + +.label-cif:hover { + color: white !important; +} + +.label-experiment { + padding-top: 0.25ex; + padding-bottom: 0.6ex; + padding-left: 0.9ex; + padding-right: 0.9ex; + border-radius: 1ex; + color: var(--md-default-fg-color) !important; + background-color: rgba(55, 189, 249, 0.1); +} + +p .label-experiment, li .label-experiment { + vertical-align: 5%; + font-size: 12px; +} + +h1 .label-experiment { + padding-top: 0.05ex; + padding-bottom: 0.4ex; + padding-left: 0.9ex; + padding-right: 0.9ex; + border-radius: 0.75ex; + color: var(--md-default-fg-color) !important; + background-color: rgba(55, 189, 249, 0.1); +} + +.label-experiment:hover { + color: white !important; +} diff --git a/docs/docs/index.md b/docs/docs/index.md new file mode 100644 index 0000000..93c9fee --- /dev/null +++ b/docs/docs/index.md @@ -0,0 +1,21 @@ +![](assets/images/logo_dark.svg#gh-dark-mode-only)![](assets/images/logo_light.svg#gh-light-mode-only) + +# Neutron imaging data analysis + +Here is a brief overview of the main documentation sections: + +- [:material-information-slab-circle: Introduction](introduction/index.md) + – Provides a description of EasyImaging, including its purpose, + licensing, latest release details, and contact information. +- [:material-cog-box: Installation & Setup](installation-and-setup/index.md) + – Guides users through system requirements, environment configuration, + and the installation process. +- [:material-book-open-variant: User Guide](user-guide/index.md) – Covers + core concepts, key terminology, workflow steps, and essential + parameters for effective use of EasyImaging. +- [:material-school: Tutorials](tutorials/index.md) – Offers practical, + step-by-step examples demonstrating common workflows and data analysis + tasks. +- [:material-code-braces-box: API Reference](api-reference/index.md) – An + auto-generated reference detailing the available functions and modules + in EasyImaging. diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md new file mode 100644 index 0000000..45643bd --- /dev/null +++ b/docs/docs/installation-and-setup/index.md @@ -0,0 +1,278 @@ +--- +icon: material/cog-box +--- + +# :material-cog-box: Installation & Setup + +**EasyImaging** is a cross-platform Python library compatible with +**Python 3.11** through **3.13**. + +To install and set up EasyImaging, we recommend using +[**Pixi**](https://pixi.prefix.dev), a modern package manager for +Windows, macOS, and Linux. + +??? note "Main benefits of using Pixi" + + - **Ease of use**: Pixi simplifies the installation process, making it + accessible even for users with limited experience in package management. + - **Python version control**: Pixi allows specifying and managing different + Python versions for each project, ensuring compatibility. + - **Isolated environments**: Pixi creates isolated environments for each + project, preventing conflicts between different package versions. + - **PyPI and Conda support**: Pixi can install packages from both PyPI and + Conda repositories, providing access to a wide range of libraries. + +An alternative installation method using the traditional **pip** package +manager is also provided. + +## Installing with Pixi recommended { #installing-with-pixi data-toc-label="Installing with Pixi" } + +This section describes the simplest way to set up EasyImaging using +**Pixi**. + +#### Installing Pixi + +- Install Pixi by following the instructions on the + [official Pixi Installation Guide](https://pixi.prefix.dev/latest/installation). + +#### Setting up EasyImaging with Pixi + + + +- Choose a project location (local drive recommended). + + ??? warning ":fontawesome-brands-windows: Windows + OneDrive" + + We **do not recommend creating a Pixi project inside OneDrive or other + synced folders**. + + By default, Pixi creates the virtual environment inside the project + directory (in `.pixi/`). On Windows, synced folders such as OneDrive + may cause file‑system issues (e.g., path-length limitations or + restricted link operations), which can lead to unexpected install + errors or environments being recreated. + + Instead, create your project in a **local directory on your drive** + where you have full write permissions. + + + +- Initialize a new Pixi project and navigate into it: + ```txt + pixi init easyimaging + cd easyimaging + ``` +- Set the Python version for the Pixi environment (e.g., 3.13): + ```txt + pixi add python=3.13 + ``` +- Add EasyImaging to the Pixi environment from PyPI: + ```txt + pixi add --pypi easyimaging + ``` +- Add a Pixi task to run EasyImaging commands easily: + ```txt + pixi task add easyimaging "python -m easyimaging" + ``` + +#### Updating Pixi and EasyImaging + +- To update all packages in the Pixi environment, including EasyImaging: + ```txt + pixi update + ``` +- To update Pixi itself to the latest version: + ```txt + pixi self-update + ``` + +#### Uninstalling Pixi + +- Follow the + [official Pixi Guide](https://pixi.prefix.dev/latest/installation/#uninstall). + +## Classical Installation + +This section describes how to install EasyImaging using the traditional +method with **pip**. It is assumed that you are familiar with Python +package management and virtual environments. + +### Environment Setup optional { #environment-setup data-toc-label="Environment Setup" } + +We recommend using a **virtual environment** to isolate dependencies and +avoid conflicts with system-wide packages. If any issues arise, you can +simply delete and recreate the environment. + +#### Creating and Activating a Virtual Environment: + + + +- Create a new virtual environment: + ```txt + python3 -m venv venv + ``` +- Activate the environment: + + === ":material-apple: macOS" + ```txt + . venv/bin/activate + ``` + === ":material-linux: Linux" + ```txt + . venv/bin/activate + ``` + === ":fontawesome-brands-windows: Windows" + ```txt + . venv/Scripts/activate # Windows with Unix-like shells + .\venv\Scripts\activate.bat # Windows with CMD + .\venv\Scripts\activate.ps1 # Windows with PowerShell + ``` + +- The terminal should now show `(venv)`, indicating that the virtual environment + is active. + + + +#### Deactivating and Removing the Virtual Environment: + + + +- Exit the environment: + ```txt + deactivate + ``` +- If this environment is no longer needed, delete it: + + === ":material-apple: macOS" + ```txt + rm -rf venv + ``` + === ":material-linux: Linux" + ```txt + rm -rf venv + ``` + === ":fontawesome-brands-windows: Windows" + ```txt + rmdir /s /q venv + ``` + + + +### Installing from PyPI { #from-pypi } + +EasyImaging is available on **PyPI (Python Package Index)** and can be +installed using `pip`. To do so, use the following command: + +```txt +pip install easyimaging +``` + +To install a specific version of EasyImaging, e.g., 1.0.3: + +```txt +pip install 'easyimaging==1.0.3' +``` + +To upgrade to the latest version: + +```txt +pip install --upgrade easyimaging +``` + +To upgrade to the latest version and force reinstallation of all +dependencies (useful if files are corrupted): + +```txt +pip install --upgrade --force-reinstall easyimaging +``` + +To check the installed version: + +```txt +pip show easyimaging +``` + +### Installing from GitHub alternative { #from-github data-toc-label="Installing from GitHub" } + +Installing unreleased versions is generally not recommended but may be +useful for testing. + +To install EasyImaging from the `develop` branch of GitHub, for example: + +```txt +pip install git+https://github.com/easyscience/imaging-lib@develop +``` + +To include extra dependencies (e.g., dev): + +```txt +pip install 'easyimaging[dev] @ git+https://github.com/easyscience/imaging-lib@develop' +``` + +## How to Run Tutorials + +EasyImaging includes a collection of **Jupyter Notebook examples** that +demonstrate key functionality. These tutorials serve as **step-by-step +guides** to help users understand the data analysis workflow. They are +available as **static HTML pages** in the +[:material-school: Tutorials](../tutorials/index.md) section. + +In the next sections, we explain how to set up Jupyter and run the +tutorials interactively in two different ways: locally or online via +Google Colab. + +If you decide to run the tutorials locally, you need to download them +first. This can be done individually via the :material-download: +**Download Notebook** button available on each tutorial page, or all at +once using the command line, as shown below. + +### Run Tutorials Locally with Pixi recommended { #running-with-pixi data-toc-label="Run Tutorials Locally with Pixi" } + +- Navigate to your existing Pixi project, created as described in the + [Installing with Pixi](#installing-with-pixi) section. +- Add JupyterLab, Interactive Python shell and the Pixi kernel for + Jupyter: + ```txt + pixi add --pypi jupyterlab ipython pixi-kernel + ``` +- Download all the EasyImaging tutorials to the `tutorials/` directory. +- Start the JupyterLab server in the `tutorials/` directory to access the + notebooks: + ```txt + pixi run jupyter lab tutorials/ + ``` +- Your web browser should open automatically. Click on one of the + `*.ipynb` files and select the `Python (Pixi)` kernel to get started. + +### Classical Run Tutorials Locally + +- Install Jupyter Notebook, Interactive Python shell and the IPython + kernel: + ```txt + pip install notebook ipython ipykernel + ``` +- Add the virtual environment as a Jupyter kernel: + ```txt + python -m ipykernel install --user --name=venv --display-name "EasyImaging Python kernel" + ``` +- Download all the EasyImaging tutorials to the `tutorials/` directory. +- Start the Jupyter Notebook server in the `tutorials/` directory to + access the notebooks: + ```txt + jupyter notebook tutorials/ + ``` +- Your web browser should open automatically. Click on one of the + `*.ipynb` files and select the `EasyImaging Python kernel` to get + started. + +### Run Tutorials via Google Colab + +**Google Colab** lets you run Jupyter Notebooks in the cloud without any +local installation. This is the fastest way to start experimenting with +EasyImaging. + +- Ensure you have a **Google account**. +- Go to the **[:material-school: Tutorials](../tutorials/index.md)** + section. +- Click the :google-colab: **Open in Google Colab** button on any + tutorial. diff --git a/docs/docs/introduction/index.md b/docs/docs/introduction/index.md new file mode 100644 index 0000000..d5e42c1 --- /dev/null +++ b/docs/docs/introduction/index.md @@ -0,0 +1,72 @@ +--- +icon: material/information-slab-circle +--- + +# :material-information-slab-circle: Introduction + +## Description + +**EasyImaging** is a software for performing Bragg-edge calculations +based on a crystalliographic model and refining its parameters against +experimental data. + +**EasyImaging** is developed both as a Python library and as a +cross-platform desktop application. + +Here, we focus on the Python library. For the graphical user interface +(GUI), please see the corresponding +[GUI resources](https://easyscience.github.io/imaging-app). + + + +## License + +**EasyImaging** library is released under the +[BSD 3-Clause License](https://raw.githubusercontent.com/easyscience/imaging-lib/master/LICENSE). + +## Releases + +The latest version of the **EasyImaging** library is +[{{ vars.release_version }}](https://github.com/easyscience/imaging-lib/releases/latest). + +For a complete list of new features, bug fixes, and improvements, see the +[GitHub Releases page](https://github.com/easyscience/imaging-lib/releases). + +## Citation + +If you use **EasyImaging** library in your work, please cite the specific +version you used. + +All official releases of the **EasyImaging** library are archived on +Zenodo, each with a version-specific Digital Object Identifier (DOI). + +Citation details in various styles (e.g., APA, MLA) and formats (e.g., +BibTeX, JSON) are available on the +[Zenodo archive page](https://doi.org/10.5281/zenodo.18163581). + +## Contributing + +We welcome contributions of any kind! + +**EasyImaging** is intended to be a community-driven, open-source project +supported by a diverse group of contributors. + +The project is maintained by the +[European Spallation Source (ESS)](https://ess.eu). + +If you would like to report a bug or request a new feature, please use +the +[GitHub Issue Tracker](https://github.com/easyscience/imaging-lib/issues) +(A free GitHub account is required.) + +To contribute code, documentation, or tests, please see our +[:material-account-plus: Contributing Guidelines](https://github.com/easyscience/imaging-lib/blob/master/CONTRIBUTING.md) +for detailed development instructions. + +## Get in Touch + +For general questions or feedback, please contact us at +[support@easyscience.org](mailto:support@easyscience.org). diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md new file mode 100644 index 0000000..6152008 --- /dev/null +++ b/docs/docs/tutorials/index.md @@ -0,0 +1,22 @@ +--- +icon: material/school +--- + +# :material-school: Tutorials + +This section presents a collection of **Jupyter Notebook** tutorials that +demonstrate how to use EasyImaging for various tasks. These tutorials +serve as self-contained, step-by-step **guides** to help users grasp the +workflow of data analysis using EasyImaging. + +Instructions on how to run the tutorials are provided in the +[:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials) +section of the documentation. + +The tutorials are organized into the following categories: + +## Getting Started + +- [The **Measurement** class](measurement.ipynb) – A tutorial which + explores the purpose and functions of the core-component: The + **Measurement** class. diff --git a/docs/docs/tutorials/measurement.ipynb b/docs/docs/tutorials/measurement.ipynb new file mode 100644 index 0000000..f356556 --- /dev/null +++ b/docs/docs/tutorials/measurement.ipynb @@ -0,0 +1,592 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0bfd5e51", + "metadata": {}, + "source": [ + "# The **Measurement** class\n", + "### The class reponsible for holding and handing the measurement data" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "bfb22357", + "metadata": {}, + "outputs": [], + "source": [ + "import scipp as sc\n", + "\n", + "from easyimaging import Measurement" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "49155b72", + "metadata": {}, + "outputs": [], + "source": [ + "from easyimaging.datasets import iron_alpha_scitiff\n", + "\n", + "scitiff_path = iron_alpha_scitiff() # If you use your own file, simply specify the path like: 'some_path/some_file.tiff'" + ] + }, + { + "cell_type": "markdown", + "id": "747b6794", + "metadata": {}, + "source": [ + "The **Measurement** class can be created in 3 different ways. The preffered way is by loading a scitiff which holds all the neccesary meta-data, using the `from_scitiff` method." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c4e759bd", + "metadata": {}, + "outputs": [], + "source": [ + "from easyimaging.datasets import iron_alpha_scitiff\n", + "\n", + "measurement = Measurement.from_scitiff(filename=scitiff_path)" + ] + }, + { + "cell_type": "markdown", + "id": "12aa16b3", + "metadata": {}, + "source": [ + "Alternatively, the **Measurement** class can also be created using a regular Tiff stack, using the `from_tiff_stack` method, and supplying the list of time-of-flights for each frame in the Tiff stack and optionally the x- and y-positions of the pixels." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "de262785", + "metadata": {}, + "outputs": [], + "source": [ + "from easyimaging.datasets import iron_alpha_tiff\n", + "\n", + "tiff_path = iron_alpha_tiff()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "45d76213", + "metadata": {}, + "outputs": [], + "source": [ + "from easyimaging.datasets import iron_alpha_tiff\n", + "\n", + "measurement = Measurement.from_tiff_stack(\n", + " filename=tiff_path,\n", + " time_of_flights=sc.arange('t', 0, 1501, 1, unit='s'), # mandatory\n", + " # x_positions=sc.arange('x', 0, 50, 1, unit='mm'), # optional\n", + " # y_positions=sc.arange('y', 0, 50, 1, unit='mm'), # optional\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "bbfb8209", + "metadata": {}, + "source": [ + "The *x_positions* and *y_positions* of the pixels can also be set or overwritten later with the method `set_physical_coord_positions`" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8081110a", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.set_physical_coord_positions(\n", + " x_positions=sc.arange('x', -8, 8, 1, unit='cm'),\n", + " y_positions=sc.arange('y', -8, 8, 1, unit='cm'),\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "700d641a", + "metadata": {}, + "source": [ + "Finally the **Measurement** class can also be created by directly passing an appropriate scipp `DataArray`. This is useful if working in the same notebook as the reduction is performed. Please be aware that there are strict requirements on the format, coordinates and meta-data of this `DataArray`. Here is an example:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "decf64b7", + "metadata": {}, + "outputs": [], + "source": [ + "tof = sc.arange('t', 0, 10, 1, unit='s')\n", + "x = sc.arange('x', 0, 7, 1, unit='m') # optional\n", + "y = sc.arange('y', 0, 7, 1, unit='m') # optional\n", + "data = sc.ones(dims=['x', 'y', 't'], shape=[6, 6, 10])\n", + "scipp_array = sc.DataArray(data=data, coords={'tof': tof, 'x': x, 'y': y})" + ] + }, + { + "cell_type": "markdown", + "id": "7e6f0618", + "metadata": {}, + "source": [ + "Note that the *x* and *y* coordinates, corresponding to the previous *x_positions* and *y_positions*, is 1 element longer than the data. That is because we work with bin-edges rathar than bin-centers in the **Measurement** class. You can also provide a bin-center list, but it will internally be converted to bin-edges assuming even bin-sizes.\n", + "\n", + "Another point to note is that the time-of-flight coordinate is called *'tof'* but it has to have the dimension 't'.\n", + "\n", + "With this correct DataArray, we can then construct the **Measurement** class" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "531b3ea0", + "metadata": {}, + "outputs": [], + "source": [ + "measurement = Measurement(data_array=scipp_array)" + ] + }, + { + "cell_type": "markdown", + "id": "e2273160", + "metadata": {}, + "source": [ + "To continue to show off the **Measurement** class, we will use the preffered creation method, using the scitiff file." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "577cc5ad", + "metadata": {}, + "outputs": [], + "source": [ + "measurement = Measurement.from_scitiff(filename=scitiff_path)" + ] + }, + { + "cell_type": "markdown", + "id": "15eb7fef", + "metadata": {}, + "source": [ + "The **Measurements** *x_positions*, *y_positions* and *time_of_flights* can all be viewed" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5aa49556", + "metadata": {}, + "outputs": [], + "source": [ + "display(measurement.x_positions) # If available\n", + "display(measurement.y_positions) # If available\n", + "display(measurement.time_of_flights)" + ] + }, + { + "cell_type": "markdown", + "id": "c3e3409d", + "metadata": {}, + "source": [ + "The **Measurement** class has a number of plotting methods relying on the underlying *plopp* library from scipp. The simplest plot is a plot of the Tiff stack" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7e9950e2", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.plot()" + ] + }, + { + "cell_type": "markdown", + "id": "5b8525e3", + "metadata": {}, + "source": [ + "By default, this plot is summed over the time-of-flight frames, but a specific time-of-flight can also be plotted" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d7db0974", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.plot(time_of_flight=0)" + ] + }, + { + "cell_type": "markdown", + "id": "17e3e327", + "metadata": {}, + "source": [ + "Pixels with invalid data values, like infinity or NaN, will appear as red. \n", + "For further customization of the plot, see https://scipp.github.io/plopp/plotting/image-plot.html and https://scipp.github.io/plopp/generated/plopp.plot.html. Any of the arguments supported here is also supported in the `plot` method.\n", + "\n", + "In case of invalid data-points, it can often be beneficial to rebin the data. When rebinning, invalid data-points are ignored when pixels are averaged, yielding clean data-sets without errenous data-points.\n", + "EasyImaging only supports rebinning by divisible whole integers, to avoid having to \"guess\" how much of a transmission belongs to each bin." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f3cd2bd3", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.rebin(dimensions={'x': 2, 'y': 2})" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15023563", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.plot(time_of_flight=0)" + ] + }, + { + "cell_type": "markdown", + "id": "3b37262c", + "metadata": {}, + "source": [ + "Further rebinning will rebin the reduced data-set again, yielding an even rougher binning. Rebinning can be reverted and the original data recovered by using the `revert_rebin` method" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f1f97240", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.revert_rebin()" + ] + }, + { + "cell_type": "markdown", + "id": "bb869ac9", + "metadata": {}, + "source": [ + "A more useful plotter to inspect the different time-of-flight frames is the `slicer_plot`, which is only available in Jupyter notebooks or similar environments with an interactive graphical backend. The `slicer_plot` has a time-of-flight slider to choose the desired frame to plot.\n", + "\n", + "To run it, first add the interactive matplotlib widget to your Jupyter notebook:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "75774206", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib widget" + ] + }, + { + "cell_type": "markdown", + "id": "b1352c5a", + "metadata": {}, + "source": [ + "Then the slicer plot can be called" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9d5de1be", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.slicer_plot()" + ] + }, + { + "cell_type": "markdown", + "id": "3b548b6a", + "metadata": {}, + "source": [ + "Just like with the regular plot method, any arguments accepted by the underlying plopp backend is supported to further customize the plot, see https://scipp.github.io/plopp/plotting/slicer-plot.html and https://scipp.github.io/plopp/generated/plopp.slicer.html for supported arguments.\n", + "\n", + "To get the time-of-flight spectrum, the **Measurement** provides the `spectrum` method." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "43c29518", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.spectrum()" + ] + }, + { + "cell_type": "markdown", + "id": "6cb7c47a", + "metadata": {}, + "source": [ + "By default the `spectrum` method adds up all the pixels of the **Measurement**. \n", + "The method returns a scipp `DataArray` with uncertainties and time-of-flights.\n", + "\n", + "It is also possible to plot the spectrum using the `spectrum_plot` method." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3cf946ab", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.spectrum_plot()" + ] + }, + { + "cell_type": "markdown", + "id": "6583f974", + "metadata": {}, + "source": [ + "Which also accepts plopp supported arguments for plot customization, see: https://scipp.github.io/plopp/plotting/line-plot.html and https://scipp.github.io/plopp/generated/plopp.plot.html\n", + "\n", + "It is also possible to inspect the spectra of individual pixels using the `spectrum_inspector` plot method. This is also an interactive plot which is only supported in Jupyter notebooks and similar. In the plotted **Measurement**, individual pixels can be clicked (after selecting the point-clicker in the menu on the left) to show their spectrum in the spectrum plot underneath." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e6da5628", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.spectrum_inspector()" + ] + }, + { + "cell_type": "markdown", + "id": "d444bc2d", + "metadata": {}, + "source": [ + "Where again the plot(s) can be customized, see https://scipp.github.io/plopp/plotting/inspector-plot.html and https://scipp.github.io/plopp/generated/plopp.inspector.html\n", + "\n", + "It is also possible to define a region of interest (ROI) to provide the spectrum of a specific designated area. To do this, first the ROI has to be created" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4969d839", + "metadata": {}, + "outputs": [], + "source": [ + "from easyimaging.measurement.regions import RectROI" + ] + }, + { + "cell_type": "markdown", + "id": "04f49975", + "metadata": {}, + "source": [ + "It is possible to define the ROI in code by hand, or draw it by hand (as shown further down)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6de05015", + "metadata": {}, + "outputs": [], + "source": [ + "roi = RectROI(\n", + " x_pixel_range=(15, 35), # mandatory\n", + " y_pixel_range=(15, 35), # mandatory\n", + " x_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')), # optional\n", + " y_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')), # optional\n", + " unique_name='center_roi', # custom name for the ROI, optional, has to be unique in computer memory\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "82bd5ce3", + "metadata": {}, + "source": [ + "The ROI needs the x and y pixel ranges, as they are used as fallback for when the ROI is used on a **Measurement** without *x_positions* and *y_positions*. The *x_range* and *y_range* are optional physical ranges which are prioritized when used on a **Measurement** with *x_positions* and *y_positions*.\n", + "\n", + "This ROI can then be passed to the `spectrum` method and the `spectrum_plot` method to only sum up the spectrum of this region." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ed81cad4", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.spectrum(roi=roi)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1e142cfe", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.spectrum_plot(roi=roi)" + ] + }, + { + "cell_type": "markdown", + "id": "e3a815ca", + "metadata": {}, + "source": [ + "In general, an ROI should be added to a **Measurement** class to be used later in fitting" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "123de71f", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.regions_of_interest.append(roi)" + ] + }, + { + "cell_type": "markdown", + "id": "82322c4f", + "metadata": {}, + "source": [ + "When the ROI is added to a **Measurement**, it can also be used in `spectrum` and `spectrum_plot` methods by simply passing its unique name" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "01bb61d2", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.spectrum_plot(roi='center_roi')" + ] + }, + { + "cell_type": "markdown", + "id": "d0b28a05", + "metadata": {}, + "source": [ + "As prevously promised, the ROI can also be drawn easily by hand, using the `roi_creator` tool. After opening the tool, click the bottom option in the control panel on the left to activate the ROI drawing tool.\n", + "\n", + "Controls when ROI drawing tool is activated:\n", + "- Left-click to make new ROI's\n", + "- Left-click and hold on ROI vertices to resize ROI's\n", + "- Right-click and hold to drag/move the entire ROI\n", + "- Middle-click to delete an ROI" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7ff41a8e-7dd2-4a19-9d09-8a9221963459", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.roi_creator()" + ] + }, + { + "cell_type": "markdown", + "id": "5dec8e7c", + "metadata": {}, + "source": [ + "The ROI's drawn with the `roi_creator` tool will appear in the **Measurements** list of regions of interest with default _unique_names_." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5ef8713d-4844-4afa-ac26-309ed2154613", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.regions_of_interest" + ] + }, + { + "cell_type": "markdown", + "id": "185948f8", + "metadata": {}, + "source": [ + "To easier identify specific ROI's, rename ROI's with memorable unique_names. Be aware that each unique_name can only exist once in memory, if a desired unique_name is currently occupied by another object, you might have to restart the notebook to clear the memory." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "41a4cd39", + "metadata": { + "tags": [ + "remove-cell" + ] + }, + "outputs": [], + "source": [ + "figs = measurement.roi_creator()\n", + "# Draw a rectangle\n", + "figs[0].toolbar['inspect']._tool.start()\n", + "figs[0].toolbar['inspect']._tool.click(x=2.5, y=2.5, button=1)\n", + "figs[0].toolbar['inspect']._tool.click(x=5.0, y=5.0, button=1)\n", + "figs[0].toolbar['inspect']._tool.stop()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f02fe391", + "metadata": {}, + "outputs": [], + "source": [ + "measurement.regions_of_interest[1].unique_name = 'best_roi' # Requires that an ROI was drawn using the roi_creator tool." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "default", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/docs/user-guide/index.md b/docs/docs/user-guide/index.md new file mode 100644 index 0000000..0bf0eae --- /dev/null +++ b/docs/docs/user-guide/index.md @@ -0,0 +1,24 @@ +--- +icon: material/book-open-variant +--- + +# :material-book-open-variant: User Guide + +This section provides an overview of the **core concepts**, **key +parameters** and **workflow steps** required for using EasyImaging +effectively. + +Here is a brief overview of the User Guide sections: + +- [Glossary](#) – Defines common terms and labels used throughout the + documentation. +- [Concept](#) – Introduces the overall idea behind data analysis in + EasyImaging. +- [Data Format](#) – Explains the data structures and file formats used + by EasyImaging. +- [Parameters](#) – Describes how parameters are structured, named, and + accessed within the EasyImaging. +- [First Steps](#) – Shows how to begin using EasyImaging in Python or + Jupyter notebooks. +- [Analysis Workflow](#) – Breaks down the data analysis pipeline into + practical, sequential steps. diff --git a/docs/includes/abbreviations.md b/docs/includes/abbreviations.md new file mode 100644 index 0000000..682f16f --- /dev/null +++ b/docs/includes/abbreviations.md @@ -0,0 +1,15 @@ + + +*[CIF]: Crystallographic Information File. +*[curl]: Command-line tool for transferring data with URLs. +*[GitHub]: A web-based platform for version control and collaboration. +*[Google Colab]: Cloud service that allows you to run Jupyter Notebooks in the cloud. +*[IUCr]: International Union of Crystallography. +*[Jupyter Notebook]: An open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. +*[JupyterLab]: Web-based interactive development environment for notebooks, code, and data. +*[pip]: Package installer for Python. +*[PyPI]: The Python Package Index is a repository of software for the Python programming language. +*[Conda]: Conda is a cross-platform, language-agnostic binary package manager. +*[Pixi]: A modern package manager for Windows, macOS, and Linux. + + diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml new file mode 100644 index 0000000..5bf28fe --- /dev/null +++ b/docs/mkdocs.yml @@ -0,0 +1,185 @@ +# Project information +site_name: EasyImaging Library +site_url: https://easyscience.github.io/imaging-lib + +# Repository +repo_url: https://github.com/easyscience/imaging-lib +edit_uri: edit/develop/docs/ + +# Copyright +copyright: © 2024-2026 EasyImaging + +# Sets the theme and theme-specific configuration +theme: + name: material + custom_dir: overrides + features: + #- content.action.edit # Temporary disable edit button (until decided on which branch to use and where to host the notebooks) + #- content.action.view + - content.code.annotate + - content.code.copy # Auto generated button to copy a code block's content + - content.tooltips + - navigation.footer + - navigation.indexes + #- navigation.instant # Instant loading, but it causes issues with rendering equations + #- navigation.sections + - navigation.top # Back-to-top button + - navigation.tracking # Anchor tracking + - search.highlight + - search.share + - search.suggest + - toc.follow + palette: + # Palette toggle for light mode + - media: '(prefers-color-scheme: light)' + scheme: default + primary: custom + toggle: + icon: fontawesome/solid/sun + name: Switch to dark mode + # Palette toggle for dark mode + - media: '(prefers-color-scheme: dark)' + scheme: slate + primary: custom + toggle: + icon: fontawesome/solid/moon + name: Switch to light mode + font: + text: Mulish + code: Roboto Mono + icon: + edit: material/file-edit-outline + favicon: assets/images/favicon.png + logo_dark_mode: assets/images/logo_dark.svg + logo_light_mode: assets/images/logo_light.svg + +# A set of key-value pairs, where the values can be any valid YAML +# construct, that will be passed to the template +extra: + generator: false # Disable `Made with Material for MkDocs` (bottom left) + social: # Extra icons in the bottom right corner + - icon: easyscience # File: overrides/.icons/easyscience.svg + link: https://easyscience.org + name: EasyScience Framework Webpage + - icon: easyimaging # File: overrides/.icons/easyimaging.svg + link: https://easyscience.github.io/imaging + name: EasyImaging Main Webpage + - icon: app # File: overrides/.icons/app.svg + link: https://easyscience.github.io/imaging-app + name: EasyImaging Application Docs + - icon: fontawesome/brands/github # Name as in Font Awesome + link: https://github.com/easyscience/imaging-lib + name: EasyImaging Library Source Code on GitHub + # Set custom variables to be used in Markdown and HTML files + vars: + ci_branch: !ENV CI_BRANCH + github_repository: !ENV GITHUB_REPOSITORY + release_version: !ENV RELEASE_VERSION + docs_version: !ENV DOCS_VERSION + notebooks_dir: !ENV NOTEBOOKS_DIR + # Renders a version selector in the header + version: + provider: mike + +# Customization to be included by the theme +extra_css: + - assets/stylesheets/extra.css + +extra_javascript: + - assets/javascripts/extra.js + # MathJax for rendering mathematical expressions + - assets/javascripts/mathjax.js # Custom MathJax config to ensure compatibility with mkdocs-jupyter + - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js # Official MathJax CDN + +# A list of extensions beyond the ones that MkDocs uses by default (meta, toc, tables, and fenced_code) +markdown_extensions: + - abbr + - admonition + - attr_list + - def_list + - footnotes + - pymdownx.arithmatex: # rendering of equations and integrates with MathJax or KaTeX + generic: true + - pymdownx.blocks.caption + - pymdownx.details + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg + options: + custom_icons: + - docs/overrides/.icons + - pymdownx.highlight: # whether highlighting should be carried out during build time by Pygments + use_pygments: true + pygments_lang_class: true + - pymdownx.snippets: + auto_append: + - docs/includes/abbreviations.md + - pymdownx.superfences: # whether highlighting should be carried out during build time by Pygments + custom_fences: + - name: mermaid + class: mermaid + format: !!python/name:pymdownx.superfences.fence_code_format + - pymdownx.tabbed: # enables content tabs + alternate_style: true + - pymdownx.tasklist: + custom_checkbox: true + - toc: + toc_depth: 3 + +# A list of plugins (with optional configuration settings) to use when building the site +plugins: + - autorefs + - inline-svg + - markdownextradata # Plugin that injects the mkdocs.yml extra variables into the Markdown template + - mike # Plugin that makes it easy to deploy multiple versions of the docs + - mkdocs-jupyter: + include: ['*.ipynb'] # Default: ['*.py', '*.ipynb'] + execute: false # Do not execute notebooks during build. They are expected to be pre-executed. + allow_errors: false + include_source: true + include_requirejs: true # Required for Plotly + #custom_mathjax_url: 'https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js' # See 'extra_javascript' above + ignore_h1_titles: true # Use titles defined in the nav section below + remove_tag_config: + remove_input_tags: + - hide-in-docs + - mkdocstrings: + handlers: + python: + paths: ['src'] # Change 'src' to your actual sources directory + options: + annotations_path: source + docstring_style: numpy + group_by_category: true + members_order: source + heading_level: 1 + show_root_heading: true + show_root_full_path: false + show_submodules: true + show_source: true + - search + +# Determines additional directories to watch when running mkdocs serve +watch: + - includes + - overrides + - ../src + +# Exclude files and folders from the global navigation +not_in_nav: | + index.md + +# Format and layout of the global navigation for the site +nav: + - Introduction: + - Introduction: introduction/index.md + - Installation & Setup: + - Installation & Setup: installation-and-setup/index.md + - User Guide: + - User Guide: user-guide/index.md + - Tutorials: + - Tutorials: tutorials/index.md + - Getting Started: + - Dummy tutorial: tutorials/plotting.ipynb + - API Reference: + - API Reference: api-reference/index.md diff --git a/docs/overrides/.icons/app.svg b/docs/overrides/.icons/app.svg new file mode 100644 index 0000000..b4fdd4f --- /dev/null +++ b/docs/overrides/.icons/app.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/docs/overrides/.icons/easyimaging.svg b/docs/overrides/.icons/easyimaging.svg new file mode 100644 index 0000000..ab7b2ba --- /dev/null +++ b/docs/overrides/.icons/easyimaging.svg @@ -0,0 +1,17 @@ + + + + + + + + + + + Logo + + Main circle + + + + \ No newline at end of file diff --git a/docs/overrides/.icons/easyscience.svg b/docs/overrides/.icons/easyscience.svg new file mode 100644 index 0000000..fb51491 --- /dev/null +++ b/docs/overrides/.icons/easyscience.svg @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/overrides/.icons/google-colab.svg b/docs/overrides/.icons/google-colab.svg new file mode 100644 index 0000000..9cd9d1b --- /dev/null +++ b/docs/overrides/.icons/google-colab.svg @@ -0,0 +1,7 @@ + + + + + + + diff --git a/docs/overrides/main.html b/docs/overrides/main.html new file mode 100644 index 0000000..2e14682 --- /dev/null +++ b/docs/overrides/main.html @@ -0,0 +1,39 @@ +{% extends "base.html" %} + +{% block content %} + +{% if page.nb_url %} + {# Parse notebook path/URL #} + {% set parts = page.nb_url.split('/') %} + {% set tutorial_name = parts[-2] %} + {% set filename = parts[-1] %} + + {# Colab url #} + {% set base_colab_url = "https://colab.research.google.com/github/" %} + {% set colab_url = + base_colab_url ~ config.extra.vars.github_repository ~ + "/blob/gh-pages/" ~ config.extra.vars.docs_version ~ + "/tutorials/" ~ tutorial_name ~ "/" ~ filename + %} + + {# Download link: relative to the current page #} + {% set file_url = filename %} + + {# Open in Colab (absolute GitHub URL; works anywhere) #} + + {% include ".icons/google-colab.svg" %} + + + {# Download: use a RELATIVE link to the file next to this page #} + + {% include ".icons/material/download.svg" %} + +{% endif %} + +{{ super() }} +{% endblock content %} diff --git a/docs/overrides/partials/logo.html b/docs/overrides/partials/logo.html new file mode 100644 index 0000000..78fa69c --- /dev/null +++ b/docs/overrides/partials/logo.html @@ -0,0 +1,15 @@ +{% if ( config.theme.logo_light_mode and config.theme.logo_dark_mode ) %} +logo +logo +{% elif config.theme.logo %} +logo +{% else %} {% set icon = config.theme.icon.logo or "material/library" %} {% +include ".icons/" ~ icon ~ ".svg" %} {% endif %} diff --git a/pixi.lock b/pixi.lock index 2b05de2..3713a70 100644 --- a/pixi.lock +++ b/pixi.lock @@ -2,1542 +2,3424 @@ version: 6 environments: default: channels: + - 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This is a workaround for +# Pixi, see https://github.com/prefix-dev/pixi/issues/5667 +macos = '14.0' + +# Non-default features: + +# Set specific Python versions to be used in CI testing. + +[feature.py-min.dependencies] +python = '3.11.*' + +[feature.py-max.dependencies] +python = '3.13.*' + +# Development dependencies for local development and testing with +# editable installations. + +[feature.dev.dependencies] +nodejs = '*' # Required for Prettier (non-Python formatting) +jupyterlab = '*' # Jupyter notebooks +ipython = '*' # Interactive Python shell +pixi-kernel = '*' # Pixi Jupyter kernel [feature.dev.pypi-dependencies] -# Development dependencies -easyimaging = { path = ".", extras = ["dev"], editable = true } +pip = '*' +easyimaging = { path = '.', editable = true, extras = ['dev'] } + +# User-like behavior for testing with pip-installed dependencies instead +# of editable installations. -[feature.docs.pypi-dependencies] -# Documentation dependencies -easyimaging = { path = ".", extras = ["docs"], editable = true } +[feature.user.dependencies] +jupyterlab = '*' # Jupyter notebooks +ipython = '*' # Interactive Python shell +pixi-kernel = '*' # Pixi Jupyter kernel -[feature.build.pypi-dependencies] -# build dependencies -easyimaging = { path = ".", extras = ["build"], editable = true } +[feature.user.pypi-dependencies] +pip = '*' +easyimaging = '*' + +############## +# ENVIRONMENTS +############## [environments] -# Default environment with basic build setup -default = ["build"] -# Development environment with build, dev, and docs features -dev = ["build", "dev", "docs"] + +# The `default` feature is always included in all environments. +# Additional features can be specified per environment. + +# Specific environments for CI testing with different Python versions. +py-311-env = { features = ['py-min', 'dev'] } +py-313-env = { features = ['py-max', 'dev'] } + +# The `default` environment is developer-oriented for local development +# and testing with editable installation of the current package. +default = { features = ['py-max', 'dev'] } + +# The `user` environment allows testing with pip-installed dependencies +# instead of editable installation of the current package. +user = { features = ['py-max', 'user'] } + +####### +# TASKS +####### [tasks] -# Development tasks -test = "pytest --cov=src/easyimaging tests --cov-branch --cov-report=xml:coverage-unit.xml" -test-unit = "pytest tests/unit_tests" -test-integration = "pytest tests/integration_tests" -# Code quality tasks -lint-check = "ruff check ." -lint = "ruff check . --fix" -format-check = "ruff format . --check" -format = "ruff format ." +################## +# 🧪 Testing Tasks +################## + +unit-tests = 'python -m pytest tests/unit/ --color=yes -v' +functional-tests = 'python -m pytest tests/functional/ --color=yes -v' +integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v' +notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --color=yes -n auto -v' + +test = { depends-on = ['unit-tests'] } + +########### +# ✔️ Checks +########### + +pyproject-check = 'python -m validate_pyproject pyproject.toml' +docstring-lint-check = 'pydoclint --quiet src/' +notebook-lint-check = 'nbqa ruff docs/docs/tutorials/' +py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/' +py-format-check = 'ruff format --check src/ tests/ docs/docs/tutorials/' +nonpy-format-check = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .' +nonpy-format-check-modified = 'python tools/nonpy_prettier_modified.py' + +check = 'pre-commit run --hook-stage manual --all-files' + +########## +# 🛠️ Fixes +########## + +docstring-transform = 'pixi run docstripy src/ -s=numpy -w' +docstring-format-fix = 'format-docstring src/' +notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/' +py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/' +py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/' +py-format-fix = 'ruff format src/ tests/ docs/docs/tutorials/' +nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .' +nonpy-format-fix-modified = 'python tools/nonpy_prettier_modified.py --write' +success-message = 'echo "✅ All auto-formatting steps completed successfully!"' + +fix = { depends-on = [ + 'docstring-format-fix', + 'py-format-fix', + 'py-lint-fix', + 'nonpy-format-fix', + 'notebook-lint-fix', + 'success-message', +] } + +#################### +# 🧮 Code Complexity +#################### + +complexity-check = 'radon cc -s src/' +complexity-check-json = 'radon cc -s -j src/' +maintainability-check = 'radon mi src/' +maintainability-check-json = 'radon mi -j src/' +raw-metrics = 'radon raw -s src/' +raw-metrics-json = 'radon raw -s -j src/' + +############# +# 📊 Coverage +############# + +unit-tests-coverage = 'pixi run unit-tests --cov=src/easyimaging --cov-report=term-missing' +functional-tests-coverage = 'pixi run functional-tests --cov=src/easyimaging --cov-report=term-missing' +integration-tests-coverage = 'pixi run integration-tests --cov=src/easyimaging --cov-report=term-missing' +docstring-coverage = 'interrogate -c pyproject.toml src/easyimaging' + +cov = { depends-on = [ + 'docstring-coverage', + 'unit-tests-coverage', + 'integration-tests-coverage', +] } + +######################## +# 📓 Notebook Management +######################## + +notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb' +notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb' +notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/' +notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v' + +notebook-prepare = { depends-on = [ + #'notebook-convert', + 'notebook-strip', + #'notebook-tweak', +] } + +######################## +# 📚 Documentation Tasks +######################## + +docs-vars = "JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS='ignore::RuntimeWarning'" +docs-pre = 'pixi run docs-vars python -m mkdocs' +docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml' +docs-serve-dirty = 'pixi run docs-serve --dirty' +docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml' +docs-build-local = 'pixi run docs-build --no-directory-urls' + +docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect' +docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages' + +docs-update-assets = 'python tools/update_docs_assets.py' + +############################## +# 📦 Template Management Tasks +############################## + +copier-copy = 'copier copy gh:easyscience/templates . --data-file ../imaging/.copier-answers.yml --data template_type=lib' +copier-recopy = 'copier recopy --data-file ../imaging/.copier-answers.yml --data template_type=lib' +copier-update = 'copier update --data-file ../imaging/.copier-answers.yml --data template_type=lib' + +##################### +# 🪝 Pre-commit Hooks +##################### + +pre-commit-clean = 'pre-commit clean' +pre-commit-install = 'pre-commit install --hook-type pre-commit --hook-type pre-push --overwrite' +pre-commit-uninstall = 'pre-commit uninstall --hook-type pre-commit --hook-type pre-push' +pre-commit-setup = { depends-on = [ + 'pre-commit-clean', + 'pre-commit-uninstall', + 'pre-commit-install', +] } + +################# +# 🐙️ GitHub Tasks +################# + +repo-wiki = 'gh api -X PATCH repos/easyscience/imaging-lib -f has_wiki=false' +repo-discussions = 'gh api -X PATCH repos/easyscience/imaging-lib -f has_discussions=true' +repo-description = "gh api -X PATCH repos/easyscience/imaging-lib -f description='Neutron imaging data analysis'" +repo-homepage = "gh api -X PATCH repos/easyscience/imaging-lib -f homepage='https://easyscience.github.io/imaging-lib'" +repo-config = { depends-on = [ + 'repo-wiki', + 'repo-discussions', + 'repo-description', + 'repo-homepage', +] } + +master-protection = 'gh api -X POST repos/easyscience/imaging-lib/rulesets --input .github/configs/rulesets-master.json' +develop-protection = 'gh api -X POST repos/easyscience/imaging-lib/rulesets --input .github/configs/rulesets-develop.json' +gh-pages-protection = 'gh api -X POST repos/easyscience/imaging-lib/rulesets --input .github/configs/rulesets-gh-pages.json' +branch-protection = { depends-on = [ + 'master-protection', + 'develop-protection', + 'gh-pages-protection', +] } + +pages-deployment = 'gh api -X POST repos/easyscience/imaging-lib/pages --input .github/configs/pages-deployment.json' + +github-labels = 'python tools/update_github_labels.py' + +######################### +# ⚖️ SPDX License Headers +######################### + +license-remove = 'python tools/license_headers.py remove src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' +license-add = 'python tools/license_headers.py add src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' +license-check = 'python tools/license_headers.py check src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' + +#################################### +# 🚀 Other Development & Build Tasks +#################################### -# Build tasks -build = "python -m build" -clean = "rm -rf dist/ build/ *.egg-info/" -update-lock = "pixi update" +default-build = 'python -m build' +dist-build = 'python -m build --wheel --outdir dist' -# Tox tasks -tox = "tox" +npm-config = 'npm config set registry https://registry.npmjs.org/' +prettier-install = 'npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml' -# Documentation tasks -docs-build = "sphinx-build -b html docs/src docs/_build/html" -docs-clean = "rm -rf docs/_build/" +clean-pycache = "find . -type d -name '__pycache__' -prune -exec rm -rf '{}' +" -[pypi-dependencies] # == [feature.default.pypi-dependencies] -# Editable install of the package itself -easyimaging = { path = ".", editable = true } +post-install = { depends-on = [ + 'npm-config', + 'prettier-install', + #'pre-commit-setup', +] } +########################## +# 🔗 Main Package Shortcut +########################## +easyimaging = 'python -m easyimaging' diff --git a/prettierrc.toml b/prettierrc.toml new file mode 100644 index 0000000..2e02224 --- /dev/null +++ b/prettierrc.toml @@ -0,0 +1,22 @@ +plugins = [ + "prettier-plugin-toml", # use the TOML plugin +] + +endOfLine = 'lf' # change line endings to LF +proseWrap = 'always' # change wrapping in Markdown files +semi = false # remove semicolons +singleQuote = true # use single quotes instead of double quotes +tabWidth = 2 # change tab width to 2 spaces +useTabs = false # use spaces instead of tabs + +printWidth = 88 # wrap lines at 88 characters + +[[overrides]] +files = ["*.md"] +[overrides.options] +printWidth = 73 # wrap Markdown files at 73 characters + +[[overrides]] +files = ["*.yml", "*.yaml"] +[overrides.options] +printWidth = 88 # wrap YAML files at 88 characters diff --git a/pyproject.toml b/pyproject.toml index 8135388..74a093a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,163 +1,345 @@ -[build-system] -requires = [ - "hatchling<=1.21.0", - "setuptools-git-versioning", -] -build-backend = "hatchling.build" - -[tool.setuptools-git-versioning] -enabled = true +############################### +# Configuration for the project +############################### [project] -name = "EasyImaging" -dynamic = ["version"] -description = "Python package for bragg-edge analysis" -readme = "README.md" -authors = [{name = "EasyScience contributors"}] -license = { file = "LICENSE" } +name = 'easyimaging' +dynamic = ['version'] # Use versioningit to manage the version +description = 'Neutron imaging data analysis' +authors = [{ name = 'EasyScience contributors' }] +readme = 'README.md' +license = 'BSD-3-Clause' +license-files = ['LICENSE'] classifiers = [ - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", - "Topic :: Scientific/Engineering", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Programming Language :: Python :: 3.13", - "Development Status :: 3 - Alpha" + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering', + 'License :: OSI Approved :: BSD License', + 'Operating System :: OS Independent', + 'Programming Language :: Python :: 3 :: Only', + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', + 'Programming Language :: Python :: 3.13', + 'Development Status :: 3 - Alpha', ] -requires-python = ">=3.11,<3.14" +requires-python = '>=3.11, <3.14' dependencies = [ - "easyscience>=2.2.0", - "scitiff", - "essimaging", - "plopp", - "ncrystal[composer]" + 'easyscience>=2.2.0', # The base library of the EasyScience framework + 'scitiff', # The data-format loader/saver for neutron tiffs + 'essimaging', # The ESS imaging reduction module + 'plopp', # The plotting library of scipp + 'ncrystal[composer]', # The backend calculator + 'pooch', # Data downloader ] [project.optional-dependencies] -build = [ - "hatchling <= 1.21.0", - "setuptools-git-versioning", - "build" -] dev = [ - "build", - "codecov>=2.1.11", - "flake8>=6.0.0", - "ipykernel", - "jupyter>=1.0.0", - "jupyterlab", - "plopp", - "pytest>=5.2", - "pytest-cov>=3.0.0", - "ruff", - "tox-gh-actions", - "ipython==9.7.0", - "matplotlib==3.10.7", - "ipympl==0.9.8", -] -docs = [ - "doc8", - "readme-renderer", - "sphinx_autodoc_typehints", - "sphinx_book_theme", - "sphinx_gallery", - "toml" + 'GitPython', # Interact with Git repositories + 'build', # Building the package + 'pre-commit', # Pre-commit hooks + 'jinja2', # Templating + 'nbmake', # Building notebooks + 'nbstripout', # Strip output from notebooks + 'nbqa', # Linting and formatting notebooks + 'pytest', # Testing + 'pytest-cov', # Test coverage + 'pytest-xdist', # Enable parallel testing + 'ruff', # Linting and formatting code + 'radon', # Code complexity and maintainability + 'validate-pyproject[all]', # Validate pyproject.toml + 'versioningit', # Automatic versioning from git tags + 'jupytext', # Jupyter notebook text format support + 'jupyterquiz', # Quizzes in Jupyter notebooks + 'pydoclint', # Docstring linter + 'format-docstring', # Docstring formatter + 'docstripy', # Convert docstrings to other formats + 'interrogate', # Docstring coverage checker + 'copier', # Template management + 'mike', # MkDocs: Versioned documentation support + 'mkdocs', # Static site generator + 'mkdocs-material', # Documentation framework on top of MkDocs + 'mkdocs-autorefs', # MkDocs: Auto-references support + 'mkdocs-jupyter', # MkDocs: Jupyter notebook support + 'mkdocs-plugin-inline-svg', # MkDocs: Inline SVG support + 'mkdocs-markdownextradata-plugin', # MkDocs: Markdown extra data support, such as global variables + 'mkdocstrings-python', # MkDocs: Python docstring support + 'pyyaml', # YAML parser + 'spdx-headers', # SPDX license header validation ] [project.urls] -homepage = "https://docs.easyimaging.org" -documentation = "https://docs.easyimaging.org" +Homepage = 'https://easyscience.github.io/imaging' +Documentation = 'https://easyscience.github.io/imaging-lib' +'Release Notes' = 'https://github.com/easyscience/imaging-lib/releases' +'Source Code' = 'https://github.com/easyscience/imaging-lib' +'Issue Tracker' = 'https://github.com/easyscience/imaging-lib/issues' -[tool.hatch.version] -path = "src/easyimaging/__version__.py" +############################ +# Build system configuration +############################ + +[build-system] +build-backend = 'hatchling.build' +requires = ['hatchling', 'versioningit'] + +############################# +# Configuration for hatchling +############################# + +# 'hatch' -- Build system for Python +# https://hatch.pypa.io/ + +[tool.hatch.build.targets.wheel] +packages = ['src/easyimaging'] [tool.hatch.metadata] allow-direct-references = true -[tool.hatch.build.targets.sdist] -packages = ["src"] +[tool.hatch.version] +source = 'versioningit' # Use versioningit to manage the version + +################################ +# Configuration for versioningit +################################ -[tool.hatch.build.targets.wheel] -packages = ["src/easyimaging"] +# 'versioningit' -- Versioning from git tags +# https://versioningit.readthedocs.io/ + +# Versioningit generates versions from git tags, so we don't need to +# either specify them statically in pyproject.toml or save them in the +# source code. Do not use {distance} in the version format, as it +# forces a version bump for every commit, which triggers unnecessary +# pixi.lock update without any changes to the source code. + +[tool.versioningit.format] +distance = '{base_version}+dev{distance}' # example: 1.2.3.post4+dev3 +dirty = '{base_version}+dirty{distance}' # example: 0.5.8+dirty3 +distance-dirty = '{base_version}+devdirty{distance}' # example: 0.5.8+devdirty3 + +# Configure how versioningit detects versions from Git +# - 'match' ensures it only considers tags starting with 'v' +# - 'default-tag' is used as a fallback when no matching tag is found +[tool.versioningit.vcs] +method = 'git' +match = ['v*'] +default-tag = 'v999.0.0' + +################################ +# Configuration for interrogate +################################ + +# 'interrogate' -- Docstring coverage checker +# https://interrogate.readthedocs.io/en/latest/ + +[tool.interrogate] +fail-under = 0 # Minimum docstring coverage percentage to pass +verbose = 1 +#exclude = ['src/**/__init__.py'] + +####################################### +# Configuration for coverage/pytest-cov +####################################### + +# 'coverage' -- Code coverage measurement tool +# https://coverage.readthedocs.io/en/latest/ [tool.coverage.run] -source = ["src/easyimaging"] +branch = true # Measure branch coverage as well +source = ['src'] # Limit coverage to the source code directory + +[tool.coverage.report] +show_missing = true # Show missing lines +skip_covered = false # Skip files with 100% coverage in the report +fail_under = 0 # Minimum coverage percentage to pass + +########################## +# Configuration for pytest +########################## + +# 'pytest' -- Testing framework +# https://docs.pytest.org/en/stable/ -[tool.github.info] -organization = 'easyScience' -repo = "easyimaging" +[tool.pytest.ini_options] +addopts = '--import-mode=importlib' +markers = ['fast: mark test as fast (should be run on every push)'] +testpaths = ['tests'] + +######################## +# Configuration for ruff +######################## + +# 'ruff' -- Python linter and code formatter +# https://docs.astral.sh/ruff/rules/ [tool.ruff] -line-length = 127 -exclude = [ - "docs", - "ProofOfConcept*", -] +exclude = ['ProofOfConcept*', 'tmp'] +indent-width = 4 +line-length = 127 # See also `max-line-length` in [tool.ruff.lint.pycodestyle] +preview = true # Enable new rules that are not yet stable, like DOC +builtins = ['display'] # Clutch-fix/patch to https://github.com/nbQA-dev/nbQA/issues/882 + +# Formatting options for Ruff [tool.ruff.format] -quote-style = "single" +docstring-code-format = true # Whether to format code snippets in docstrings +docstring-code-line-length = 127 # Line length for code snippets in docstrings +indent-style = 'space' # PEP 8 recommends using spaces over tabs +quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 257) -[tool.ruff.lint.per-file-ignores] -# allow asserts in test files -"*test_*.py" = ["S101"] +# Linting rules to use with Ruff [tool.ruff.lint] -ignore-init-module-imports = true select = [ - # flake8 settings from existing CI setup - "E9", "F63", "F7", "F82", - # Code should be polished to fulfill all cases below - # https://docs.astral.sh/ruff/rules/ - # pycodestyle - "E", - # Pyflakes - "F", - # pyupgrade -# "UP", - # flake8-bugbear -# "B", - # flake8-simplify -# "SIM", - # isort - "I", - # flake8-bandit - "S", + # Various rules + #'C90', # https://docs.astral.sh/ruff/rules/#mccabe-c90 + #'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + 'F', # https://docs.astral.sh/ruff/rules/#pyflakes-f + #'FLY', # https://docs.astral.sh/ruff/rules/#flynt-fly + #'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb + 'I', # https://docs.astral.sh/ruff/rules/#isort-i + #'N', # https://docs.astral.sh/ruff/rules/#pep8-naming-n + #'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy + #'PGH', # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh + #'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf + #'RUF', # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf + #'TRY', # https://docs.astral.sh/ruff/rules/#tryceratops-try + #'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up + # pycodestyle (E, W) rules + 'E', # https://docs.astral.sh/ruff/rules/#error-e + 'W', # https://docs.astral.sh/ruff/rules/#warning-w + # Pylint (PL) rules + #'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc + #'PLE', # https://docs.astral.sh/ruff/rules/#error-ple + #'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr + #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw + # flake8 rules + #'A', # https://docs.astral.sh/ruff/rules/#flake8-builtins-a + #'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + #'ARG', # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg + #'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async + #'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + #'BLE', # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble + #'C4', # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 + #'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com + #'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz + #'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + #'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa + #'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt + #'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix + #'G', # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g + #'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn + #'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp + #'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc + #'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log + #'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie + #'PT', # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt + #'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth + #'PYI', # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi + #'RET', # https://docs.astral.sh/ruff/rules/#flake8-return-ret + #'RSE', # https://docs.astral.sh/ruff/rules/#flake8-raise-rse + 'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s + #'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim + #'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf + #'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot + #'T20', # https://docs.astral.sh/ruff/rules/#flake8-print-t20 + #'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc + #'TD', # https://docs.astral.sh/ruff/rules/#flake8-todos-td + #'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid +] + +# Exceptions to the linting rules + +# Ignore specific rules globally +ignore = [ + 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ + # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout + 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/ +] + +# Ignore specific rules in certain files or directories +[tool.ruff.lint.per-file-ignores] +'*/__init__.py' = [ + 'F401', # re-exports are intentional in __init__.py +] +'tests/**' = [ + 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'S101', # https://docs.astral.sh/ruff/rules/assert/ +] +'docs/**' = [ + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'T201', # https://docs.astral.sh/ruff/rules/print/ ] +'docs/docs/tutorials/**' = [ + 'E402', # https://docs.astral.sh/ruff/rules/module-import-not-at-top-of-file/ +] + +# Specific options for certain rules + +[tool.ruff.lint.flake8-tidy-imports] +# Disallow all relative imports +#ban-relative-imports = 'all' [tool.ruff.lint.isort] +# Forces all from imports to appear on their own line force-single-line = true -[tool.tox] -legacy_tox_ini = """ -[tox] -isolated_build = True -envlist = py{3.11,3.12,3.13} -[gh-actions] -python = - 3.11: py311 - 3.12: py312 - 3.13: py313 -[gh-actions:env] -PLATFORM = - ubuntu-latest: linux - macos-latest: macos - macos-15-intel: macos-intel - windows-latest: windows -[testenv] -passenv = - CI - GITHUB_ACTIONS - GITHUB_ACTION - GITHUB_REF - GITHUB_REPOSITORY - GITHUB_HEAD_REF - GITHUB_RUN_ID - GITHUB_SHA - COVERAGE_FILE -deps = coverage -commands = - pip install -e '.[dev]' - pytest --cov --cov-report=xml -""" +[tool.ruff.lint.mccabe] +# Cyclomatic complexity threshold (default is 10) +max-complexity = 10 + +[tool.ruff.lint.pycodestyle] +# PEP 8 line length guidance: +# https://peps.python.org/pep-0008/#maximum-line-length +# Use 127 characters as the project-wide maximum for regular code lines. +# Use 127 characters for docstrings. +max-line-length = 127 # See also `line-length` in [tool.ruff] +max-doc-length = 127 + +[tool.ruff.lint.pydocstyle] +convention = 'numpy' + +[tool.ruff.lint.pylint] +# Ruff counts `self`/`cls` in max-args; traditional pylint does not. +# Setting 6 here matches pylint's default of 5 (excluding self). +max-args = 6 +max-positional-args = 6 + +############################# +# Configuration for pydoclint +############################# + +# 'pydoclint' -- Docstring linter, a faster alternative to +# 'darglint' or 'darglint2'. +# https://pypi.org/project/pydoclint/ + +# This is a more advanced docstring linter compared to Ruff's built-in +# docstring check rules D or DOC. For example, among many other things, +# it can check that arguments in the docstring, which are used by MkDocs +# and IDEs to render parameter documentation, remain synchronized with +# the parameter declarations in the code (in function's signature). + +[tool.pydoclint] +exclude = '\.' # Temporarily disable pydoclint until we are ready +style = 'numpy' +check-style-mismatch = true +check-arg-defaults = true +allow-init-docstring = true + +#################################### +# Configuration for format-docstring +#################################### + +# 'format-docstring' -- Code formatter for docstrings +# https://github.com/jsh9/format-docstring + +[tool.format_docstring] +exclude = '\.' # Temporarily disable format-docstring until we are ready +docstring_style = 'numpy' +line_length = 127 +fix_rst_backticks = true +verbose = 'default' diff --git a/src/easyimaging/__init__.py b/src/easyimaging/__init__.py index fdd01c7..b5a0e5b 100644 --- a/src/easyimaging/__init__.py +++ b/src/easyimaging/__init__.py @@ -1,16 +1,12 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2024 Easyscience contributors (https://github.com/EasyScience) -# flake8: noqa -import importlib.metadata +"""EasyImaging library.""" -try: - __version__ = importlib.metadata.version(__package__ or __name__) -except importlib.metadata.PackageNotFoundError: - __version__ = '0.0.0' - -del importlib +from importlib.metadata import version from .measurement import Measurement -__all__ = [Measurement] +__version__ = version(__package__) + +__all__ = [Measurement, __version__] diff --git a/src/easyimaging/__version__.py b/src/easyimaging/__version__.py deleted file mode 100644 index b8023d8..0000000 --- a/src/easyimaging/__version__.py +++ /dev/null @@ -1 +0,0 @@ -__version__ = '0.0.1' diff --git a/src/easyimaging/datasets.py b/src/easyimaging/datasets.py new file mode 100644 index 0000000..439018f --- /dev/null +++ b/src/easyimaging/datasets.py @@ -0,0 +1,55 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + + +import pooch + +BRAIN = pooch.create( + # Use the default cache folder for the operating system + path=pooch.os_cache('easyimaging'), + # The remote data is on Github + base_url='https://raw.githubusercontent.com/easyscience/imaging/refs/heads/master/data/', + version=None, + # If this is a development version, get the data from the "main" branch + version_dev='master', + registry={ + 'iron_alpha_scitiff/iron_alpha_v1.tiff': 'sha256:efb923947e5f5c0f46788c0f18836a3fce916745a05ad5fb8483e5ff17e08a1a', + 'iron_alpha_tiff/iron_alpha_v1.tiff': 'sha256:a1e4a14bfff3d7c0e92cc42f65f7931536d01f763ba7df2a0e4c0aac851f3594', + 'small_test_scitiff/small_test_scitiff_v1.tiff': ( + 'sha256:2ce4088fad10437a1180855fba4ebfefad0c98b252be36d6fc046a1aa6ca922d' + ), + 'small_test_tiff/small_test_tiff_v1.tiff': 'sha256:99e5558db28d0d5d5ca46d159791b3649d5a61b6cb4ff67bedaf5485b7d6ea35', + }, +) + + +def iron_alpha_scitiff(): + """ + Load the Iron Alpha sample data as a scitiff. + """ + fname = BRAIN.fetch('iron_alpha_scitiff/iron_alpha_v1.tiff') + return fname + + +def iron_alpha_tiff(): + """ + Load the Iron Alpha sample data as a tiff. + """ + fname = BRAIN.fetch('iron_alpha_tiff/iron_alpha_v1.tiff') + return fname + + +def small_test_scitiff(): + """ + Load a small test scitiff file. + """ + fname = BRAIN.fetch('small_test_scitiff/small_test_scitiff_v1.tiff') + return fname + + +def small_test_tiff(): + """ + Load a small test tiff file. + """ + fname = BRAIN.fetch('small_test_tiff/small_test_tiff_v1.tiff') + return fname diff --git a/src/easyimaging/measurement/__init__.py b/src/easyimaging/measurement/__init__.py index b773640..eb1f0c1 100644 --- a/src/easyimaging/measurement/__init__.py +++ b/src/easyimaging/measurement/__init__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from .measurement import Measurement __all__ = [Measurement] diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py index 56e3a2f..c8dfc14 100644 --- a/src/easyimaging/measurement/measurement.py +++ b/src/easyimaging/measurement/measurement.py @@ -1,6 +1,6 @@ -# SPDX-FileCopyrightText: 2026 EasyImaging contributors -# SPDX-License-Identifier: BSD-3-Clause -# © 2021-2026 Contributors to the EasyImaging project +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations import warnings @@ -26,9 +26,7 @@ class Measurement(NewBase): - """ - Class responsible for managing the measurement data of a time-of-flight neutron imaging experiment. - """ + """Class responsible for managing the measurement data of a time-of-flight neutron imaging experiment.""" def __init__( self, @@ -47,6 +45,12 @@ def __init__( if any(data_array.coords['tof'].to(unit='s') < sc.scalar(0, unit='s')): raise ValueError('time_of_flight values must be non-negative.') + # Coordinate names were changed in scitiff. + if 'x_pixel_offset' in data_array.coords: + data_array.coords['x'] = data_array.coords.pop('x_pixel_offset') + if 'y_pixel_offset' in data_array.coords: + data_array.coords['y'] = data_array.coords.pop('y_pixel_offset') + if 'x' in data_array.coords and 'y' in data_array.coords: self._validate_data_array_coordinate(data_array, 'x', 'x', 'length', 'm') self._validate_data_array_coordinate(data_array, 'y', 'y', 'length', 'm') @@ -82,17 +86,17 @@ def __init__( def from_scitiff( cls, filename: str | Path, unique_name: str | None = None, display_name: str | None = None ) -> Measurement: # noqa: E501 - """ - Create a Measurement instance by loading data from a SciTIFF file. + """Create a Measurement instance by loading data from a SciTIFF file. Parameters ---------- + cls : filename : str | Path Path to the SciTIFF file. - unique_name : str | None - Unique identifier for the measurement. - display_name : str | None - Display name for the measurement. + unique_name : str | None, optional + Unique identifier for the measurement. By default, None. + display_name : str | None, optional + Display name for the measurement. By default, None. Returns ------- @@ -121,26 +125,26 @@ def from_tiff_stack( unique_name: str | None = None, display_name: str | None = None, ) -> Measurement: - """ - Create a Measurement instance by loading data from a TIFF stack file. + """Create a Measurement instance by loading data from a TIFF stack file. Parameters ---------- + cls : filename : str | Path Path to the TIFF stack file. time_of_flights : sc.Variable | np.ndarray Array of time-of-flight values corresponding to the frames in the TIFF stack. If a numpy array is provided, the unit is assumed to be seconds. - x_positions : sc.Variable | np.ndarray | None + x_positions : sc.Variable | np.ndarray | None, optional Array of x-coordinate positions for the pixels. - If a numpy array is provided, the unit is assumed to be meters. - y_positions : sc.Variable | np.ndarray | None + If a numpy array is provided, the unit is assumed to be meters. By default, None. + y_positions : sc.Variable | np.ndarray | None, optional Array of y-coordinate positions for the pixels. - If a numpy array is provided, the unit is assumed to be meters. - unique_name : str | None - Unique identifier for the measurement. - display_name : str | None - Display name for the measurement. + If a numpy array is provided, the unit is assumed to be meters. By default, None. + unique_name : str | None, optional + Unique identifier for the measurement. By default, None. + display_name : str | None, optional + Display name for the measurement. By default, None. Returns ------- @@ -198,8 +202,8 @@ def from_tiff_stack( return instance def save_scitiff(self, filename: str | Path) -> None: - """ - Save the measurement data to a SciTIFF file with its time-of-flight and physical coordinate information. + """Save the measurement data to a SciTIFF file with its time-of-flight and physical coordinate information. + Note that it is the rebinned data array that is saved if rebinning has been applied. Parameters @@ -226,14 +230,15 @@ def save_scitiff(self, filename: str | Path) -> None: @property def data_array_copy(self) -> sc.DataArray: - """ - Get the current data array of the measurement, either rebinned or the original full resolution. + """Get the current data array of the measurement, either rebinned or the original full resolution. + Note that this will make a full copy of the data array, so it should be used with caution for large datasets. """ return self._data_array.copy(deep=True) @data_array_copy.setter def data_array_copy(self, value: sc.DataArray) -> None: + """Data array copy.""" raise AttributeError( 'Cannot set data_array, it is a read-only property. ' 'Please make a new Measurement instance if you want to use a different data array.' @@ -241,30 +246,26 @@ def data_array_copy(self, value: sc.DataArray) -> None: @property def _data_array(self) -> sc.DataArray: - """ - Get the current data array, either rebinned or the original full resolution. - """ + """Get the current data array, either rebinned or the original full resolution.""" if hasattr(self, '_rebinned_data_array'): return self._rebinned_data_array return self._full_data_array @_data_array.setter def _data_array(self, value: sc.DataArray) -> None: + """Data array.""" raise AttributeError('Cannot set _data_array, it is a read-only property.') @property def x_positions(self) -> sc.Variable | None: - """ - Get the x-coordinate positions of the pixels, if available. - """ + """Get the x-coordinate positions of the pixels, if available.""" if self._has_physical_coords: return self._data_array.coords['x'].copy() return None @x_positions.setter def x_positions(self, value: sc.Variable | np.ndarray) -> None: - """ - Set the x-coordinate positions of the pixels. + """Set the x-coordinate positions of the pixels. Parameters ---------- @@ -290,17 +291,14 @@ def x_positions(self, value: sc.Variable | np.ndarray) -> None: @property def y_positions(self) -> sc.Variable | None: - """ - Get the y-coordinate positions of the pixels, if available. - """ + """Get the y-coordinate positions of the pixels, if available.""" if self._has_physical_coords: return self._data_array.coords['y'].copy() return None @y_positions.setter def y_positions(self, value: sc.Variable | np.ndarray) -> None: - """ - Set the y-coordinate positions of the pixels. + """Set the y-coordinate positions of the pixels. Parameters ---------- @@ -327,8 +325,7 @@ def y_positions(self, value: sc.Variable | np.ndarray) -> None: def set_physical_coord_positions( self, x_positions: sc.Variable | np.ndarray, y_positions: sc.Variable | np.ndarray ) -> None: - """ - Set the physical coordinate positions for the measurement corresponding to the pixel indices. + """Set the physical coordinate positions for the measurement corresponding to the pixel indices. Parameters ---------- @@ -362,9 +359,7 @@ def set_physical_coord_positions( self._has_physical_coords = True def delete_physical_coord_positions(self) -> None: - """ - Delete the physical coordinate positions for the measurement. - """ + """Delete the physical coordinate positions for the measurement.""" if self._has_physical_coords: del self._data_array.coords['x'] del self._data_array.coords['y'] @@ -374,15 +369,12 @@ def delete_physical_coord_positions(self) -> None: @property def time_of_flights(self) -> sc.Variable: - """ - Get the time-of-flight values of the measurement. - """ + """Get the time-of-flight values of the measurement.""" return self._data_array.coords['tof'].copy() @time_of_flights.setter def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: - """ - Set the time-of-flight values of the measurement. + """Set the time-of-flight values of the measurement. Parameters ---------- @@ -405,29 +397,29 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None: @property def regions_of_interest(self) -> EasyList[RectROI]: - """ - Get the list of regions of interest (ROIs) defined for this measurement. - """ + """Get the list of regions of interest (ROIs) defined for this measurement.""" return self._regions_of_interest @regions_of_interest.setter def regions_of_interest(self, value: EasyList[RectROI]) -> None: + """Regions of interest.""" raise AttributeError( 'Cannot set regions_of_interest, it is a read-only property. ' 'Please simply add or remove ROIs directly from the list.' ) def rebin(self, dimensions: dict[str, Numeric]) -> None: - """ - Rebin the measurement image stack. This operation reduces the resolution of the data by combining adjacent pixels or time bins. + """Rebin the measurement image stack. + + This operation reduces the resolution of the data by combining adjacent pixels or time bins. The rebinned dimensions must be evenly divisible by their specific rebin factor. Parameters ---------- - dimensions : dict[str, int] + dimensions : dict[str, Numeric] A dictionary specifying the rebinning factors for each dimension. For example, {'t': 2} will rebin the time dimension by a factor of 2. - """ # noqa: E501 + """ if not isinstance(dimensions, dict): raise TypeError('dimensions must be a dictionary mapping dimension names to rebin factors.') if all(isinstance(value, Numeric) and value == 1 for value in dimensions.values()): # Reverts to original data @@ -458,17 +450,18 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None: self._rebinned_data_array = temp_array def revert_rebin(self) -> None: - """ - Revert any rebinning applied to the measurement data, restoring it to its original resolution. - """ + """Revert any rebinning applied to the measurement data, restoring it to its original resolution.""" if hasattr(self, '_rebinned_data_array'): del self._rebinned_data_array else: - warnings.warn('No rebinning to revert. The data array is already in its original state.', UserWarning) + warnings.warn( + 'No rebinning to revert. The data array is already in its original state.', + UserWarning, + ) def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> None: - """ - Plot the measurement image at a specific time-of-flight. + """Plot the measurement image at a specific time-of-flight. + If no time-of-flight is provided, the plot will average over all time-of-flight values. This method uses the plopp library for plotting: @@ -476,9 +469,9 @@ def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> Non Parameters ---------- - time_of_flight : int | sc.Variable | None - The time-of-flight value to plot. If None, the time-of-flight axis is averaged. - kwargs : dict + time_of_flight : int | sc.Variable | None, optional + The time-of-flight value to plot. If None, the time-of-flight axis is averaged. By default, None. + **kwargs : dict Additional keyword arguments to pass to the plotting function. See https://scipp.github.io/plopp/generated/plopp.plot.html for options. """ @@ -513,26 +506,23 @@ def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> Non plot.show() def slicer_plot(self, **kwargs) -> None: - """ - Launch an interactive slicer plot for exploring the measurement data. + """Launch an interactive slicer plot for exploring the measurement data. This method uses the plopp library for interactive slicing: https://scipp.github.io/plopp/plotting/slicer-plot.html Parameters ---------- - kwargs : dict + **kwargs : dict Additional keyword arguments to pass to the slicer function. See https://scipp.github.io/plopp/generated/plopp.slicer.html for options. """ slicer_kwargs_defaults = self._plot_defaults() - slicer_kwargs_defaults.update( - { - 'title': self.display_name + ' - Time of Flight Slicer', - 'keep': ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'], - 'mode': 'single', - } - ) + slicer_kwargs_defaults.update({ + 'title': self.display_name + ' - Time of Flight Slicer', + 'keep': ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'], + 'mode': 'single', + }) slicer_kwargs_defaults['coords'].append('tof') # Overwrite defaults with any user-provided kwargs @@ -544,30 +534,27 @@ def slicer_plot(self, **kwargs) -> None: raise RuntimeError('Interactive slicer is only supported in Jupyter notebooks.') def spectrum_inspector(self, **kwargs) -> None: - """ - Launch an interactive spectrum inspector plot for exploring the measurement data. + """Launch an interactive spectrum inspector plot for exploring the measurement data. This method uses the plopp library for interactive inspection: https://scipp.github.io/plopp/plotting/inspector-plot.html Parameters ---------- - kwargs : dict + **kwargs : dict Additional keyword arguments to pass to the inspector function. See https://scipp.github.io/plopp/generated/plopp.inspector.html for options. """ inspector_kwargs_defaults = self._plot_defaults() inspector_kwargs_defaults['ymax'] = inspector_kwargs_defaults['cmax'] - inspector_kwargs_defaults.update( - { - 'title': self.display_name + ' - Spectrum Inspector', - 'ymin': 0.0, - 'dim': 't', - 'orientation': 'vertical', - 'operation': 'mean', - 'mode': 'point', - } - ) + inspector_kwargs_defaults.update({ + 'title': self.display_name + ' - Spectrum Inspector', + 'ymin': 0.0, + 'dim': 't', + 'orientation': 'vertical', + 'operation': 'mean', + 'mode': 'point', + }) # Overwrite defaults with any user-provided kwargs inspector_kwargs_defaults.update(kwargs) @@ -577,8 +564,7 @@ def spectrum_inspector(self, **kwargs) -> None: raise RuntimeError('Interactive spectrum inspector is only supported in Jupyter notebooks.') def roi_creator(self, **kwargs) -> None: - """ - Launch an interactive ROI creator for defining regions of interest on the measurement data. + """Launch an interactive ROI creator for defining regions of interest on the measurement data. This method uses the plopp library for interactive ROI creation: https://scipp.github.io/plopp/plotting/roi-selector.html @@ -591,7 +577,7 @@ def roi_creator(self, **kwargs) -> None: Parameters ---------- - kwargs : dict + **kwargs : dict Additional keyword arguments to pass to the ROI creator function. See https://scipp.github.io/plopp/generated/plopp.inspector.html for options. """ @@ -601,16 +587,14 @@ def roi_creator(self, **kwargs) -> None: roi_selector_kwargs_defaults = self._plot_defaults() roi_selector_kwargs_defaults['ymax'] = roi_selector_kwargs_defaults['cmax'] - roi_selector_kwargs_defaults.update( - { - 'title': self.display_name + ' - ROI Creator', - 'ymin': 0.0, - 'dim': 't', - 'orientation': 'vertical', - 'operation': 'mean', - 'mode': 'rectangle', - } - ) + roi_selector_kwargs_defaults.update({ + 'title': self.display_name + ' - ROI Creator', + 'ymin': 0.0, + 'dim': 't', + 'orientation': 'vertical', + 'operation': 'mean', + 'mode': 'rectangle', + }) # Overwrite defaults with any user-provided kwargs roi_selector_kwargs_defaults.update(kwargs) @@ -655,6 +639,7 @@ def roi_creator(self, **kwargs) -> None: # The callback to be used by the Scipp RectangleTool when drawing a new rectangle. def create_rectangle_roi(rect, roi_list, data_array): + """Create rectangle roi.""" # Get the pixel and physical coordinate ranges from the rectangle vertices using the helper method. x_pixel_range, y_pixel_range, x_range, y_range = Measurement._ranges_from_rectangle(rect, data_array) new_roi = RectROI( @@ -668,6 +653,7 @@ def create_rectangle_roi(rect, roi_list, data_array): # The callback to be used by the Scipp RectangleTool when dragging the corners of an existing rectangle. def edit_rectangle_roi(rect, roi_list, data_array): + """Edit rectangle roi.""" x_pixel_range, y_pixel_range, x_range, y_range = Measurement._ranges_from_rectangle(rect, data_array) # Find the ROI corresponding to the rectangle being edited based on the stored rectangle ID. for roi in roi_list: @@ -680,6 +666,7 @@ def edit_rectangle_roi(rect, roi_list, data_array): matching_roi.set_physical_coord_range(x_range, y_range) def delete_rectangle_roi(rect, roi_list): + """Delete rectangle roi.""" for roi in roi_list: if hasattr(roi, '_rect_ids') and rect.id in roi._rect_ids: roi_list.remove(roi) @@ -690,7 +677,11 @@ def delete_rectangle_roi(rect, roi_list): # ------------------------------------------------------------------------------------------------- plots[0].toolbar['inspect']._tool.on_create( - partial(create_rectangle_roi, roi_list=self.regions_of_interest, data_array=self._data_array) + partial( + create_rectangle_roi, + roi_list=self.regions_of_interest, + data_array=self._data_array, + ) ) plots[0].toolbar['inspect']._tool.on_change( @@ -704,15 +695,16 @@ def delete_rectangle_roi(rect, roi_list): return plots def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray: - """ - Extract the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + """Extract the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + If no ROI is provided, the spectrum is calculated over the entire image. Parameters ---------- - roi : RectROI | str | None + roi : RectROI | str | None, optional The region of interest for which to extract the spectrum. If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs. + By default, None. Returns ------- @@ -741,8 +733,8 @@ def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray: return spectrum_data def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None: - """ - Plot the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + """Plot the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI). + If no ROI is provided, the spectrum is calculated over the entire image. This method uses the plopp library for plotting: @@ -750,10 +742,11 @@ def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None: Parameters ---------- - roi : RectROI | str | None + roi : RectROI | str | None, optional The region of interest for which to plot the spectrum. If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs. - kwargs : dict + By default, None. + **kwargs : dict Additional keyword arguments to pass to the plotting function. See https://scipp.github.io/plopp/generated/plopp.plot.html for options. """ @@ -783,6 +776,7 @@ def _validate_data_array_coordinate( expected_dim_string: str, expected_unit: str, ) -> None: + """Validate data array coordinate.""" if data_array.coords[coord_name].dims != (expected_dim,): raise DimensionError(f"'{coord_name}' coordinate must be of dimension '{expected_dim}'.") try: @@ -802,6 +796,7 @@ def _validate_provided_coord( expected_dim_string: str, expected_unit: str, ) -> sc.Variable: + """Validate provided coord.""" if not (isinstance(coord, sc.Variable) and coord.sizes) and not isinstance(coord, np.ndarray): raise TypeError(f'{coord_name} must be a scipp Variable or a numpy ndarray.') if len(coord) not in (data_array.sizes[dim], data_array.sizes[dim] + 1): @@ -818,6 +813,7 @@ def _validate_provided_coord( def _ranges_from_rectangle( rect, data_array: sc.DataArray ) -> tuple[tuple[int, int], None] | tuple[tuple[int, int], tuple[sc.Variable, sc.Variable]]: # noqa: E501 + """Ranges from rectangle.""" # To be used in the roi_selector method to convert the rectangle vertices to pixel and # physical coordinate ranges for the new ROI. x_vertex_list, y_vertex_list = rect.vertices @@ -830,8 +826,14 @@ def _ranges_from_rectangle( else: x_unit = data_array.coords['x'].unit y_unit = data_array.coords['y'].unit - x_range = (sc.scalar(min(x_vertex_list), unit=x_unit), sc.scalar(max(x_vertex_list), unit=x_unit)) - y_range = (sc.scalar(min(y_vertex_list), unit=y_unit), sc.scalar(max(y_vertex_list), unit=y_unit)) + x_range = ( + sc.scalar(min(x_vertex_list), unit=x_unit), + sc.scalar(max(x_vertex_list), unit=x_unit), + ) + y_range = ( + sc.scalar(min(y_vertex_list), unit=y_unit), + sc.scalar(max(y_vertex_list), unit=y_unit), + ) sliced_data_array = data_array['x', x_range[0] : x_range[1]]['y', y_range[0] : y_range[1]] @@ -843,6 +845,7 @@ def _ranges_from_rectangle( return x_pixel_range, y_pixel_range, x_range, y_range def _plot_defaults(self): + """Plot defaults.""" return { 'title': self.display_name, 'clabel': 'Transmission', @@ -853,4 +856,5 @@ def _plot_defaults(self): } def __repr__(self): + """Repr function.""" return f'{self.display_name} with shape {self._data_array.shape} and regions of interest: {[roi.display_name for roi in self.regions_of_interest]}' # noqa: E501 diff --git a/src/easyimaging/measurement/regions.py b/src/easyimaging/measurement/regions.py index 78323e8..2708958 100644 --- a/src/easyimaging/measurement/regions.py +++ b/src/easyimaging/measurement/regions.py @@ -1,6 +1,6 @@ -# SPDX-FileCopyrightText: 2026 EasyImaging contributors -# SPDX-License-Identifier: BSD-3-Clause -# © 2021-2026 Contributors to the EasyImaging project +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations from typing import Any @@ -30,8 +30,7 @@ def __init__( unique_name: str | None = None, display_name: str | None = None, ) -> None: - """ - Initialize a RectROI instance. + """Initialize a RectROI instance. Parameters: x_pixel_range (Sequence[int]): The pixel range for the x-coordinate. @@ -53,6 +52,7 @@ def __init__( def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Sequence[int]) -> None: """Set the pixel coordinate ranges for the ROI. + Parameters: x_pixel_range (Sequence[int]): The start and end pixel coordinates in the x direction. y_pixel_range (Sequence[int]): The start and end pixel coordinates in the y direction. @@ -67,6 +67,7 @@ def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Seq def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequence[sc.Variable]) -> None: """Set the physical coordinate ranges for the ROI. + Parameters: x_range (Sequence[sc.Variable]): The start and end physical coordinates in the x direction. y_range (Sequence[sc.Variable]): The start and end physical coordinates in the y direction. @@ -94,16 +95,20 @@ def delete_physical_coord_range(self) -> None: def pixel_slice(self) -> Tuple[slice, slice]: """Get the pixel slice corresponding to the ROI. - Returns: - tuple: Two (x,y) slice objects representing the pixel range of the ROI. + Returns + ------- + tuple + Two (x,y) slice objects representing the pixel range of the ROI. """ return slice(self._x_pixel_start, self._x_pixel_end), slice(self._y_pixel_start, self._y_pixel_end) def slice(self) -> Tuple[slice, slice]: """Get the slice corresponding to the ROI, using physical coordinates if available. - Returns: - tuple: Two (x,y) slice objects representing the range of the ROI. + Returns + ------- + tuple + Two (x,y) slice objects representing the range of the ROI. """ if self._has_physical_coords: return slice(self._x_start, self._x_end), slice(self._y_start, self._y_end) @@ -112,42 +117,51 @@ def slice(self) -> Tuple[slice, slice]: @property def x_pixel_start(self) -> int: + """X pixel start.""" return self._x_pixel_start.value @x_pixel_start.setter def x_pixel_start(self, value: int): + """X pixel start.""" self._check_index(value, 'x_pixel_start') self._x_pixel_start = sc.scalar(value) @property def x_pixel_end(self) -> int: + """X pixel end.""" return self._x_pixel_end.value @x_pixel_end.setter def x_pixel_end(self, value: int): + """X pixel end.""" self._check_index(value, 'x_pixel_end') self._x_pixel_end = sc.scalar(value) @property def y_pixel_start(self) -> int: + """Y pixel start.""" return self._y_pixel_start.value @y_pixel_start.setter def y_pixel_start(self, value: int): + """Y pixel start.""" self._check_index(value, 'y_pixel_start') self._y_pixel_start = sc.scalar(value) @property def y_pixel_end(self) -> int: + """Y pixel end.""" return self._y_pixel_end.value @y_pixel_end.setter def y_pixel_end(self, value: int): + """Y pixel end.""" self._check_index(value, 'y_pixel_end') self._y_pixel_end = sc.scalar(value) @property def x_start(self) -> sc.Variable: + """X start.""" if self._has_physical_coords: return self._x_start.copy() else: @@ -155,12 +169,14 @@ def x_start(self) -> sc.Variable: @x_start.setter def x_start(self, value: sc.Variable): + """X start.""" self._single_coord_setter_check(value, 'x_start') self._check_scalar(value, 'x_start') self._x_start = value @property def x_end(self) -> sc.Variable: + """X end.""" if self._has_physical_coords: return self._x_end.copy() else: @@ -168,12 +184,14 @@ def x_end(self) -> sc.Variable: @x_end.setter def x_end(self, value: sc.Variable): + """X end.""" self._single_coord_setter_check(value, 'x_end') self._check_scalar(value, 'x_end') self._x_end = value @property def y_start(self) -> sc.Variable: + """Y start.""" if self._has_physical_coords: return self._y_start.copy() else: @@ -181,12 +199,14 @@ def y_start(self) -> sc.Variable: @y_start.setter def y_start(self, value: sc.Variable): + """Y start.""" self._single_coord_setter_check(value, 'y_start') self._check_scalar(value, 'y_start') self._y_start = value @property def y_end(self) -> sc.Variable: + """Y end.""" if self._has_physical_coords: return self._y_end.copy() else: @@ -194,14 +214,13 @@ def y_end(self) -> sc.Variable: @y_end.setter def y_end(self, value: sc.Variable): + """Y end.""" self._single_coord_setter_check(value, 'y_end') self._check_scalar(value, 'y_end') self._y_end = value def _check_input_sequence(self, value: Sequence, name: str, typename: str, expected_type: any) -> None: - """ - Check if the input value is a sequence of the expected type and length. - """ + """Check if the input value is a sequence of the expected type and length.""" if not isinstance(value, Sequence) or len(value) != 2: raise TypeError(f'{name} must be a tuple or a list of two {typename}, got a {type(value).__name__}.') if not (isinstance(value[0], expected_type) and isinstance(value[1], expected_type)): @@ -211,18 +230,14 @@ def _check_input_sequence(self, value: Sequence, name: str, typename: str, expec ) def _check_index(self, value: int, name: str) -> None: - """ - Check if the input value is a valid index (non-negative integer). - """ + """Check if the input value is a valid index (non-negative integer).""" if not isinstance(value, int): raise TypeError(f'{name} index must be an integer.') if value < 0: raise ValueError(f'{name} index must be non-negative.') def _check_scalar(self, value: sc.Variable, name: str) -> None: - """ - Check if the input value is a scipp scalar with a unit of length. - """ + """Check if the input value is a scipp scalar with a unit of length.""" if value.dims: raise ValueError(f'{name} must be a scipp scalar (0-dimensional Variable).') try: @@ -232,9 +247,7 @@ def _check_scalar(self, value: sc.Variable, name: str) -> None: raise UnitError(f"{name} must be a scipp scalar with a unit of length (e.g., 'm').") from e def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None: - """ - Check if the input value is a scipp scalar and if physical coordinates are set. - """ + """Check if the input value is a scipp scalar and if physical coordinates are set.""" if not isinstance(value, sc.Variable): raise TypeError(f'{name} must be a scipp scalar.') if not self._has_physical_coords: @@ -256,12 +269,32 @@ def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]: out_dict['y_pixel_range'] = [int(self.y_pixel_start), int(self.y_pixel_end)] if self._has_physical_coords: out_dict['x_range'] = [ - {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.x_start)}, - {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.x_end)}, + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.x_start), + }, + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.x_end), + }, ] out_dict['y_range'] = [ - {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.y_start)}, - {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.y_end)}, + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.y_start), + }, + { + '@module': 'scipp', + '@version': sc.__version__, + '@class': 'scalar', + 'dict': sc.to_dict(self.y_end), + }, ] return out_dict @@ -275,6 +308,7 @@ def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI: return super().from_dict(temp_dict) def __repr__(self) -> str: + """Repr function.""" repr_str = ( f'RectROI(x_pixel_range=({self._x_pixel_start}, {self._x_pixel_end}), ' f'y_pixel_range=({self._y_pixel_start}, {self._y_pixel_end})' diff --git a/src/easyimaging/utils/__init__.py b/src/easyimaging/utils/__init__.py index c680399..7f816d2 100644 --- a/src/easyimaging/utils/__init__.py +++ b/src/easyimaging/utils/__init__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from .jupyter_notebook_utilities import _is_notebook from .scipp_utilities import _to_edges diff --git a/src/easyimaging/utils/jupyter_notebook_utilities.py b/src/easyimaging/utils/jupyter_notebook_utilities.py index 9c19dc0..883c945 100644 --- a/src/easyimaging/utils/jupyter_notebook_utilities.py +++ b/src/easyimaging/utils/jupyter_notebook_utilities.py @@ -1,7 +1,9 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + + def _is_notebook() -> bool: - """ - Check if the code is running in a Jupyter notebook environment. - """ + """Check if the code is running in a Jupyter notebook environment.""" try: shell = get_ipython().__class__.__name__ # pyright: ignore[reportUndefinedVariable] if shell == 'ZMQInteractiveShell': diff --git a/src/easyimaging/utils/scipp_utilities.py b/src/easyimaging/utils/scipp_utilities.py index 3626a1b..a00ccd1 100644 --- a/src/easyimaging/utils/scipp_utilities.py +++ b/src/easyimaging/utils/scipp_utilities.py @@ -1,10 +1,11 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import scipp as sc def _to_edges(centers: sc.Variable) -> sc.Variable: - """ - Convenience method to convert center coordinates to edge coordinates. - """ + """Convenience method to convert center coordinates to edge coordinates.""" interior_edges = sc.midpoints(centers) return sc.concat( [ diff --git a/tests/integration/integration/fitting/test_dummy.py b/tests/integration/integration/fitting/test_dummy.py new file mode 100644 index 0000000..c61e754 --- /dev/null +++ b/tests/integration/integration/fitting/test_dummy.py @@ -0,0 +1,17 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +import pytest + + +@pytest.mark.fast +def test_dummy_fast(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected + + +# def test_dummy_slow(): +# calculated = sum(i * j for i in range(10000) for j in range(10000)) +# expected = 2499500025000000 +# assert calculated == expected diff --git a/tests/integration/integration/scipp-analysis/test_dummy.py b/tests/integration/integration/scipp-analysis/test_dummy.py new file mode 100644 index 0000000..c61e754 --- /dev/null +++ b/tests/integration/integration/scipp-analysis/test_dummy.py @@ -0,0 +1,17 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +import pytest + + +@pytest.mark.fast +def test_dummy_fast(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected + + +# def test_dummy_slow(): +# calculated = sum(i * j for i in range(10000) for j in range(10000)) +# expected = 2499500025000000 +# assert calculated == expected diff --git a/tests/package_test.py b/tests/package_test.py index 4197cf3..8594634 100644 --- a/tests/package_test.py +++ b/tests/package_test.py @@ -1,5 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2024 Easyscience contributors (https://github.com/EasyScience) + import easyimaging as pkg diff --git a/tests/small_scitiff.tiff b/tests/small_scitiff.tiff deleted file mode 100644 index 5ec25b7..0000000 Binary files a/tests/small_scitiff.tiff and /dev/null differ diff --git a/tests/small_tiff.tiff b/tests/small_tiff.tiff deleted file mode 100644 index b99b895..0000000 Binary files a/tests/small_tiff.tiff and /dev/null differ diff --git a/tests/unit_tests/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py similarity index 91% rename from tests/unit_tests/measurement/test_measurement.py rename to tests/unit/measurement/test_measurement.py index e031bae..c5d2fe2 100644 --- a/tests/unit_tests/measurement/test_measurement.py +++ b/tests/unit/measurement/test_measurement.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import warnings from copy import copy from pathlib import Path @@ -13,6 +16,8 @@ from scipp import DimensionError from easyimaging import Measurement +from easyimaging.datasets import small_test_scitiff +from easyimaging.datasets import small_test_tiff from easyimaging.measurement.regions import RectROI @@ -90,7 +95,11 @@ def valid_roi(self): def test_init_valid_data_array(self, valid_data_array): # When Then - measurement = Measurement(data_array=valid_data_array, unique_name='test_measurement', display_name='Test Measurement') + measurement = Measurement( + data_array=valid_data_array, + unique_name='test_measurement', + display_name='Test Measurement', + ) # Expect assert measurement._data_array is not valid_data_array # Ensure a copy was made assert not sc.any(measurement._data_array.masks['non_finite']).value @@ -150,15 +159,31 @@ def test_init_invalid_data_array_type(self): @pytest.mark.parametrize( 'new_tof_coordinate, error, expected_message', [ - (None, ValueError, "data array must have a 'tof' coordinate for time-of-flight information."), - (sc.scalar(5.0, unit='s'), DimensionError, "'tof' coordinate must be of dimension 't'."), - (sc.arange('x', 0, 6, 1, unit='s'), DimensionError, "'tof' coordinate must be of dimension 't'."), + ( + None, + ValueError, + "data array must have a 'tof' coordinate for time-of-flight information.", + ), + ( + sc.scalar(5.0, unit='s'), + DimensionError, + "'tof' coordinate must be of dimension 't'.", + ), + ( + sc.arange('x', 0, 6, 1, unit='s'), + DimensionError, + "'tof' coordinate must be of dimension 't'.", + ), ( sc.arange('t', 0, 10, 1, unit='m'), sc.UnitError, "'tof' coordinate must have a unit of time, such as \\('s'\\).", ), # noqa: E501 # fmt: skip - (sc.arange('t', -5, 5, 1, unit='s'), ValueError, 'time_of_flight values must be non-negative.'), + ( + sc.arange('t', -5, 5, 1, unit='s'), + ValueError, + 'time_of_flight values must be non-negative.', + ), ], ids=[ 'missing_tof', @@ -182,8 +207,16 @@ def test_init_invalid_tof_coordinates(self, valid_data_array, new_tof_coordinate 'new_x_coordinate, error, expected_message', [ (sc.scalar(5.0, unit='m'), DimensionError, "'x' coordinate must be of dimension 'x'"), - (sc.arange('t', 0, 10, 1, unit='m'), DimensionError, "'x' coordinate must be of dimension 'x'."), - (sc.arange('x', 0, 6, 1, unit='s'), sc.UnitError, "'x' coordinate must have a unit of length, such as \\('m'\\)."), # noqa: E501 + ( + sc.arange('t', 0, 10, 1, unit='m'), + DimensionError, + "'x' coordinate must be of dimension 'x'.", + ), + ( + sc.arange('x', 0, 6, 1, unit='s'), + sc.UnitError, + "'x' coordinate must have a unit of length, such as \\('m'\\).", + ), # noqa: E501 ], ids=[ 'scalar_x', @@ -203,8 +236,16 @@ def test_init_invalid_x_coordinates(self, valid_data_array, new_x_coordinate, er 'new_y_coordinate, error, expected_message', [ (sc.scalar(5.0, unit='m'), DimensionError, "'y' coordinate must be of dimension 'y'."), - (sc.arange('t', 0, 10, 1, unit='m'), DimensionError, "'y' coordinate must be of dimension 'y'."), - (sc.arange('y', 0, 6, 1, unit='s'), sc.UnitError, "'y' coordinate must have a unit of length, such as \\('m'\\)."), # noqa: E501 + ( + sc.arange('t', 0, 10, 1, unit='m'), + DimensionError, + "'y' coordinate must be of dimension 'y'.", + ), + ( + sc.arange('y', 0, 6, 1, unit='s'), + sc.UnitError, + "'y' coordinate must have a unit of length, such as \\('m'\\).", + ), # noqa: E501 ], ids=[ 'scalar_y', @@ -232,7 +273,10 @@ def test_init_missing_single_wrong_dimension(self, valid_data_array, dimension): def test_init_missing_both_wrong_dimensions(self, valid_data_array_no_xy_coords): # When - invalid_data_array = valid_data_array_no_xy_coords.rename_dims({'x': 'wrong_x', 'y': 'wrong_y'}) + invalid_data_array = valid_data_array_no_xy_coords.rename_dims({ + 'x': 'wrong_x', + 'y': 'wrong_y', + }) # Then Expect with pytest.raises(DimensionError, match="data array must have both 'x' and 'y' dimensions."): Measurement(data_array=invalid_data_array) @@ -247,7 +291,9 @@ def test_init_missing_single_physical_coordinate(self, valid_data_array, coordin Measurement(data_array=invalid_data_array) @pytest.mark.parametrize( - 'path', ['tests/small_scitiff.tiff', Path('tests/small_scitiff.tiff')], ids=['str_path', 'Path_object'] + 'path', + [small_test_scitiff(), Path(small_test_scitiff())], + ids=['str_path', 'Path_object'], ) def test_from_scitiff_valid(self, path): # When Then @@ -277,14 +323,19 @@ def test_from_scitiff_non_existent_file(self): def test_from_scitiff_not_a_scitiff(self): # When - path = 'tests/small_tiff.tiff' # This is a regular TIFF, not a SciTIFF + path = small_test_tiff() # This is a regular TIFF, not a SciTIFF + path = path.replace('\\', '/') # Ensure consistent path format across platforms # Then Expect with pytest.raises(RuntimeError, match=f"Tiff file '{path}' not a proper SciTIFF file:"): Measurement.from_scitiff( filename=path, ) - @pytest.mark.parametrize('path', ['tests/small_tiff.tiff', Path('tests/small_tiff.tiff')], ids=['str_path', 'Path_object']) + @pytest.mark.parametrize( + 'path', + [small_test_tiff(), Path(small_test_tiff())], + ids=['str_path', 'Path_object'], + ) def test_from_tiff_stack_valid_paths(self, path): # When Then measurement = Measurement.from_tiff_stack( @@ -311,7 +362,7 @@ def test_from_tiff_stack_valid_paths(self, path): def test_from_tiff_stack_valid_time_of_flights(self, coord, expected): # When Then measurement = Measurement.from_tiff_stack( - filename='tests/small_tiff.tiff', + filename=small_test_tiff(), time_of_flights=coord, ) # Expect @@ -331,7 +382,7 @@ def test_from_tiff_stack_valid_time_of_flights(self, coord, expected): def test_from_tiff_stack_valid_x_positions(self, coord, expected): # When Then measurement = Measurement.from_tiff_stack( - filename='tests/small_tiff.tiff', + filename=small_test_tiff(), time_of_flights=sc.arange('t', 0, 240, 1, unit='s'), x_positions=coord, y_positions=sc.arange('y', 0, 1020, 20, unit='cm'), @@ -354,7 +405,7 @@ def test_from_tiff_stack_valid_x_positions(self, coord, expected): def test_from_tiff_stack_valid_y_positions(self, coord, expected): # When Then measurement = Measurement.from_tiff_stack( - filename='tests/small_tiff.tiff', + filename=small_test_tiff(), time_of_flights=sc.arange('t', 0, 240, 1, unit='s'), y_positions=coord, x_positions=sc.arange('x', 0, 510, 10, unit='cm'), @@ -379,14 +430,26 @@ def test_from_tiff_stack_invalid_path(self, path, error): @pytest.mark.parametrize( 'coord, error, expected_message', [ - ('not_a_valid_type', TypeError, 'time_of_flight must be a scipp Variable or a numpy ndarray.'), + ( + 'not_a_valid_type', + TypeError, + 'time_of_flight must be a scipp Variable or a numpy ndarray.', + ), ( sc.arange('t', 0, 5, 1, unit='s'), ValueError, 'Length of time_of_flight array does not match the number of frames in the TIFF stack.', ), # noqa: E501 - (sc.scalar(5.0, unit='s'), TypeError, 'time_of_flight must be a scipp Variable or a numpy ndarray.'), - (sc.arange('t', 0, 240, 1, unit='m'), sc.UnitError, "time_of_flight must have a unit of time, such as 's'"), + ( + sc.scalar(5.0, unit='s'), + TypeError, + 'time_of_flight must be a scipp Variable or a numpy ndarray.', + ), + ( + sc.arange('t', 0, 240, 1, unit='m'), + sc.UnitError, + "time_of_flight must have a unit of time, such as 's'", + ), ], ids=[ 'invalid_type', @@ -399,20 +462,28 @@ def test_from_tiff_stack_invalid_time_of_flights(self, coord, error, expected_me # When Then Expect with pytest.raises(error, match=expected_message): Measurement.from_tiff_stack( - filename='tests/small_tiff.tiff', + filename=small_test_tiff(), time_of_flights=coord, ) @pytest.mark.parametrize( 'coord, error, expected_message', [ - ('not_a_valid_type', TypeError, 'x_positions must be a scipp Variable or a numpy ndarray.'), + ( + 'not_a_valid_type', + TypeError, + 'x_positions must be a scipp Variable or a numpy ndarray.', + ), ( sc.arange('x', 0, 10, 1, unit='m'), ValueError, 'Length of x_positions array does not match the number of pixels in the x dimension.', ), # noqa: E501 - (sc.arange('x', 0, 50, 1, unit='s'), sc.UnitError, "x_positions must have a unit of length, such as 'm'"), + ( + sc.arange('x', 0, 50, 1, unit='s'), + sc.UnitError, + "x_positions must have a unit of length, such as 'm'", + ), ], ids=[ 'invalid_type_x', @@ -424,7 +495,7 @@ def test_from_tiff_stack_invalid_x_positions(self, coord, error, expected_messag # When Then Expect with pytest.raises(error, match=expected_message): Measurement.from_tiff_stack( - filename='tests/small_tiff.tiff', + filename=small_test_tiff(), time_of_flights=sc.arange('t', 0, 240, 1, unit='s'), x_positions=coord, ) @@ -432,13 +503,21 @@ def test_from_tiff_stack_invalid_x_positions(self, coord, error, expected_messag @pytest.mark.parametrize( 'coord, error, expected_message', [ - ('not_a_valid_type', TypeError, 'y_positions must be a scipp Variable or a numpy ndarray.'), + ( + 'not_a_valid_type', + TypeError, + 'y_positions must be a scipp Variable or a numpy ndarray.', + ), ( sc.arange('y', 0, 10, 1, unit='m'), ValueError, 'Length of y_positions array does not match the number of pixels in the y dimension.', ), # noqa: E501 - (sc.arange('y', 0, 50, 1, unit='s'), sc.UnitError, "y_positions must have a unit of length, such as 'm'"), + ( + sc.arange('y', 0, 50, 1, unit='s'), + sc.UnitError, + "y_positions must have a unit of length, such as 'm'", + ), ], ids=[ 'invalid_type_y', @@ -450,7 +529,7 @@ def test_from_tiff_stack_invalid_y_positions(self, coord, error, expected_messag # When Then Expect with pytest.raises(error, match=expected_message): Measurement.from_tiff_stack( - filename='tests/small_tiff.tiff', + filename=small_test_tiff(), time_of_flights=sc.arange('t', 0, 240, 1, unit='s'), y_positions=coord, ) @@ -588,7 +667,10 @@ def test_positions_setter_invalid(self, valid_data_array_no_xy_coords, coordinat # When measurement = Measurement(data_array=valid_data_array_no_xy_coords) # Then Expect - with pytest.raises(ValueError, match=f'Cannot set {coordinate} before setting all physical coordinate positions.'): + with pytest.raises( + ValueError, + match=f'Cannot set {coordinate} before setting all physical coordinate positions.', + ): setattr(measurement, coordinate, sc.arange('x', 0, 10, 1, unit='m')) # Just a single test, other test-cases are covered by from_tiff_stack tests as both use _validate_provided_coord() @@ -644,7 +726,10 @@ def test_delete_physical_coord_positions_no_coords(self, valid_data_array_no_xy_ # When measurement = Measurement(data_array=valid_data_array_no_xy_coords) # Then Expect - with pytest.raises(ValueError, match='Cannot delete physical coordinate positions because they are not set.'): + with pytest.raises( + ValueError, + match='Cannot delete physical coordinate positions because they are not set.', + ): measurement.delete_physical_coord_positions() def test_time_of_flights(self, valid_data_array): @@ -872,7 +957,10 @@ def test_rebin_invalid_dimension_type(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(TypeError, match='dimensions must be a dictionary mapping dimension names to rebin factors.'): + with pytest.raises( + TypeError, + match='dimensions must be a dictionary mapping dimension names to rebin factors.', + ): measurement.rebin(dimensions=['x']) def test_rebin_time_dimension(self, valid_data_array): @@ -900,21 +988,30 @@ def test_rebin_invalid_dimensions_value_type(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(ValueError, match="Rebin size for dimension 'x' must be a positive integer of at least 1."): + with pytest.raises( + ValueError, + match="Rebin size for dimension 'x' must be a positive integer of at least 1.", + ): measurement.rebin(dimensions={'x': 'not_an_integer'}) def test_rebin_invalid_dimensions_value_zero(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(ValueError, match="Rebin size for dimension 'x' must be a positive integer of at least 1."): + with pytest.raises( + ValueError, + match="Rebin size for dimension 'x' must be a positive integer of at least 1.", + ): measurement.rebin(dimensions={'x': 0}) def test_rebin_invalid_dimensions_value_negative(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(ValueError, match="Rebin size for dimension 'x' must be a positive integer of at least 1."): + with pytest.raises( + ValueError, + match="Rebin size for dimension 'x' must be a positive integer of at least 1.", + ): measurement.rebin(dimensions={'x': -2}) def test_rebin_invalid_dimensions_value_non_divisable(self, valid_data_array): @@ -941,13 +1038,20 @@ def test_revert_rebin_no_rebin(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.warns(UserWarning, match='No rebinning to revert. The data array is already in its original state.'): + with pytest.warns( + UserWarning, + match='No rebinning to revert. The data array is already in its original state.', + ): measurement.revert_rebin() # Without making image comparisons, this is the best we can do to test the plot function @pytest.mark.parametrize( 'time_of_flight, title', - [(None, '(averaged over TOF)'), (0, 'at TOF index 0'), (sc.scalar(5.0, unit='s'), 'at TOF=5.0 s')], + [ + (None, '(averaged over TOF)'), + (0, 'at TOF index 0'), + (sc.scalar(5.0, unit='s'), 'at TOF=5.0 s'), + ], ids=['sum', 'indice', 'scipp_scalar'], ) def test_plot_coordinates(self, valid_data_array, time_of_flight, title, plot_setup): @@ -1083,7 +1187,10 @@ def test_spectrum_inspector_fails_outside_notebook(self, valid_data_array): # When measurement = Measurement(data_array=valid_data_array) # Then Expect - with pytest.raises(RuntimeError, match='Interactive spectrum inspector is only supported in Jupyter notebooks.'): + with pytest.raises( + RuntimeError, + match='Interactive spectrum inspector is only supported in Jupyter notebooks.', + ): measurement.spectrum_inspector() def test_spectrum_inspector(self, valid_data_array, plot_setup): @@ -1274,7 +1381,8 @@ def test_spectrum_valid_with_physical_roi(self, valid_data_array): # When valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) - # Make the physical coordinates different from the pixel coordinates to ensure they are used correctly in the spectrum calculation # noqa: E501 + # Make the physical coordinates different from the pixel coordinates + # to ensure they are used correctly in the spectrum calculation measurement.set_physical_coord_positions( x_positions=sc.arange('x', 0, 21, 3, unit='m'), y_positions=sc.arange('y', 0, 14, 2, unit='m'), @@ -1310,7 +1418,8 @@ def test_spectrum_valid_roi_by_name(self, valid_data_array): assert sc.identical(spectrum.data, sc.ones(dims=['t'], shape=[10]) * 0.625) def test_spectrum_identical_after_rebin(self, valid_data_array): - # If the roi is defined such that it includes whole rebinned pixels, then the spectrum should be identical before and after rebinning # noqa: E501 + # If the roi is defined such that it includes whole rebinned pixels, + # then the spectrum should be identical before and after rebinning valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4)) @@ -1322,7 +1431,8 @@ def test_spectrum_identical_after_rebin(self, valid_data_array): assert sc.identical(spectrum_before_rebin, spectrum_after_rebin) def test_spectrum_not_identical_after_rebin(self, valid_data_array): - # If the roi is defined such that it includes partial rebinned pixels, then the spectrum should not be identical before and after rebinning # noqa: E501 + # If the roi is defined such that it includes partial rebinned pixels, + # then the spectrum should not be identical before and after rebinning valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10]) measurement = Measurement(data_array=valid_data_array) roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 5)) @@ -1369,6 +1479,7 @@ def test_spectrum_invalid_roi_name(self, valid_data_array): measurement = Measurement(data_array=valid_data_array) # Then Expect with pytest.raises( - KeyError, match="ROI with unique name 'non_existent_roi' not found in the measurement's list of ROIs." + KeyError, + match="ROI with unique name 'non_existent_roi' not found in the measurement's list of ROIs.", ): # noqa: E501 measurement.spectrum(roi='non_existent_roi') diff --git a/tests/unit_tests/measurement/test_regions.py b/tests/unit/measurement/test_regions.py similarity index 89% rename from tests/unit_tests/measurement/test_regions.py rename to tests/unit/measurement/test_regions.py index 5fdd122..48d8fdd 100644 --- a/tests/unit_tests/measurement/test_regions.py +++ b/tests/unit/measurement/test_regions.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import pytest import scipp as sc from scipp import UnitError @@ -16,7 +19,14 @@ def roi_with_physical_coords(self): x_end = sc.scalar(10.0, unit='m') y_start = sc.scalar(0.0, unit='m') y_end = sc.scalar(5.0, unit='m') - return RectROI((10, 50), (20, 80), (x_start, x_end), (y_start, y_end), unique_name='test_roi', display_name='Test ROI') + return RectROI( + (10, 50), + (20, 80), + (x_start, x_end), + (y_start, y_end), + unique_name='test_roi', + display_name='Test ROI', + ) def test_init_valid_physical_coords(self, roi_with_physical_coords): # When Then @@ -100,12 +110,12 @@ def test_init_invalid_x_pixel_range_arguments(self, x_pixel_range): ( (sc.scalar(0.0, unit='m'), sc.array(dims=['x'], values=[1.0, 2.0], unit='m')), ValueError, - 'Physical coordinates must be a scipp scalar \(0-dimensional Variable\).', + r'Physical coordinates must be a scipp scalar \(0-dimensional Variable\).', ), # Second element not a scalar # noqa: E501 ( (sc.scalar(0.0, unit='m'), sc.scalar(1.0, unit='s')), UnitError, - "Physical coordinates must be a scipp scalar with a unit of length \(e.g., 'm'\).", + r"Physical coordinates must be a scipp scalar with a unit of length \(e.g., 'm'\).", ), # Second element with wrong unit # noqa: E501 ], ids=[ @@ -182,7 +192,9 @@ def test_pixel_coordinate_setter(self, roi_basic, attribute): assert getattr(roi, attribute) == 15 @pytest.mark.parametrize( - 'attribute', ['x_pixel_end', 'y_pixel_start', 'y_pixel_end'], ids=['x_pixel_end', 'y_pixel_start', 'y_pixel_end'] + 'attribute', + ['x_pixel_end', 'y_pixel_start', 'y_pixel_end'], + ids=['x_pixel_end', 'y_pixel_start', 'y_pixel_end'], ) @pytest.mark.parametrize( 'invalid_value, error, message', @@ -234,7 +246,9 @@ def test_physical_coordinate_getter(self, roi_with_physical_coords, attribute, s assert getattr(roi, attribute) is not getattr(roi, f'_{attribute}') # Ensure a copy is returned @pytest.mark.parametrize( - 'attribute', ['x_start', 'x_end', 'y_start', 'y_end'], ids=['x_start', 'x_end', 'y_start', 'y_end'] + 'attribute', + ['x_start', 'x_end', 'y_start', 'y_end'], + ids=['x_start', 'x_end', 'y_start', 'y_end'], ) def test_physical_coordinate_setter(self, roi_with_physical_coords, attribute): # When @@ -246,17 +260,24 @@ def test_physical_coordinate_setter(self, roi_with_physical_coords, attribute): assert sc.identical(getattr(roi, attribute), new_value) @pytest.mark.parametrize( - 'attribute', ['x_start', 'x_end', 'y_start', 'y_end'], ids=['x_start', 'x_end', 'y_start', 'y_end'] + 'attribute', + ['x_start', 'x_end', 'y_start', 'y_end'], + ids=['x_start', 'x_end', 'y_start', 'y_end'], ) def test_physical_coordinate_setter_setting_single_coordinate(self, roi_basic, attribute): # When roi = roi_basic # Then Expect - with pytest.raises(ValueError, match=f'Cannot set {attribute} before setting all physical coordinate ranges.'): + with pytest.raises( + ValueError, + match=f'Cannot set {attribute} before setting all physical coordinate ranges.', + ): setattr(roi, attribute, sc.scalar(1.0, unit='m')) @pytest.mark.parametrize( - 'attribute', ['x_start', 'x_end', 'y_start', 'y_end'], ids=['x_start', 'x_end', 'y_start', 'y_end'] + 'attribute', + ['x_start', 'x_end', 'y_start', 'y_end'], + ids=['x_start', 'x_end', 'y_start', 'y_end'], ) @pytest.mark.parametrize( 'invalid_value, error, message', @@ -265,12 +286,12 @@ def test_physical_coordinate_setter_setting_single_coordinate(self, roi_basic, a ( sc.array(dims=['x'], values=[1.0, 2.0], unit='m'), ValueError, - 'must be a scipp scalar \(0-dimensional Variable\).', + r'must be a scipp scalar \(0-dimensional Variable\).', ), # Not a scalar # noqa: E501 ( sc.scalar(1.0, unit='s'), UnitError, - "must be a scipp scalar with a unit of length \(e.g., 'm'\).", + r"must be a scipp scalar with a unit of length \(e.g., 'm'\).", ), # Wrong unit # noqa: E501 ], ids=['not_scipp_variable', 'not_scalar', 'wrong_unit'], @@ -318,8 +339,14 @@ def test_to_dict_with_physical_coords(self, roi_with_physical_coords): # When Then roi_dict = roi_with_physical_coords.to_dict() # Expect - assert roi_dict['x_pixel_range'] == [roi_with_physical_coords.x_pixel_start, roi_with_physical_coords.x_pixel_end] - assert roi_dict['y_pixel_range'] == [roi_with_physical_coords.y_pixel_start, roi_with_physical_coords.y_pixel_end] + assert roi_dict['x_pixel_range'] == [ + roi_with_physical_coords.x_pixel_start, + roi_with_physical_coords.x_pixel_end, + ] + assert roi_dict['y_pixel_range'] == [ + roi_with_physical_coords.y_pixel_start, + roi_with_physical_coords.y_pixel_end, + ] assert isinstance(roi_dict['x_range'], list) and len(roi_dict['x_range']) == 2 assert isinstance(roi_dict['y_range'], list) and len(roi_dict['y_range']) == 2 assert isinstance(roi_dict['x_range'][0], dict) and roi_dict['x_range'][0]['@module'] == 'scipp' diff --git a/tools/license_headers.py b/tools/license_headers.py new file mode 100644 index 0000000..f276ca1 --- /dev/null +++ b/tools/license_headers.py @@ -0,0 +1,321 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Add, remove, or check SPDX headers in Python files.""" + +from __future__ import annotations + +import argparse +import fnmatch +import tomllib +from datetime import datetime +from pathlib import Path +from typing import Any +from typing import Optional +from typing import Union + +from git import Repo +from spdx_headers.core import find_repository_root +from spdx_headers.core import get_copyright_info +from spdx_headers.core import has_spdx_header +from spdx_headers.data import load_license_data +from spdx_headers.operations import add_header_to_single_file +from spdx_headers.operations import remove_header_from_single_file + +LICENSE_DATABASE = load_license_data() + + +def load_pyproject(repo_path: Union[str, Path]) -> dict[str, Any]: + """ + Load and return parsed ``pyproject.toml`` data for the repository. + """ + repo_root = find_repository_root(repo_path) + pyproject_path = repo_root / 'pyproject.toml' + + with pyproject_path.open('rb') as file_handle: + return tomllib.load(file_handle) + + +def get_pyproject_value(pyproject_data: dict[str, Any], dotted_key: str) -> Any: + """Return a nested ``pyproject.toml`` value from a dotted key.""" + value: Any = pyproject_data + for part in dotted_key.split('.'): + if not isinstance(value, dict) or part not in value: + raise KeyError(dotted_key) + value = value[part] + return value + + +def normalize_pattern(pattern: str) -> str: + """Normalize an exclude pattern to a POSIX-style relative path.""" + normalized = Path(pattern).as_posix() + if normalized.startswith('./'): + normalized = normalized[2:] + return normalized.rstrip('/') + + +def get_exclude_patterns( + repo_path: Union[str, Path], + exclude_values: list[str], + exclude_from_pyproject_toml: Optional[str], +) -> list[str]: + """ + Return normalized exclude patterns from CLI and ``pyproject.toml``. + """ + pyproject_data = load_pyproject(repo_path) + patterns: list[str] = [] + + if exclude_from_pyproject_toml: + value = get_pyproject_value(pyproject_data, exclude_from_pyproject_toml) + if not isinstance(value, list) or not all(isinstance(item, str) for item in value): + raise ValueError( + f'{exclude_from_pyproject_toml} in pyproject.toml must be a list of strings.', + ) + patterns.extend(value) + + for item in exclude_values: + try: + value = get_pyproject_value(pyproject_data, item) + except KeyError: + patterns.append(item) + continue + + if not isinstance(value, list) or not all(isinstance(entry, str) for entry in value): + raise ValueError(f'{item} in pyproject.toml must be a list of strings.') + patterns.extend(value) + + normalized_patterns: list[str] = [] + seen: set[str] = set() + for pattern in patterns: + normalized = normalize_pattern(pattern) + if normalized and normalized not in seen: + normalized_patterns.append(normalized) + seen.add(normalized) + + return normalized_patterns + + +def get_file_creation_year(file_path: Union[str, Path]) -> str: + """Return the year the file was first added to Git history. + + If the year cannot be determined, fall back to the current year. + """ + file_path = Path(file_path) + + repo = Repo(file_path, search_parent_directories=True) + root = Path(repo.working_tree_dir).resolve() + rel_path = file_path.resolve().relative_to(root) + + rel_path_git = rel_path.as_posix() + + log_output = repo.git.log( + '--follow', + '--diff-filter=A', + '--reverse', + '--format=%ad', + '--date=format:%Y', + '--', + rel_path_git, + ).strip() + + year = log_output.splitlines()[0].strip() if log_output else '' + + return year or str(datetime.now().year) + + +def get_org_url(repo_path: Union[str, Path]) -> str: + """ + Return the organization URL derived from the repository source URL. + """ + pyproject_data = load_pyproject(repo_path) + repo_url = pyproject_data['project']['urls']['Source Code'] + return repo_url.rsplit('/', 1)[0] + + +def get_project_license(repo_path: Union[str, Path]) -> str: + """Return the project license value from ``pyproject.toml``.""" + pyproject_data = load_pyproject(repo_path) + return pyproject_data['project']['license'] + + +def get_copyright_holder(repo_path: Union[str, Path]) -> str: + """Return the repository copyright holder name.""" + _, name, _ = get_copyright_info(repo_path) + return name + + +def add_spdx_header( + target_file: Union[str, Path], + *, + license_key: str, + copyright_holder: str, + org_url: str, +) -> None: + """Add SPDX headers to one file.""" + year = get_file_creation_year(target_file) + + add_header_to_single_file( + filepath=target_file, + license_key=license_key, + license_data=LICENSE_DATABASE, + year=year, + name=copyright_holder, + email=org_url, + ) + + +def is_excluded(relative_path: str, exclude_patterns: list[str]) -> bool: + """Return whether a relative path should be excluded.""" + for pattern in exclude_patterns: + if fnmatch.fnmatch(relative_path, pattern): + return True + if relative_path == pattern: + return True + if relative_path.startswith(f'{pattern}/'): + return True + return False + + +def iter_python_files( + paths: list[str], + *, + repo_root: Path, + exclude_patterns: list[str], + parser: argparse.ArgumentParser, +) -> list[Path]: + """Collect Python files under the given paths after exclusions.""" + files: list[Path] = [] + seen: set[Path] = set() + + for base_dir in paths: + base_path = Path(base_dir) + if not base_path.exists(): + parser.error(f'Path does not exist: {base_dir}') + + if base_path.is_file(): + candidates = [base_path] if base_path.suffix == '.py' else [] + else: + candidates = sorted(base_path.rglob('*.py')) + + for py_file in candidates: + resolved = py_file.resolve() + try: + relative_path = resolved.relative_to(repo_root).as_posix() + except ValueError: + relative_path = py_file.as_posix() + + if is_excluded(relative_path, exclude_patterns): + continue + + if resolved not in seen: + files.append(py_file) + seen.add(resolved) + + return files + + +def run_add( + files: list[Path], + *, + license_key: str, + copyright_holder: str, + org_url: str, +) -> int: + """Add SPDX headers to all selected files.""" + for py_file in files: + add_spdx_header( + py_file, + license_key=license_key, + copyright_holder=copyright_holder, + org_url=org_url, + ) + return 0 + + +def run_remove(files: list[Path]) -> int: + """Remove SPDX headers from all selected files.""" + for py_file in files: + remove_header_from_single_file(py_file) + return 0 + + +def run_check(files: list[Path]) -> int: + """Check SPDX headers in all selected files.""" + missing_files = [py_file for py_file in files if not has_spdx_header(py_file)] + + if not missing_files: + print('✓ All Python files have valid SPDX headers.') + return 0 + + print('✗ The following files are missing SPDX headers:') + for py_file in missing_files: + print(f' - {py_file.as_posix()}') + print(f'\nFound {len(missing_files)} files without SPDX headers.') + return 1 + + +def build_parser() -> argparse.ArgumentParser: + """Build the CLI argument parser.""" + parser = argparse.ArgumentParser( + description='Add, remove, or check SPDX headers in Python files.', + ) + subparsers = parser.add_subparsers(dest='command', required=True) + + for command_name in ('check', 'remove', 'add'): + command_parser = subparsers.add_parser(command_name) + command_parser.add_argument( + 'paths', + nargs='+', + help='Relative paths to scan (e.g. src tests)', + ) + command_parser.add_argument( + '--exclude', + nargs='*', + default=[], + help='Exclude paths, glob patterns, or pyproject dotted keys.', + ) + command_parser.add_argument( + '--exclude-from-pyproject-toml', + help='Read exclude patterns from a dotted key in pyproject.toml.', + ) + + return parser + + +def main(argv: Optional[list[str]] = None) -> int: + """Run the SPDX header CLI.""" + parser = build_parser() + args = parser.parse_args(argv) + + repo_path = Path('.').resolve() + repo_root = find_repository_root(repo_path).resolve() + exclude_patterns = get_exclude_patterns( + repo_path, + args.exclude, + args.exclude_from_pyproject_toml, + ) + files = iter_python_files( + args.paths, + repo_root=repo_root, + exclude_patterns=exclude_patterns, + parser=parser, + ) + + if args.command == 'check': + return run_check(files) + + if args.command == 'remove': + return run_remove(files) + + license_key = get_project_license(repo_path) + copyright_holder = get_copyright_holder(repo_path) + org_url = get_org_url(repo_path) + return run_add( + files, + license_key=license_key, + copyright_holder=copyright_holder, + org_url=org_url, + ) + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/tools/update_docs_assets.py b/tools/update_docs_assets.py new file mode 100644 index 0000000..fa31665 --- /dev/null +++ b/tools/update_docs_assets.py @@ -0,0 +1,91 @@ +""" +Update documentation assets from the assets-branding repository. + +This script fetches branding assets (logos, icons, images) from the +easyscience/assets-branding GitHub repository and copies them to the +appropriate locations in the documentation directory. +""" + +import shutil +from pathlib import Path + +import pooch + +# Configuration: Define what to fetch and where to copy +GITHUB_REPO = 'easyscience/assets-branding' +GITHUB_BRANCH = 'master' +BASE_URL = f'https://raw.githubusercontent.com/{GITHUB_REPO}/refs/heads/{GITHUB_BRANCH}' +PROJECT_NAME = 'easyimaging' + +# Mapping of source files to destination paths +# Format: "source_path_in_repo": "destination_path_in_project" +ASSETS_MAP = { + # Logos + f'{PROJECT_NAME}/logos/dark.svg': 'docs/docs/assets/images/logo_dark.svg', + f'{PROJECT_NAME}/logos/light.svg': 'docs/docs/assets/images/logo_light.svg', + # Favicon + f'{PROJECT_NAME}/icons/color.png': 'docs/docs/assets/images/favicon.png', + # Icon overrides + f'{PROJECT_NAME}/icons/bw.svg': f'docs/overrides/.icons/{PROJECT_NAME}.svg', + 'easyscience-org/icons/eso-icon_bw.svg': 'docs/overrides/.icons/easyscience.svg', +} + + +def fetch_and_copy_asset( + source_path: str, + dest_path: str, + cache_dir: Path, +) -> None: + """ + Fetch an asset from GitHub and copy it to the destination. + + Args: + source_path: Path to the file in the GitHub repository + dest_path: Destination path in the project + cache_dir: Directory to cache downloaded files + """ + url = f'{BASE_URL}/{source_path}' + + # Create a unique cache filename based on source path + cache_filename = source_path.replace('/', '_') + + # Download file using pooch + file_path = pooch.retrieve( + url=url, + known_hash=None, # Skip hash verification + path=cache_dir, + fname=cache_filename, + ) + + # Create destination directory if it doesn't exist + dest = Path(dest_path) + dest.parent.mkdir(parents=True, exist_ok=True) + + # Copy the file to destination + shutil.copy2(file_path, dest) + print(f'Copied {file_path} -> {dest_path}') + + +def main(): + """Main function to update all documentation assets.""" + print('📥 Updating documentation assets...') + print(f' Repository: {GITHUB_REPO}') + print(f' Branch: {GITHUB_BRANCH}\n') + + # Use a temporary cache directory + cache_dir = Path.home() / '.cache' / GITHUB_REPO + cache_dir.mkdir(parents=True, exist_ok=True) + + # Fetch and copy each asset + for source_path, dest_path in ASSETS_MAP.items(): + try: + fetch_and_copy_asset(source_path, dest_path, cache_dir) + print() + except Exception as e: + print(f'❌ Failed to fetch {source_path}: {e}') + + print('\n✅ Documentation assets updated successfully!') + + +if __name__ == '__main__': + main() diff --git a/tools/update_github_labels.py b/tools/update_github_labels.py new file mode 100644 index 0000000..84de575 --- /dev/null +++ b/tools/update_github_labels.py @@ -0,0 +1,341 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Set/update GitHub labels for current or specified easyscience +repository. + +Requires: + - gh CLI installed + - gh auth login completed + +Usage: + python update_github_labels.py + python update_github_labels.py --dry-run + python update_github_labels.py --repo easyscience/my-repo + python update_github_labels.py --repo easyscience/my-repo --dry-run +""" + +from __future__ import annotations + +import argparse +import json +import shlex +import subprocess # noqa: S404 +import sys +from dataclasses import dataclass + +EASYSCIENCE_ORG = 'easyscience' + + +# Data structures + + +@dataclass(frozen=True) +class Label: + """A GitHub label with name, color, and description.""" + + name: str + color: str + description: str = '' + + +@dataclass(frozen=True) +class LabelRename: + """Mapping from old label name to new label name.""" + + old: str + new: str + + +class Colors: + """Hex color codes for label groups.""" + + SCOPE = 'd73a4a' + MAINTAINER = '0e8a16' + PRIORITY = 'fbca04' + BOT = '5319e7' + + +LABEL_RENAMES = [ + # Default GitHub labels to rename (if they exist) + LabelRename('bug', '[scope] bug'), + LabelRename('documentation', '[scope] documentation'), + LabelRename('duplicate', '[maintainer] duplicate'), + LabelRename('enhancement', '[scope] enhancement'), + LabelRename('good first issue', '[maintainer] good first issue'), + LabelRename('help wanted', '[maintainer] help wanted'), + LabelRename('invalid', '[maintainer] invalid'), + LabelRename('question', '[maintainer] question'), + LabelRename('wontfix', '[maintainer] wontfix'), + # Custom label renames (if they exist) + LabelRename('[bot] pull request', '[bot] release'), +] + +LABELS = [ + # Scope labels + Label( + '[scope] bug', + Colors.SCOPE, + 'Bug report or fix (major.minor.PATCH)', + ), + Label( + '[scope] documentation', + Colors.SCOPE, + 'Documentation only changes (major.minor.patch.POST)', + ), + Label( + '[scope] enhancement', + Colors.SCOPE, + 'Adds/improves features (major.MINOR.patch)', + ), + Label( + '[scope] maintenance', + Colors.SCOPE, + 'Code/tooling cleanup, no feature or bugfix (major.minor.PATCH)', + ), + Label( + '[scope] significant', + Colors.SCOPE, + 'Breaking or major changes (MAJOR.minor.patch)', + ), + Label( + '[scope] ⚠️ label needed', + Colors.SCOPE, + 'Automatically added to issues and PRs without a [scope] label', + ), + # Maintainer labels + Label( + '[maintainer] duplicate', + Colors.MAINTAINER, + 'Already reported or submitted', + ), + Label( + '[maintainer] good first issue', + Colors.MAINTAINER, + 'Good entry-level issue for newcomers', + ), + Label( + '[maintainer] help wanted', + Colors.MAINTAINER, + 'Needs additional help to resolve or implement', + ), + Label( + '[maintainer] invalid', + Colors.MAINTAINER, + 'Invalid, incorrect or outdated', + ), + Label( + '[maintainer] question', + Colors.MAINTAINER, + 'Needs clarification, discussion, or more information', + ), + Label( + '[maintainer] wontfix', + Colors.MAINTAINER, + 'Will not be fixed or continued', + ), + # Priority labels + Label( + '[priority] lowest', + Colors.PRIORITY, + 'Very low urgency', + ), + Label( + '[priority] low', + Colors.PRIORITY, + 'Low importance', + ), + Label( + '[priority] medium', + Colors.PRIORITY, + 'Normal/default priority', + ), + Label( + '[priority] high', + Colors.PRIORITY, + 'Should be prioritized soon', + ), + Label( + '[priority] highest', + Colors.PRIORITY, + 'Urgent. Needs attention ASAP', + ), + Label( + '[priority] ⚠️ label needed', + Colors.PRIORITY, + 'Automatically added to issues without a [priority] label', + ), + # Bot label + Label( + '[bot] release', + Colors.BOT, + 'Automated release PR. Excluded from changelog/versioning', + ), + Label( + '[bot] backmerge', + Colors.BOT, + 'Automated backmerge master → develop failed due to conflicts', + ), +] + + +# Helpers + + +@dataclass(frozen=True) +class CmdResult: + """Result of a shell command execution.""" + + returncode: int + stdout: str + stderr: str + + +def run_cmd( + args: list[str], + *, + dry_run: bool, + check: bool = True, +) -> CmdResult: + """Run a command (or print it in dry-run mode).""" + cmd_str = ' '.join(shlex.quote(a) for a in args) + + if dry_run: + print(f' [dry-run] {cmd_str}') + return CmdResult(0, '', '') + + proc = subprocess.run( + args=args, + text=True, + capture_output=True, + ) + result = CmdResult( + proc.returncode, + proc.stdout.strip(), + proc.stderr.strip(), + ) + + if check and proc.returncode != 0: + raise RuntimeError(f'Command failed ({proc.returncode}): {cmd_str}\n{result.stderr}') + + return result + + +def get_current_repo() -> str: + """Get the current repository name in 'owner/repo' format.""" + result = subprocess.run( + args=[ + 'gh', + 'repo', + 'view', + '--json', + 'nameWithOwner', + ], + text=True, + capture_output=True, + check=True, + ) + data = json.loads(result.stdout) + name_with_owner = data.get('nameWithOwner', '') + + if '/' not in name_with_owner: + raise RuntimeError('Could not determine current repository name') + + return name_with_owner + + +def rename_label( + repo: str, + rename: LabelRename, + *, + dry_run: bool, +) -> None: + """Rename a label, silently skipping if it doesn't exist.""" + result = run_cmd( + args=[ + 'gh', + 'label', + 'edit', + rename.old, + '--name', + rename.new, + '--repo', + repo, + ], + dry_run=dry_run, + check=False, + ) + + if dry_run or result.returncode == 0: + print(f' Rename: {rename.old!r} → {rename.new!r}') + else: + print(f' Skip (not found): {rename.old!r}') + + +def upsert_label( + repo: str, + label: Label, + *, + dry_run: bool, +) -> None: + """Create or update a label.""" + run_cmd( + [ + 'gh', + 'label', + 'create', + label.name, + '--color', + label.color, + '--description', + label.description, + '--force', + '--repo', + repo, + ], + dry_run=dry_run, + ) + print(f' Upsert: {label.name!r}') + + +# Main + + +def main() -> int: + """Entry point: parse arguments and sync labels.""" + parser = argparse.ArgumentParser(description='Sync GitHub labels for easyscience repos') + parser.add_argument( + '--repo', + help='Target repository (owner/name)', + ) + parser.add_argument( + '--dry-run', + action='store_true', + help='Print actions without applying changes', + ) + args = parser.parse_args() + + repo = args.repo or get_current_repo() + org = repo.split('/')[0] + + if org.lower() != EASYSCIENCE_ORG: + print(f"Error: repository '{repo}' is not under '{EASYSCIENCE_ORG}'", file=sys.stderr) + return 2 + + print(f'Repository: {repo}') + if args.dry_run: + print('Mode: DRY-RUN (no changes will be made)\n') + + print('\nRenaming default labels...') + for rename in LABEL_RENAMES: + rename_label(repo, rename, dry_run=args.dry_run) + + print('\nUpserting labels...') + for label in LABELS: + upsert_label(repo, label, dry_run=args.dry_run) + + print('\nDone.') + return 0 + + +if __name__ == '__main__': + raise SystemExit(main())