Refactor core objects, improve validation, and update API

.badgery.yaml

@@ -52,6 +52,7 @@ cards:
   - group: Coverage
     type: codecov
     title: Unit test coverage (Codecov)
+    flag: unittests
     enabled: true
 
   - group: Coverage

.github/workflows/dashboard.yaml

@@ -41,33 +41,34 @@ jobs:
 
       - name: Install and setup development dependencies
         shell: bash
-        run: pixi run dev
+        run: |
+          pixi run dev
+          pixi add --pypi --git https://github.com/enhantica/badgery badgery
 
       - 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
+            if [ -d "../$BRANCH" ]; then
               echo "Branch $BRANCH already processed, skipping"
               continue
             fi
-            git worktree add ../worktree-$BRANCH origin/$BRANCH
+            git worktree add ../$BRANCH origin/$BRANCH
             mkdir -p reports/$BRANCH
             echo "Docstring coverage for branch $BRANCH"
-            pixi run interrogate -c pyproject.toml --fail-under=0 ../worktree-$BRANCH/src > reports/$BRANCH/coverage-docstring.txt
+            pixi run interrogate -c pyproject.toml --fail-under=0 ../$BRANCH/src > reports/$BRANCH/coverage-docstring.txt
             echo "Cyclomatic complexity for branch $BRANCH"
-            pixi run radon cc -s -j ../worktree-$BRANCH/src --exclude ../worktree-$BRANCH/src/easydiffraction/crystallography/space_group_lookup_table.py > reports/$BRANCH/cyclomatic-complexity.json
+            pixi run radon cc -s -j ../$BRANCH/src > reports/$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
+            pixi run radon mi -j ../$BRANCH/src > reports/$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
+            pixi run radon raw -s -j ../$BRANCH/src > reports/$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
+        run: >
+          pixi run python -m badgery --config .badgery.yaml --repo ${{
+          github.repository }} --branch ${{ env.CI_BRANCH }} --output index.html
 
       - name: Prepare publish directory
         run: |

.github/workflows/pypi-test.yaml

@@ -20,6 +20,7 @@ env:
   DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
 
 jobs:
+  # Job 1: Test installation from PyPI on multiple OS
   pypi-package-tests:
     strategy:
       matrix:
@@ -54,10 +55,8 @@ jobs:
       - 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: Install package from PyPI with all extras
+        run: pixi add --pypi "easydiffraction[all]"
 
       - name: Run unit tests to verify the installation
         run: pixi run unit-tests
@@ -70,8 +69,31 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          pixi run tutorials-list
-          pixi run tutorials-fetch
+          pixi run easydiffraction --version
+          pixi run easydiffraction list-tutorials
+          pixi run easydiffraction fetch-tutorials
 
       - name: Test tutorials as notebooks
         run: pixi run notebook-tests
+
+  # Job 2: Trigger dashboard build
+  dashboard-build-trigger:
+    needs: pypi-package-tests
+
+    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 }}"
+            });

.github/workflows/test.yaml

@@ -147,6 +147,10 @@ jobs:
         shell: bash
         run: pixi remove --pypi easydiffraction
 
+      - 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 Python package for the next job
@@ -156,6 +160,7 @@ jobs:
           path: |
             dist/
             tests/
+            pytest.ini
             pixi.toml
             pixi.lock
           if-no-files-found: 'error'

.github/workflows/tutorial-tests.yaml

@@ -22,7 +22,12 @@ 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 }}
+
 jobs:
+  # Job 1: Test tutorials as scripts and notebooks on multiple OS
   tutorial-tests:
     strategy:
       fail-fast: false
@@ -60,3 +65,25 @@ jobs:
       - name: Test tutorials as notebooks
         shell: bash
         run: pixi run notebook-tests
+
+  # Job 2: Trigger dashboard build
+  dashboard-build-trigger:
+    needs: tutorial-tests
+
+    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 }}"
+            });

.gitignore

@@ -4,9 +4,18 @@ __pycache__
 .coverage
 .pyc
 
+# PyTest
+.pytest_cache
+
+# MyPy
+.mypy_cache
+
 # Pixi
 .pixi
 
+# Ruff
+.ruff_cache
+
 # Jupyter Notebooks
 .ipynb_checkpoints
 

.pre-commit-config.yaml

@@ -49,9 +49,9 @@ repos:
         pass_filenames: false
         stages: [pre-push]
 
-      - id: pixi-unit-tests
-        name: pixi run unit-tests
-        entry: pixi run unit-tests
-        language: system
-        pass_filenames: false
-        stages: [pre-push]
+      #- id: pixi-unit-tests
+      #  name: pixi run unit-tests
+      #  entry: pixi run unit-tests
+      #  language: system
+      #  pass_filenames: false
+      #  stages: [pre-push]

.prettierignore

@@ -1,2 +1,6 @@
 # Pixi
+.pixi
 pixi.lock
+
+# MyPy
+.mypy_cache