Applying the Copier templates

.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

.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

.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

.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 }}

.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 }}

.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

.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 }}
+        post-cleanup: ${{ inputs.post-cleanup }}

.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 }}

.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 }}

.github/configs/pages-deployment.json

@@ -0,0 +1,6 @@
+{
+  "source": {
+    "branch": "gh-pages",
+    "path": "/"
+  }
+}