easydiffraction 0.7.2__tar.gz → 0.7.3__tar.gz

easydiffraction-0.7.3/.badgery.yaml

@@ -0,0 +1,73 @@
+default_branch: master
+develop_branch: develop
+
+cards:
+  - group: Tests
+    type: gh_action
+    title: Code/package tests (GitHub)
+    file: test.yaml
+    enabled: true
+
+  - group: Tests
+    type: gh_action
+    title: Tutorial tests (GitHub)
+    file: tutorial-tests.yaml
+    enabled: true
+
+  - group: Tests
+    type: gh_action
+    title: Package tests (PyPI)
+    file: pypi-test.yaml
+    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)
+    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.yaml
+    enabled: true
+
+  - group: Build & Release
+    type: gh_action
+    title: Docs build/deployment
+    workflow: docs.yaml
+    enabled: true

easydiffraction-0.7.3/.github/workflows/backmerge-pr.yaml

@@ -0,0 +1,44 @@
+# This workflow creates a backmerge PR from DEFAULT_BRANCH into `develop`
+# whenever a new version tag is pushed (v*).
+#
+# Usage:
+#   - Triggered automatically on tag push (v*).
+#   - Creates a PR titled "Backmerge: DEFAULT_BRANCH into develop".
+#   - Adds the label "[maintainer] auto-pull-request" so it is excluded from changelogs.
+
+name: Backmerge PR creation
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+
+jobs:
+  create-backmerge-pr:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout ${{ env.DEFAULT_BRANCH }} branch
+        uses: actions/checkout@v5
+        with:
+          ref: ${{ env.DEFAULT_BRANCH }}
+
+      - name: Create PR from ${{ env.DEFAULT_BRANCH }} to develop
+        run: |
+          gh pr create \
+            --base develop \
+            --head ${{ env.DEFAULT_BRANCH }} \
+            --title "Backmerge: ${{ env.DEFAULT_BRANCH }} into develop" \
+            --label "[maintainer] auto-pull-request" \
+            --body "⚠️ This PR is created automatically for backmerges changes from \`${{ env.DEFAULT_BRANCH }}\` into \`develop\`, following a new release tag push.
+
+            It is labeled \`[maintainer] auto-pull-request\` and is excluded from release notes and version bump logic."
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_API_PERSONAL_ACCESS_TOKEN }}

easydiffraction-0.7.2/.github/workflows/delete-old-runs.yml → easydiffraction-0.7.3/.github/workflows/cleanup.yaml

@@ -2,7 +2,7 @@
 # parameters.
 # https://github.com/Mattraks/delete-workflow-runs
 
-name: Delete old workflow runs
+name: Old workflow runs cleanup
 
 on:
   # Run monthly, at 00:00 on the 1st day of month.

easydiffraction-0.7.3/.github/workflows/coverage.yaml

@@ -0,0 +1,145 @@
+name: Coverage checks
+
+on:
+  # Trigger the workflow on push
+  push:
+  # 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, 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: Run docstring coverage
+  docstring-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v5
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          environments: default
+          activate-environment: default
+          run-install: true
+          frozen: true
+          cache: false
+          post-cleanup: false
+
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
+
+      - 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@v5
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          environments: default
+          activate-environment: default
+          run-install: true
+          frozen: true
+          cache: false
+          post-cleanup: false
+
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
+
+      - 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: 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 }}
+
+  # Job 2: Run functional tests with coverage and upload to Codecov
+  func-tests-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v5
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          environments: default
+          activate-environment: default
+          run-install: true
+          frozen: true
+          cache: false
+          post-cleanup: false
+
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
+
+      - name: Run functional tests with coverage
+        run: pixi run func-tests-coverage --cov-report=xml:coverage-func.xml
+
+      - name: Upload functional tests coverage to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/codecov-action@v5
+        with:
+          name: func-tests-job
+          flags: functional
+          files: ./coverage-func.xml
+          fail_ci_if_error: true
+          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  # Job 4: Trigger dashboard build
+  dashboard-build-trigger:
+    needs: [docstring-coverage, unit-tests-coverage, func-tests-coverage] # depend on the previous jobs
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v5
+
+      - name: Trigger dashboard build
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            await github.rest.actions.createWorkflowDispatch({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              workflow_id: "dashboard.yaml",
+              ref: "${{ env.CI_BRANCH }}"
+            });

easydiffraction-0.7.3/.github/workflows/dashboard.yaml

@@ -0,0 +1,89 @@
+name: Dashboard build and publish
+
+on:
+  workflow_dispatch:
+  workflow_call:
+
+# 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 }}
+  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@v5
+        with:
+          fetch-depth: 0
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          environments: default
+          activate-environment: default
+          run-install: true
+          frozen: true
+          cache: false
+          post-cleanup: false
+
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
+
+      - name: Run docstring coverage and code complexity/maintainability checks
+        run: |
+          for BRANCH in ${{ env.DEFAULT_BRANCH }} ${{ env.DEVELOP_BRANCH }} ${{ env.CI_BRANCH }}; do
+            echo "=== Processing branch $BRANCH ==="
+            if [ -d "../worktree-$BRANCH" ]; then
+              echo "Branch $BRANCH already processed, skipping"
+              continue
+            fi
+            git worktree add ../worktree-$BRANCH origin/$BRANCH
+            mkdir -p reports/$BRANCH
+            echo "Docstring coverage for branch $BRANCH"
+            pixi run interrogate -c pyproject.toml --fail-under=0 ../worktree-$BRANCH/src > reports/$BRANCH/coverage-docstring.txt
+            echo "Cyclomatic complexity for branch $BRANCH"
+            pixi run radon cc -s -j ../worktree-$BRANCH/src --exclude ../worktree-$BRANCH/src/easydiffraction/crystallography/space_group_lookup_table.py > reports/$BRANCH/cyclomatic-complexity.json
+            echo "Maintainability index for branch $BRANCH"
+            pixi run radon mi -j ../worktree-$BRANCH/src --exclude ../worktree-$BRANCH/src/easydiffraction/crystallography/space_group_lookup_table.py > reports/$BRANCH/maintainability-index.json
+            echo "Raw metrics for branch $BRANCH"
+            pixi run radon raw -s -j ../worktree-$BRANCH/src --exclude ../worktree-$BRANCH/src/easydiffraction/crystallography/space_group_lookup_table.py > reports/$BRANCH/raw-metrics.json
+          done
+
+      - name: Generate dashboard HTML
+        run: |
+          pixi add --pypi --git https://github.com/enhantica/badgery badgery
+          pixi run pip show badgery
+          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 }}
+
+      - name: Publish to main branch of ${{ github.repository }}
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          external_repository: ${{ env.REPO_OWNER }}/dashboard
+          publish_branch: ${{ env.DEFAULT_BRANCH }}
+          personal_token: ${{ secrets.GH_API_PERSONAL_ACCESS_TOKEN }}
+          publish_dir: ./_dashboard_publish
+          keep_files: true
+
+      - name: Add dashboard link to summary
+        run: |
+          URL="https://${{ env.REPO_OWNER }}.github.io/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }}"
+          echo "Dashboard link: [$URL]($URL)" >> $GITHUB_STEP_SUMMARY

easydiffraction-0.7.2/.github/workflows/build-docs.yml → easydiffraction-0.7.3/.github/workflows/docs.yaml

@@ -14,17 +14,17 @@
 # and inspecting, as well as links to both the development and production versions of
 # the deployed documentation site.
 
-name: Build and deploy docs
+name: Docs build and deployment
 
 on:
   # Trigger the workflow on pull request
   pull_request:
     # Selected branches
-    branches: [master, develop]
+    branches: [master, main, develop]
   # Trigger the workflow on push
   push:
     # Selected branches
-    branches: [master, develop]
+    branches: [master, main, develop]
     # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
     tags: ['v*']
   # Allows you to run this workflow manually from the Actions tab
@@ -86,14 +86,17 @@ jobs:
       - name: Set up pixi
         uses: prefix-dev/setup-pixi@v0.9.0
         with:
-          environments: >-
-            py313-docs
-          activate-environment: py313-docs
+          environments: default
+          activate-environment: default
           run-install: true
           frozen: true
           cache: false
           post-cleanup: false
 
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
+
       - name: Clone easyscience/assets-docs and easyscience/assets-branding
         run: |
           cd ..
@@ -226,7 +229,7 @@ jobs:
       # which triggers deployment to the custom domain via webhook.
       #
       # To be able to push to the gh_pages branch, the personal GitHub API access
-      # token GH_API_PERSONAL_ACCSESS_TOKEN must be set for this repository via
+      # token GH_API_PERSONAL_ACCESS_TOKEN must be set for this repository via
       # https://github.com/easyscience/diffraction-lib/settings/secrets/actions
       # Then the gh_pages branch is used to deploy the site to the custom domain.
       # Deploying is done with a webhook added via:
@@ -234,7 +237,7 @@ jobs:
       - name: PROD deployment to gh_pages for custom domain
         uses: s0/git-publish-subdir-action@develop
         env:
-          GITHUB_TOKEN: ${{ secrets.GH_API_PERSONAL_ACCSESS_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GH_API_PERSONAL_ACCESS_TOKEN }}
           REPO: self
           BRANCH: gh_pages
           FOLDER: site

easydiffraction-0.7.3/.github/workflows/labels.yaml

@@ -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.
+
+name: PR label checks
+
+on:
+  pull_request_target:
+    types: [opened, labeled, unlabeled, synchronize]
+
+permissions:
+  pull-requests: read
+
+jobs:
+  require-label:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Validate required labels
+        run: |
+          PR_LABELS=$(echo '${{ toJson(github.event.pull_request.labels.*.name) }}' | jq -r '.[]')
+          echo "Current PR labels: $PR_LABELS"
+          VALID_LABELS=(
+            "[maintainer] auto-pull-request"
+            "[scope] bug"
+            "[scope] documentation"
+            "[scope] enhancement"
+            "[scope] maintenance"
+            "[scope] significant"
+          )
+
+          found=false
+          for label in "${VALID_LABELS[@]}"; do
+            if echo "$PR_LABELS" | grep -Fxq "$label"; then
+              echo "✅ Found valid label: $label"
+              found=true
+              break
+            fi
+          done
+
+          if [ "$found" = false ]; then
+            echo "ERROR: PR must have at least one of the following labels:"
+            for label in "${VALID_LABELS[@]}"; do
+              echo "       - $label"
+            done
+            exit 1
+          fi

easydiffraction-0.7.2/.github/workflows/publish-pypi.yml → easydiffraction-0.7.3/.github/workflows/pypi-publish.yaml

@@ -1,7 +1,7 @@
 # Builds a Python package and publish it to PyPI when a new tag is
 # created.
 
-name: Publish to PyPI
+name: PyPI publishing
 
 on:
   # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
@@ -20,19 +20,22 @@ jobs:
         with:
           fetch-depth: '0' # full history with tags to get the version number by versioningit
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
         with:
-          python-version: '3.13'
+          environments: default
+          activate-environment: default
+          run-install: true
+          frozen: true
+          cache: false
+          post-cleanup: false
 
-      - name: Upgrade package installer for Python
-        run: pip install --upgrade pip
-
-      - name: Install build tool
-        run: pip install --upgrade build
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
 
       - name: Create Python package
-        run: python -m build
+        run: pixi run python -m build
 
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

easydiffraction-0.7.2/.github/workflows/test-package-pypi.yaml → easydiffraction-0.7.3/.github/workflows/pypi-test.yaml

@@ -1,4 +1,4 @@
-name: Test unpinned PyPI package
+name: PyPI package tests
 
 on:
   # Run daily, at 00:00.
@@ -14,8 +14,13 @@ concurrency:
     ${{ github.workflow }}-${{ 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 }}
+  DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+
 jobs:
-  test-package:
+  pypi-package-tests:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
@@ -30,22 +35,30 @@ jobs:
           cache: false
           post-cleanup: false
 
-      - name: Download the pixi configuration file from the master branch
+      - name:
+          Download the pixi configuration file from the ${{ env.CI_BRANCH}}
+          branch
+        shell: bash
         run: |
-          curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi/prod/pixi.toml
+          curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/${CI_BRANCH}/pixi.toml
 
-      - name: Download the tests from the master branch
+      - name: Download the tests from the ${{ env.DEFAULT_BRANCH }} branch
         shell: bash
         run: |
-          curl -LO https://github.com/easyscience/diffraction-lib/archive/refs/heads/master.zip
-          unzip master.zip -d .
+          curl -LO https://github.com/easyscience/diffraction-lib/archive/refs/heads/${DEFAULT_BRANCH}.zip
+          unzip ${DEFAULT_BRANCH}.zip -d .
           mkdir -p tests
-          cp -r diffraction-lib-master/tests/* tests/
-          rm -rf master.zip diffraction-lib-master
+          cp -r diffraction-lib-${DEFAULT_BRANCH}/tests/* tests/
+          rm -rf ${DEFAULT_BRANCH}.zip diffraction-lib-${DEFAULT_BRANCH}
 
       - name: Create the environment and install dependencies
         run: pixi install
 
+      - name: Install package from PyPI with dev and visualization extras
+        run: |
+          pixi add --pypi "easydiffraction[dev,visualization]"
+          pixi run easydiffraction --version
+
       - name: Run unit tests to verify the installation
         run: pixi run unit-tests
 

easydiffraction-0.7.3/.github/workflows/quality.yaml

@@ -0,0 +1,123 @@
+# The workflow is divided into several steps to ensure code quality:
+#    - Check the validity of pyproject.toml
+#    - Check code linting
+#    - Check code formatting
+#    - Check formatting of docstrings in the code
+#    - Check formatting of Markdown, YAML, TOML, etc. files
+
+name: Code quality checks
+
+on:
+  # Trigger the workflow on push
+  push:
+    # Every branch
+    branches: ['**']
+    # 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
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          environments: default
+          activate-environment: default
+          run-install: true
+          frozen: true
+          cache: false
+          post-cleanup: false
+
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
+
+      # Check the validity of pyproject.toml
+      - name: Check validity of pyproject.toml
+        id: check_pyproject
+        continue-on-error: true
+        shell: bash
+        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 py-lint-check
+
+      # 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 py-format-check
+
+      # Check formatting of docstrings in the code with docformatter
+      - name: Check formatting of docstrings in the code
+        id: check_docs_formatting
+        continue-on-error: true
+        shell: bash
+        run: pixi run docs-format-check
+
+      # Check formatting of MD, YAML, TOML, etc. files with Prettier in
+      # the project root
+      - name: Check formatting of MD, YAML, TOML, etc. files
+        id: check_others_formatting
+        continue-on-error: true
+        shell: bash
+        run: pixi run nonpy-format-check
+
+      # Check formatting of Jupyter Notebooks in the tutorials folder
+      - name: Convert tutorial scripts to 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
+        if: always()
+        shell: bash
+        run: |
+          {
+            echo "## 🧪 Code Quality Checks Summary"
+            echo ""
+            echo "| Check | Status |"
+            echo "|-------|--------|"
+            echo "| pyproject.toml   | ${{ steps.check_pyproject.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| py lint          | ${{ steps.check_code_linting.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| py format        | ${{ steps.check_code_formatting.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| docstring format | ${{ steps.check_docs_formatting.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| nonpy format     | ${{ steps.check_others_formatting.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| notebooks format | ${{ steps.check_notebooks_formatting.outcome == 'success' && '✅' || '❌' }} |"
+          } >> "$GITHUB_STEP_SUMMARY"
+
+      # Fail job requirement
+      - name: Fail job if any check failed
+        if: failure()
+        shell: bash
+        run: exit 1