Standardize Pixi and CI workflow configurations (#82)

* Move tests directory inside the package structure

* Update PyPI install command

* Update workflow to trigger only on the master branch

* Fix default values in delete-old-runs workflow to be strings

* Update build-docs workflow to restrict branch triggers and adjust Pixi version

* Update pixi lock file

* Refactor test paths in workflows and update dependencies in pixi.toml files

* Remove step to move tests inside the package in the publish to PyPI workflow

* Add tests directory to the package distribution

* Update test command paths in pixi.toml for consistency

* Move pixi-kernel dependency to the pypi-dependencies section in pixi.toml

* Reorganize pixi.toml files: move libcblas dependency to target section and ensure pixi-kernel is listed under pypi-dependencies

* Refactor pixi.toml: standardize formatting for libcblas dependency

* Update pixi.toml

* Update test-package-pypi.yaml: enhance download steps for pixi configuration and tests

* Remove step to move tests inside the package in the workflow

* Fix formatting in test-package-pypi.yaml: adjust line endings for consistency in download steps

* Rename test script commands for consistency in pixi.toml and update workflow references in test-tutorials.yaml

* Update workflows: change default values to integers in delete-old-runs.yml and streamline curl command in test-package-pypi.yaml

* Refactor Pixi commands for consistency across workflows and documentation

* Refactor workflow scripts and documentation for consistency

* Updates pixi.lock

* Removes test __init__.py files

* Add SPDX license headers to __main__.py

Author: AndrewSazonov

.github/workflows/build-docs.yml

@@ -4,7 +4,7 @@ on:
   # Trigger the workflow on push
   push:
     # Selected branches
-    branches: [develop, master, docs, patch, pixi]
+    branches: [master, develop, docs, patch]
     # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
     tags:
       - 'v*'
@@ -82,39 +82,34 @@ jobs:
           git clone https://github.com/easyscience/assets-branding.git
 
       - name: Add files from cloned repositories
-        run: pixi run add-assets-to-docs
+        run: pixi run docs-assets
 
       # Convert python scripts in the notebooks directory to Jupyter notebooks
       # Strip output from the notebooks
       # Prepare the notebooks for documentation (add colab cell, etc.)
       # Run the notebooks to generate the output cells using multiple cores
       # The notebooks are then used to build the documentation site
       - name: Convert tutorial scripts to notebooks
-        run: pixi run make-notebooks
+        run: pixi run notebook-prepare
 
       - name: Run notebooks
-        run: pixi run run-notebooks
+        run: pixi run notebook-exec
 
       - name: Move notebooks to docs/tutorials
-        run: pixi run move-notebooks-to-docs
-
-      # The following step is needed to avoid the following message during the build:
-      # "Matplotlib is building the font cache; this may take a moment"
-      #- name: Pre-build site step
-      #  run: pixi run python -c "import easydiffraction"
+        run: pixi run docs-notebooks
 
       # Create the mkdocs.yml configuration file
       # The file is created by merging two files:
       # - assets-docs/mkdocs.yml - the common configuration (theme, plugins, etc.)
       # - docs/mkdocs.yml - the project-specific configuration (project name, TOC, etc.)
       - name: Create mkdocs.yml file
-        run: pixi run create-mkdocs-yml
+        run: pixi run docs-config
 
       # Build the static files
       # Input: docs/ directory containing the Markdown files
       # Output: site/ directory containing the generated HTML files
       - name: Build site with MkDocs
-        run: pixi run build-docs
+        run: pixi run docs-build
 
       # Set up the Pages action to configure the static files to be deployed
       # NOTE: The repository must have GitHub Pages enabled and configured to build using GitHub Actions

.github/workflows/draft-release-notes.yml

@@ -6,9 +6,7 @@ name: Update release draft
 on:
   # Runs on pushes targeting the default branch (updates the real draft release)
   push:
-    branches:
-      - main
-      - master
+    branches: [master]
 
 jobs:
   draft-release-notes:

.github/workflows/test-code.yaml

@@ -76,52 +76,55 @@ jobs:
         shell: bash
         run: |
           pixi run npm config set registry https://registry.npmjs.org/
-          pixi run install-prettier
+          pixi run prettier-install
 
       # Check the validity of pyproject.toml
       - name: Check validity of pyproject.toml
         id: check_pyproject
         continue-on-error: true
         shell: bash
-        run: pixi run check-pyproject
+        run: pixi run pyproject-check
 
       # Check code linting with Ruff in the project root
       - name: Check code linting
         id: check_code_linting
         continue-on-error: true
         shell: bash
-        run: pixi run check-lint-py
+        run: pixi run py-lint-check
 
       - name: Suggestion to fix code linting issues (*.py files)
         if: steps.check_code_linting.outcome == 'failure'
         shell: bash
-        run: echo "In project root run 'pixi run lint-py' and commit changes"
+        run:
+          echo "In project root run 'pixi run py-lint-fix' and commit changes"
 
       # Check code formatting with Ruff in the project root
       - name: Check code formatting
         id: check_code_formatting
         continue-on-error: true
         shell: bash
-        run: pixi run check-format-py
+        run: pixi run py-format-check
 
       - name: Suggestion to fix code formatting issues (*.py files)
         if: steps.check_code_formatting.outcome == 'failure'
         shell: bash
-        run: echo "In project root run 'pixi run format-py' and commit changes"
+        run:
+          echo "In project root run 'pixi run py-format-fix' and commit changes"
 
       # Check formatting of Markdown, YAML, TOML, etc. files with Prettier in
       # the project root
       - name: Check formatting of Markdown, YAML, TOML, etc. files
         id: check_others_formatting
         continue-on-error: true
         shell: bash
-        run: pixi run check-format-non-py
+        run: pixi run nonpy-format-check
 
       - name: Suggestion to fix non-code formatting issues (*.md, *.yml, etc.)
         if: steps.check_others_formatting.outcome == 'failure'
         shell: bash
         run:
-          echo "In project root run 'pixi run format-non-py' and commit changes"
+          echo "In project root run 'pixi run nonpy-format-fix' and commit
+          changes"
 
       - name: Force fail if any of the previous steps failed
         if: |
@@ -185,16 +188,12 @@ jobs:
         if: startsWith(github.ref , 'refs/tags/v') != true
         run: git tag --delete $(git tag)
 
-      - name: Move tests inside the package
-        shell: bash
-        run: mv tests/ src/easydiffraction/tests/
-
       - name: Create Python package
         shell: bash
         run: |
           for env in ${{ env.PIXI_ENVS }}; do
             echo "🔹🔸🔹🔸🔹   Current env: $env   🔹🔸🔹🔸🔹"
-            pixi run -e $env build
+            pixi run -e $env dist-build
             env_prefix="${env%%-*}"
             echo "📦 Moving built wheel to dist/$env_prefix/"
             pixi run mkdir -p dist/$env_prefix
@@ -209,6 +208,7 @@ jobs:
           name: edl_${{ matrix.os }}_${{ runner.arch }}
           path: |
             dist/
+            tests/
             pixi/wheel/pixi.toml
           if-no-files-found: 'error'
           compression-level: 0
@@ -225,7 +225,6 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     env:
-      PIXI_PROJECT_MANIFEST: 'pixi/wheel/pixi.toml'
       PIXI_ENVS: 'py311-wheel py312-wheel py313-wheel'
 
     steps:

.github/workflows/test-package-pypi.yaml

@@ -30,10 +30,16 @@ jobs:
           cache: false
           post-cleanup: false
 
-      - name: Download the pixi configuration file for EasyDiffraction
-        run:
-          curl -LO
-          https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml
+      - name: Download the pixi configuration file from the master branch
+        run: |
+          curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml
+
+      - name: Download the tests from the master branch
+        run: |
+          curl -LO https://github.com/easyscience/diffraction-lib/archive/refs/heads/master.zip
+          unzip master.zip "diffraction-lib-master/tests/*" -d . 
+          mv diffraction-lib-master/tests ./tests 
+          rm -rf master.zip diffraction-lib-master
 
       - name: Create the environment and install dependencies
         run: pixi install
@@ -45,10 +51,10 @@ jobs:
         run: pixi run func-tests
 
       - name: List the available EasyDiffraction tutorials
-        run: pixi run list-tutorials
+        run: pixi run tutorials-list
 
       - name: Fetch the EasyDiffraction tutorials
-        run: pixi run fetch-tutorials
+        run: pixi run tutorials-fetch
 
       - name: Test tutorials as notebooks
-        run: pixi run test-notebooks
+        run: pixi run notebook-tests

.github/workflows/test-tutorials.yaml

@@ -54,19 +54,19 @@ jobs:
 
       - name: Convert tutorial scripts to notebooks
         shell: bash
-        run: pixi run make-notebooks
+        run: pixi run notebook-prepare
 
       - name: Check notebooks formatting
         id: check_formatting
         continue-on-error: true
         shell: bash
-        run: pixi run check-format-notebooks
+        run: pixi run notebook-format-check
 
       - name: Suggestion to fix notebook formatting
         if: steps.check_formatting.outcome == 'failure'
         shell: bash
         run: |
-          echo "Run 'pixi run fix-format-notebooks' and commit changes."
+          echo "Run 'pixi run notebook-format-fix' and commit changes."
           exit 1
 
   # Job 2: Test tutorials as Python scripts and Jupyter Notebooks
@@ -97,12 +97,12 @@ jobs:
 
       - name: Test tutorials as python scripts
         shell: bash
-        run: pixi run test-scripts
+        run: pixi run script-tests
 
       - name: Convert tutorial scripts to notebooks
         shell: bash
-        run: pixi run make-notebooks
+        run: pixi run notebook-prepare
 
       - name: Test tutorials as notebooks
         shell: bash
-        run: pixi run test-notebooks
+        run: pixi run notebook-tests

.github/workflows/validate-pixi.yaml

@@ -55,8 +55,9 @@ jobs:
 
       - name: Add PyPI dependencies
         run: >
-          pixi add --pypi "easydiffraction[visualization] @
-          git+https://github.com/easyscience/diffraction-lib@${{env.CI_BRANCH}}"
+          pixi add --pypi 'easydiffraction[dev, visualization]' --git
+          https://github.com/easyscience/diffraction-lib.git --branch ${{
+          env.CI_BRANCH }}
 
       - name: Add a task to run EasyDiffraction from the command line
         run: pixi task add easydiffraction "python -m easydiffraction"

DEVELOPMENT.md

@@ -26,7 +26,7 @@ This is an example of a workflow that describes the development process.
   ```
 - Install Prettier for non-Python files formatting
   ```bash
-  pixi run install-prettier
+  pixi run prettier-install
   ```
 
 ## Making changes
@@ -61,35 +61,35 @@ This is an example of a workflow that describes the development process.
   ```
 - Test tutorials as python scripts
   ```bash
-  pixi run test-scripts
+  pixi run script-tests
   ```
 - Convert tutorial scripts to notebooks
   ```bash
-  pixi run make-notebooks
+  pixi run notebook-prepare
   ```
 - Test tutorials as notebooks
   ```bash
-  pixi run test-notebooks
+  pixi run notebook-tests
   ```
 
 ## Building and checking documentation with MkDocs
 
 - Move notebooks to docs/tutorials
   ```bash
-  pixi run move-notebooks-to-docs
+  pixi run docs-notebooks
   ```
 - Add extra files to build documentation (from `../assets-docs/` and
   `../assets-branding/` directories)
   ```bash
-  pixi run add-assets-to-docs
+  pixi run docs-assets
   ```
 - Create mkdocs.yml file
   ```bash
-  pixi run create-mkdocs-yml
+  pixi run docs-config
   ```
 - Build documentation
   ```bash
-  pixi run build-docs
+  pixi run docs-build
   ```
 - Test the documentation locally (built in the `site/` directory). E.g., on
   macOS, open the site in the default browser via the terminal
@@ -98,7 +98,7 @@ This is an example of a workflow that describes the development process.
   ```
 - Clean up after checking documentation
   ```bash
-  pixi run cleanup-docs
+  pixi run docs-clean
   ```
 
 ## Committing and pushing changes

docs/installation-and-setup/index.md

@@ -217,11 +217,11 @@ approach.
 
     === "curl"
         ```bash
-        curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/pixi/pixi/prod/pixi.toml
+        curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml
         ```
     === "wget"
         ```bash
-        wget https://raw.githubusercontent.com/easyscience/diffraction-lib/pixi/pixi/prod/pixi.toml
+        wget https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml
         ```
 
 - Create the environment defined in `pixi.toml` and install all necessary