Reapply updated Copier templates and streamline developer workflow (#97)

AndrewSazonov · henrikjacobsenfys · commit 809e3a79a3a0 · 2026-02-06T11:17:51.000+01:00
* Update pixi.lock

* Reapply templates from v0.4.0

* pixi run fix-all

* Switch to manual pre-commit and simplify tasks

* Enable PyPI Trusted Publishing via OIDC

* Reorder imports and widget magic in notebooks

* Normalize notebook cell IDs
diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.0.5
+_commit: v0.4.2
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18163581
diff --git a/.github/actions/publish-to-pypi/action.yml b/.github/actions/publish-to-pypi/action.yml
@@ -1,13 +1,14 @@
 name: 'Publish to PyPI'
-description: 'Publish a built distribution to PyPI using pypa/gh-action-pypi-publish'
+description: 'Publish dist/ to PyPI via Trusted Publishing (OIDC)'
 inputs:
-  password:
-    description: 'PyPI API token (or password) for authentication'
-    required: true
+  packages_dir:
+    description: 'Directory containing the built packages to upload'
+    required: false
+    default: 'dist'
 
 runs:
   using: 'composite'
   steps:
     - uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        password: ${{ inputs.password }}
+        packages-dir: ${{ inputs.packages_dir }}
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -107,11 +107,8 @@ jobs:
       - name: Pre-build site step
         run: pixi run python -c "import easydynamics"
 
-      # Convert Python scripts in the docs/docs/tutorials/ directory to Jupyter
-      # notebooks.
-      # This step also strips any existing output from the notebooks and
-      # prepares them for documentation.
-      - name: Convert tutorial scripts to notebooks
+      # 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.).
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
@@ -14,6 +14,10 @@ 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@v5
@@ -23,10 +27,18 @@ jobs:
       - 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/easydynamics/settings/publishing/
+      # Use the following data:
+      # Owner: easyscience
+      # Repository name: dynamics-lib
+      # Workflow name: pypi-publish.yml
       - name: Publish to PyPI
         uses: ./.github/actions/publish-to-pypi
-        with:
-          password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/quality.yml b/.github/workflows/quality.yml
@@ -79,6 +79,14 @@ jobs:
         continue-on-error: true
         shell: bash
         run: pixi run nonpy-format-check
+      # Check formatting of Jupyter Notebooks in the tutorials folder
+      - name: Prepare notebooks and check formatting
+        id: check_notebooks_formatting
+        continue-on-error: true
+        shell: bash
+        run: |
+          pixi run notebook-prepare
+          pixi run notebook-format-check
 
       # Add summary
       - name: Add quality checks summary
diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml
@@ -46,7 +46,7 @@ jobs:
         shell: bash
         run: pixi run script-tests
 
-      - name: Convert tutorial scripts to notebooks
+      - name: Prepare notebooks
         shell: bash
         run: pixi run notebook-prepare
 
diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,11 @@ __pycache__/
 .venv/
 .coverage
 
+# PyInstaller
+dist/
+build/
+*.spec
+
 # MkDocs
 docs/site/
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,57 +1,54 @@
 repos:
   - repo: local
     hooks:
-      # -----------------
-      # Pre-commit checks
-      # -----------------
+      # -------------
+      # Manual checks
+      # -------------
       - id: pixi-pyproject-check
         name: pixi run pyproject-check
         entry: pixi run pyproject-check
         language: system
         pass_filenames: false
-        stages: [pre-commit]
+        stages: [manual]
 
-      - id: pixi-py-lint-check-staged
-        name: pixi run py-lint-check-staged
-        entry: pixi run py-lint-check-pre
+      - id: pixi-py-lint-check
+        name: pixi run py-lint-check
+        entry: pixi run py-lint-check
         language: system
         pass_filenames: false
-        stages: [pre-commit]
+        stages: [manual]
 
-      - id: pixi-py-format-check-staged
-        name: pixi run py-format-check-staged
-        entry: pixi run py-format-check-pre
+      - id: pixi-py-format-check
+        name: pixi run py-format-check
+        entry: pixi run py-format-check
         language: system
         pass_filenames: false
-        stages: [pre-commit]
+        stages: [manual]
 
-      - id: pixi-nonpy-format-check-modified
-        name: pixi run nonpy-format-check-modified
-        entry: pixi run nonpy-format-check-modified
+      - id: pixi-nonpy-format-check
+        name: pixi run nonpy-format-check
+        entry: pixi run nonpy-format-check
         language: system
         pass_filenames: false
-        stages: [pre-commit]
+        stages: [manual]
 
       - id: pixi-docs-format-check
         name: pixi run docs-format-check
         entry: pixi run docs-format-check
         language: system
         pass_filenames: false
-        stages: [pre-commit]
+        stages: [manual]
 
-      # ----------------
-      # Pre-push checks
-      # ----------------
-      - id: pixi-nonpy-format-check
-        name: pixi run nonpy-format-check
-        entry: pixi run nonpy-format-check
+      - id: pixi-notebook-format-check
+        name: pixi run notebook-format-check
+        entry: pixi run notebook-format-check
         language: system
         pass_filenames: false
-        stages: [pre-push]
+        stages: [manual]
 
       - id: pixi-unit-tests
         name: pixi run unit-tests
         entry: pixi run unit-tests
         language: system
         pass_filenames: false
-        stages: [pre-push]
+        stages: [manual]
diff --git a/README.md b/README.md
@@ -1,16 +1,18 @@
 <p>
   <picture>
     <!-- light mode logo -->
-    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/easyscience/dynamics-lib/refs/heads/master/docs/docs/assets/images/logo_light.svg'>
+    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydynamics/logos/light.svg'>
     <!-- dark mode logo -->
-    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/easyscience/dynamics-lib/refs/heads/master/docs/docs/assets/images/logo_dark.svg'>
+    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydynamics/logos/dark.svg'>
     <!-- default logo == light mode logo -->
-    <img src='https://raw.githubusercontent.com/easyscience/dynamics-lib/refs/heads/master/docs/docs/assets/images/logo_light.svg' alt='EasyDynamics'>
+    <img src='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydynamics/logos/light.svg' alt='EasyDynamics'>
   </picture>
 </p>
 
-**EasyDynamics** is a scientific software for plotting and fitting qens
-and ins powder data.
+**EasyDynamics** is a scientific software for plotting and fitting QENS
+and INS powder data.
+
+<!-- HOME REPOSITORY SECTION -->
 
 **EasyDynamics** is available both as a Python library and as a
 cross-platform desktop application.
diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css
@@ -222,9 +222,27 @@ Adjust the margins and paddings to fit the defaults in MkDocs Material and do no
   width: 100% !important;
   display: flex !important;
 }
+
 .jp-Notebook {
   padding: 0 !important;
   margin-top: -3em !important;
+
+  /* Ensure notebook content stretches across the page */
+  width: 100% !important;
+  max-width: 100% !important;
+
+  /* mkdocs-material + some notebook HTML end up as flex */
+  align-items: stretch !important;
+}
+
+.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]: */
@@ -234,11 +252,6 @@ Adjust the margins and paddings to fit the defaults in MkDocs Material and do no
   display: none !important;
 }
 
-/* Removes jupyter cell paddings */
-.jp-Cell {
-  padding-left: 0 !important;
-}
-
 /* Removes jupyter output cell padding to align with input cell text */
 .jp-RenderedText {
   padding-left: 0.85em !important;
diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md
@@ -8,8 +8,8 @@ icon: material/cog-box
 **Python 3.11** through **3.12**.
 
 To install and set up EasyDynamics, we recommend using
-[**Pixi**](https://prefix.dev), a modern package manager for Windows,
-macOS, and Linux.
+[**Pixi**](https://pixi.prefix.dev), a modern package manager for
+Windows, macOS, and Linux.
 
 !!! note "Main benefits of using Pixi"
 
@@ -46,16 +46,9 @@ This section describes the simplest way to set up EasyDynamics using
   ```txt
   pixi add python=3.12
   ```
-- Add the GNU Scientific Library (GSL) dependency:
+- Add EasyDynamics to the Pixi environment from PyPI:
   ```txt
-  pixi add gsl
-  ```
-- Add EasyDynamics with the `visualization` extras, which include
-  optional dependencies used for simplified visualization of charts and
-  tables. This can be especially useful for running the Jupyter Notebook
-  examples:
-  ```txt
-  pixi add --pypi "easydynamics[visualization]"
+  pixi add --pypi easydynamics
   ```
 - Add a Pixi task to run EasyDynamics commands easily:
   ```txt
@@ -160,20 +153,7 @@ simply delete and recreate the environment.
 ### Installing from PyPI { #from-pypi }
 
 EasyDynamics is available on **PyPI (Python Package Index)** and can be
-installed using `pip`.
-
-We recommend installing the latest release of EasyDynamics with the
-`visualization` extras, which include optional dependencies used for
-simplified visualization of charts and tables. This can be especially
-useful for running the Jupyter Notebook examples. To do so, use the
-following command:
-
-```txt
-pip install 'easydynamics[visualization]'
-```
-
-If only the core functionality is needed, the library can be installed
-simply with:
+installed using `pip`. To do so, use the following command:
 
 ```txt
 pip install easydynamics
@@ -216,10 +196,10 @@ example:
 pip install git+https://github.com/easyscience/dynamics-lib@develop
 ```
 
-To include extra dependencies (e.g., visualization):
+To include extra dependencies (e.g., dev):
 
 ```txt
-pip install 'easydynamics[visualization] @ git+https://github.com/easyscience/dynamics-lib@develop'
+pip install 'easydynamics[dev] @ git+https://github.com/easyscience/dynamics-lib@develop'
 ```
 
 ## How to Run Tutorials
diff --git a/docs/docs/introduction/index.md b/docs/docs/introduction/index.md
@@ -6,8 +6,8 @@ icon: material/information-slab-circle
 
 ## Description
 
-**EasyDynamics** is a scientific software for plotting and fitting qens
-and ins powder data.
+**EasyDynamics** is a scientific software for plotting and fitting QENS
+and INS powder data.
 
 **EasyDynamics** is available both as a Python library and as a
 cross-platform desktop application.
diff --git a/docs/docs/tutorials/components.ipynb b/docs/docs/tutorials/components.ipynb
@@ -21,6 +21,7 @@
    "source": [
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "import scipp as sc\n",
     "\n",
     "from easydynamics.sample_model import DampedHarmonicOscillator\n",
     "from easydynamics.sample_model import DeltaFunction\n",
@@ -105,8 +106,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import scipp as sc\n",
-    "\n",
     "x1 = sc.linspace(dim='x', start=-2.0, stop=2.0, num=100, unit='meV')\n",
     "x2 = sc.linspace(dim='x', start=-2.0 * 1e3, stop=2.0 * 1e3, num=101, unit='microeV')\n",
     "\n",
diff --git a/docs/docs/tutorials/detailed_balance.ipynb b/docs/docs/tutorials/detailed_balance.ipynb
@@ -23,11 +23,11 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "\n",
-    "%matplotlib widget\n",
     "import numpy as np\n",
     "\n",
-    "from easydynamics.utils import _detailed_balance_factor as detailed_balance_factor"
+    "from easydynamics.utils import _detailed_balance_factor as detailed_balance_factor\n",
+    "\n",
+    "%matplotlib widget"
    ]
   },
   {
diff --git a/docs/docs/tutorials/diffusion_model.ipynb b/docs/docs/tutorials/diffusion_model.ipynb
@@ -67,7 +67,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a50c67ec",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/docs/docs/tutorials/experiment.ipynb b/docs/docs/tutorials/experiment.ipynb
diff --git a/pixi.lock b/pixi.lock
diff --git a/pixi.toml b/pixi.toml
diff --git a/tools/update_github_labels.py b/tools/update_github_labels.py
