Merge pull request #89 from bids-standard/mnt/misc

MNT: Miscellaneous cleanups and process improvements

Author: effigies

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Mon Feb 3 13:04:18 2025 -0500 - markiewicz@stanford.edu - sty: ruff format [ignore-rev]
+5970ba32048444aa3a64a56d8122deeb4282b411

.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    groups:
+      actions-infrastructure:
+        patterns:
+          - actions/*
+  - package-ecosystem: uv
+    directory: /
+    schedule:
+      interval: weekly

.github/workflows/gh-pages.yml

@@ -7,23 +7,16 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: ["3.11"]
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python }}
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -r requirements.txt
+    - uses: actions/checkout@v4
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v6
+    - name: Sync environment
+      run: uv sync
     - name: Generate schemas
-      run: python -m bsmschema specification/schema/
+      run: uv run -m bsmschema specification/schema/
     - name: Build
-      run: jb build -W specification
+      run: uv run jb build -W specification
     - uses: peaceiris/actions-gh-pages@v3
       if: ${{ github.ref == 'refs/heads/main' }}
       with:

.github/workflows/package.yml

@@ -8,37 +8,54 @@ on:
       - rel/*
     tags:
       - '*'
+  pull_request:
+    branches:
+      - main
+      - maint/*
+  workflow_dispatch:
 
 defaults:
   run:
     shell: bash
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
 jobs:
-  package:
-    # Build packages and upload
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        include:
-          - os: ubuntu-latest
-            python-version: "3"
+  build:
+    name: Build & verify package
+    runs-on: ubuntu-latest
+    permissions:
+      attestations: write
+      id-token: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
-          submodules: recursive
           fetch-depth: 0
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - uses: hynek/build-and-inspect-python-package@v2
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
-      - name: Build sdist and wheel
-        run: pipx run build bsmschema
-      - name: Upload to PyPI (on tags)
-        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@release/v1
+          path: bsmschema
+          attest-build-provenance-github: ${{ github.event_name != 'pull_request' }}
+
+  publish:
+    name: Publish package to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    needs: [build]
+    permissions:
+      attestations: write
+      id-token: write
+
+    steps:
+      - name: Download packages built by build-and-inspect-python-package
+        uses: actions/download-artifact@v4
         with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
-          packages-dir: bsmschema/dist
+          name: Packages
+          path: dist
+
+      - name: Upload package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

Makefile

@@ -21,17 +21,19 @@ validate_cff: CITATION.cff ## Makes sure the CITATION.cff file is valid. (pip in
 	cffconvert --validate
 
 test: ## Build the book, checks for dead link and fail on warning
-	jupyter-book build specification --warningiserror --builder linkcheck
+	uv run jupyter-book build specification --warningiserror --builder linkcheck
 
-html: ## Build html version of the book
-	jupyter-book build specification
+html: specification/schema ## Build html version of the book
+	uv run jupyter-book build specification
 
 serve: html ## Serve the built website
 	python -m http.server -d specification/_build/html/
 
 pdfhtml: ## Build pdf version of the book from html (requires pyppeteer)
-	jupyter-book build specification --builder pdfhtml
+	uv run jupyter-book build specification --builder pdfhtml
 
 pdflatex: ## Build pdf version of the book from latex
-	jb build specification --builder pdflatex 
+	uv run jb build specification --builder pdflatex
 
+specification/schema:
+	uv run -m bsmschema specification/schema/

README.md

@@ -41,30 +41,29 @@ BIDSStatsModel.parse_file('stats-models/specification/examples/model-example_smd
 
 ## Building the documentation locally
 
-1) Install the requirements, including the local copy of `bsmschema`:
-
-   ```
-   pip install -r requirements.txt
-   ```
+We recommend using the [uv] tool to ensure reproducible builds.
 
 1) Build the schema files to ensure the local validator will work:
 
    ```
-   python -m bsmschema specification/schema
+   uv run -m bsmschema specification/schema
    ```
 
 
 1) Build the JupyterBook:
 
    ```
-   jb build specification
+   uv run jb build specification
    ```
 
 1) Serve the built website:
 
    ```
-   python -m http.server -d specification/_build/html/
+   uv run -m http.server -d specification/_build/html/
    ```
 
 Note that this will start a long-running web-server that will occupy your terminal. 
-`Ctrl-C` quits.
+`Ctrl-C` quits.
+
+
+[uv]: https://docs.astral.sh/uv/

bsmschema/bsmschema/__init__.py

@@ -1 +1,3 @@
 from . import models
+
+__all__ = ['models']

bsmschema/bsmschema/__main__.py

@@ -4,11 +4,11 @@
 
 if __name__ == '__main__':
     if len(sys.argv) != 2:
-        print("Usage: python -m bsmschema /path/to/schemadir")
+        print('Usage: python -m bsmschema /path/to/schemadir')
         sys.exit(1)
 
-    schemadir = Path(sys.argv[1]) 
+    schemadir = Path(sys.argv[1])
     schemadir.mkdir(parents=True, exist_ok=True)
     for mname in models.__all__:
         model = getattr(models, mname)
-        Path.write_text(schemadir / f"{mname}.json", model.schema_json(indent=2))
+        Path.write_text(schemadir / f'{mname}.json', model.schema_json(indent=2))