Merge branch 'master' into bep-016

bids-standard · Mar 29, 2024 · 48a6a42 · 48a6a42
2 parents ab2b4cd + bd08602
commit 48a6a42
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Showing 140 changed files with 11,546 additions and 1,293 deletions.
diff --git a/.all-contributorsrc b/.all-contributorsrc
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -2,7 +2,7 @@ version: 2.1
 jobs:
   build_docs:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12-node
     steps:
       # checkout code to default ~/project
       - checkout
@@ -21,14 +21,15 @@ jobs:
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
-          paths: site
+          paths:
+            - site
       - store_artifacts:
           path: ~/project/site/
           destination: dev_docs
 
   check_links:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12
     steps:
       # checkout code to default ~/project
       - checkout
@@ -131,7 +132,8 @@ jobs:
       - persist_to_workspace:
           # raw generated changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Lint and fix the auto generated changes.md file
   lint_generated_changelog:
@@ -164,7 +166,8 @@ jobs:
       - persist_to_workspace:
           # linted and fixed changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Push built changelog to repo
   commit_generated_changelog:
@@ -178,7 +181,7 @@ jobs:
       - attach_workspace:
           # fixed+linted changelog in ~/changelog_build/CHANGES.md
           at: ~/.
-      - deploy:
+      - run:
           name: Changelog deployment
           # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
           command: |
@@ -197,7 +200,6 @@ jobs:
             fi
 
 workflows:
-  version: 2
   search_build:
     jobs:
       - build_docs

diff --git a/.codespellrc b/.codespellrc
@@ -1,6 +1,6 @@
 [codespell]
-skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json
-ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,winn
+skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
+ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel
 builtin = clear,rare,en-GB_to_en-US
 # this overloads default dictionaries and I have not yet figured out
 # how to have multiple https://github.com/codespell-project/codespell/issues/2727

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
@@ -26,8 +26,8 @@ jobs:
         os: ["ubuntu-latest"]
         python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: "Install build dependencies"
@@ -44,7 +44,7 @@ jobs:
         run: python -m build tools/schemacode
       - name: "Check distribution metadata"
         run: twine check tools/schemacode/dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: tools/schemacode/dist/
@@ -56,26 +56,27 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         include:
           - os: macos-latest
             python-version: 3
           - os: windows-latest
             python-version: 3
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: "Set up Python"
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
 
       - name: "Display Python version"
         run: python -c "import sys; print(sys.version)"
 
       - name: "Fetch packages"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
@@ -90,7 +91,7 @@ jobs:
               --cov-append --cov-report=xml --cov=bidsschematools --doctest-modules
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: unit_${{ matrix.os }}_${{ matrix.python-version }}
           path: coverage.xml
@@ -107,7 +108,7 @@ jobs:
         python-version: ["3.11"]
     steps:
       - name: "Fetch packages"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
@@ -129,12 +130,12 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate schema
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set Up Python environment
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.11"
 
       - name: Install the schemacode package
         run: |
@@ -145,7 +146,7 @@ jobs:
         run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: schema_validation
           path: coverage.xml
@@ -157,13 +158,13 @@ jobs:
     needs: [test, validate_schema]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       - name: Upload to CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
           fail_ci_if_error: true
diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
@@ -16,15 +16,15 @@ jobs:
   codespell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: codespell-project/actions-codespell@master
 
   # Markdown formatting
   remark:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-node@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
           node-version: 14
       - name: Install dependencies
@@ -36,8 +36,8 @@ jobs:
   yamllint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Install dependencies
@@ -49,8 +49,8 @@ jobs:
   python-style:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - run: python -m pip install --upgrade flake8 black isort[colors]
@@ -63,8 +63,8 @@ jobs:
   latin-phrases:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Install dependencies
@@ -81,3 +81,18 @@ jobs:
         run: |
           python no-bad-latin.py
         working-directory: tools
+
+  # Validate CITATION.cff
+  validate_cff:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: 3
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install cffconvert
+    - name: Validate CITATION.cff
+      run: make validate_citation_cff
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,7 @@ venvs
 pdf_build_src/bids-spec.pdf
 pdf_build_src/bids-spec_pandoc_log.json
 pdf_build_src/src_copy
+pdf_build_src/tests/data/output
 
 # JS/NPM
 package-lock.json

diff --git a/.lgtm.yml b/.lgtm.yml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
 exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json'
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.3.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -23,7 +23,7 @@ repos:
         files: tools/schemacode
         args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
   - repo: https://github.com/pyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         files: ^tools/(?!schemacode)
@@ -33,22 +33,23 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.9-for-vscode
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
+        entry: env PRETTIER_LEGACY_CLI=1 prettier # temporary fix for https://github.com/prettier/prettier/issues/15742
         files: src/schema/.*/.*\.yaml
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.9.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

diff --git a/.remarkrc b/.remarkrc
@@ -10,6 +10,7 @@
     ["lint-maximum-heading-length", false],
     ["lint-no-shortcut-reference-link", false],
     ["lint-no-trailing-spaces"],
+    ["remark-lint-code-block-style", false],
     ["lint-no-undefined-references", false]
   ]
 }