Cookiecutter

.bumpversion.toml

@@ -24,4 +24,4 @@ post_commit_hooks = []
 filename = "pyproject.toml"
 
 [[tool.bumpversion.files]]
-filename = "ml_cli/version.py"
+filename = "pyml_cli/version.py"

.github/workflows/code-style.yaml

@@ -5,13 +5,22 @@ on: [pull_request]
 
 jobs:
   linting:
+    env:
+      UV_CACHE_DIR: /tmp/.uv-cache
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
       - name: Setup uv
-        id: setup-uv
-        uses: astral-sh/setup-uv@v5
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Setup Pixi Environment
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          enable-cache: true
-      - name: Run pre-commit
-        run: uvx pre-commit run --all-files
+          pixi-version: latest
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+
+      - name: Set up Python
+        run: uv python install
+
+      - uses: pre-commit/action@v3.0.1

.github/workflows/docs.yaml

@@ -4,6 +4,13 @@ on:
   push:
     branches:
       - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  pull-requests: write
 
 jobs:
   build-docs:
@@ -17,24 +24,62 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          fetch-depth: 0
 
-      - uses: prefix-dev/setup-pixi@v0.8.1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Setup Pixi Environment
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
+          pixi-version: latest
           cache: true
-          environments: docs
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       - name: Build docs
         run: pixi run build-docs
 
+      - name: Verify build output
+        run: |
+          # Verify that markdown files are NOT in the site directory
+          # (They should be processed into HTML by MkDocs)
+          # The markdown files are generated by the pre-build hook, processed by MkDocs,
+          # and only the resulting HTML files should be in ./site
+          if find ./site -name "*.md" | grep -q .; then
+            echo "ERROR: Markdown files found in site directory!"
+            find ./site -name "*.md"
+            exit 1
+          fi
+          echo "✓ Build verification passed: No markdown files in site directory"
+          echo "✓ Site directory contains HTML files ready for deployment"
+
       - name: Deploy website
-        uses: peaceiris/actions-gh-pages@v3
+        if: github.ref_name == 'main'
+        uses: peaceiris/actions-gh-pages@v4
         with:
           # https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-set-personal-access-token-personal_token
-          personal_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: site
+          # Note: This action deploys the contents of publish_dir (./site) to gh-pages.
+          # It does NOT check .gitignore - it simply takes all files in ./site and pushes them.
+          # Since ./site only contains HTML files (generated from markdown by MkDocs),
+          # no markdown files will be deployed. The markdown files exist only during
+          # the build process and are never committed to any branch.
+          personal_token: ${{ secrets.GHPAGES_DEPLOY_KEY }}
+          publish_dir: ./site
           publish_branch: gh-pages
           allow_empty_commit: false
           keep_files: false
           force_orphan: true
           enable_jekyll: false
+
+      - name: Deploy PR Preview
+        if: github.event_name == 'pull_request' && github.event.pull_request.base.ref == 'main'
+        uses: rossjrw/pr-preview-action@v1.6.3
+        with:
+          # Note: This action works similarly - it deploys the contents of source-dir (./site)
+          # to create a preview. It also does NOT check .gitignore, but since ./site only
+          # contains HTML files, no markdown files will be included in the preview.
+          source-dir: ./site
+          preview-branch: gh-pages

.github/workflows/pr-tests.yaml

@@ -1,61 +1,84 @@
 name: Run tests on pull requests
 
-on: [pull_request]
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+
+env:
+  OPENAI_API_KEY: dummy_key
 
 jobs:
-  run-tests:
+  check-changes:
     runs-on: ubuntu-latest
-    name: Run test suite
-
-    # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
-    defaults:
-      run:
-        shell: bash -l {0}
-
+    outputs:
+      has-code-changes: ${{ steps.changes.outputs.has-code-changes }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - uses: prefix-dev/setup-pixi@v0.8.1
+        uses: actions/checkout@v6
         with:
-          cache: true
-          environments: tests
+          fetch-depth: 0
 
-      - name: Run tests
+      - name: Check for code changes
+        id: changes
         run: |
-          pixi run test
-
-      # https://github.com/codecov/codecov-action
-      - name: Upload code coverage
-        uses: codecov/codecov-action@v2
-        with:
-          # fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
-
+          if [[ "${{ github.event_name }}" == "push" ]]; then
+            echo "has-code-changes=true" >> $GITHUB_OUTPUT
+          else
+            # For pull requests, check if there are non-docs changes
+            if git diff --name-only origin/${{ github.base_ref }}...HEAD | grep -v '^docs/' | grep -v '\.md$' | grep -q .; then
+              echo "has-code-changes=true" >> $GITHUB_OUTPUT
+            else
+              echo "has-code-changes=false" >> $GITHUB_OUTPUT
+            fi
+          fi
 
-  # This helps us check that pyproject.toml's `project` table's `dependencies`
-  # are defined completely.
-  bare-install:
+  test-matrix:
+    needs: check-changes
     runs-on: ubuntu-latest
-    name: Run bare installation test
+    name: ${{ matrix.test-type }} (Python ${{ matrix.python-version }}, ${{ matrix.environment-type }})
+    if: ${{ needs.check-changes.outputs.has-code-changes == 'true' }}
 
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+        environment-type: ['pixi']
+        test-type: ['unit-tests', 'smoke-tests']
+
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
+
+      - name: Update apt and install curl
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y curl
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      # Setup Pixi if needed
+      - name: Setup Pixi Environment
+        if: ${{ matrix.environment-type == 'pixi' }}
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          python-version: ${{ matrix.python-version }}
+          pixi-version: latest
+          cache: true
 
-      - name: Install package
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .
+      # Run the appropriate test based on matrix variables
+      - name: Run unit tests
+        if: ${{ matrix.test-type == 'unit-tests' }}
+        run: pixi run -e tests test
+
+      - name: Run smoke tests (pixi)
+        if: ${{ matrix.test-type == 'smoke-tests' && github.repository_owner == 'matdagommer' }}
+        run: pixi run pyml --help
 
-      - name: Run CLI as a smoke test.
-        run: "pyml-cli --help"
+      # Upload code coverage only for unit tests
+      - name: Upload code coverage
+        if: ${{ matrix.test-type == 'unit-tests' }}
+        uses: codecov/codecov-action@v4
+        with:
+          verbose: true

.pre-commit-config.yaml

@@ -2,19 +2,14 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
-      - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 25.11.0
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.11.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
-        exclude: ^notebooks/.*|^docs/.*$
+        exclude: ^notebooks/.*|^docs/.*|pyproject.toml|pyml_cli/templates/.*$
   - repo: https://github.com/jendrikseipp/vulture
     rev: 'v2.14'
     hooks:
@@ -23,7 +18,7 @@ repos:
     rev: 1.7.0
     hooks:
       - id: interrogate
-        exclude: ^(docs/|tests/)
+        exclude: ^(docs/|tests/|scripts/|notebooks/|pyml_cli/templates/)
         args: [-c, pyproject.toml]
   - repo: local
     hooks:

docs/api.md

@@ -1,3 +1,3 @@
 # Top-level API for pyml-cli
 
-::: ml_cli
+::: pyml_cli

docs/releases/v0.1.3.md

@@ -44,8 +44,8 @@ This release introduces automated version management and improves the release wo
 ### New Features
 
 - Add `.bumpversion.toml` for automated version management, enabling consistent version bumping and tagging. (9c8dbf) (MatDagommer)
-- Add `pyproject.toml` and `ml_cli/version.py` to the files tracked by bumpversion, ensuring all relevant files are updated during version bumps. (f105e4) (MatDagommer)
-- Include `ml_cli/version.py` in the list of files updated by bumpversion. (be0d2e) (MatDagommer)
+- Add `pyproject.toml` and `pyml_cli/version.py` to the files tracked by bumpversion, ensuring all relevant files are updated during version bumps. (f105e4) (MatDagommer)
+- Include `pyml_cli/version.py` in the list of files updated by bumpversion. (be0d2e) (MatDagommer)
 
 ### Bug Fixes