Merge branch 'bids-standard:master' into schema/rules/ephys

.circleci/config.yml

@@ -66,14 +66,16 @@ jobs:
 
   build_docs_pdf:
     docker:
-      - image: danteev/texlive:latest
+      - image: texlive/texlive:latest
     steps:
       # checkout code to default ~/project
       - checkout
       - run:
           name: install dependencies
           command: |
-            apt-get update && apt install -y python3-pip
+            apt-get update && apt install -y python3-pip python3-venv pandoc
+            python3 -m venv .venv
+            source .venv/bin/activate
             python3 -m pip install --upgrade pip
             python3 -m pip install -r  ~/project/requirements.txt
             python3 -m pip install ~/project/tools/schemacode/[render]
@@ -83,6 +85,7 @@ jobs:
       - run:
           name: generate pdf version docs
           command: |
+            source .venv/bin/activate
             cd ~/project/pdf_build_src
             bash build_pdf.sh
             mv ~/project/pdf_build_src/bids-spec.pdf ~/project/bids-spec.pdf

.codecov.yml

@@ -1,3 +1,5 @@
 ignore:
-    - "*/*/tests/*"
-    - "**/tests/*"
+  - "*/*/tests/*"
+  - "**/tests/*"
+codecov:
+  token: 7e84a7fb-8f7e-45f5-8dcc-9f5219fa3855

.codespell_dict

@@ -1,6 +1,11 @@
 sub-directory->subdirectory
+Sub-directory->Subdirectory
 sub-directories->subdirectories
+Sub-directories->Subdirectories
 file name->filename
+File name->Filename
 file names->filenames
+File names->Filenames
 folder->directory
-folders->directories
+Folder->Directory
+Folders->Directories

.codespellrc

@@ -1,6 +1,8 @@
 [codespell]
-skip = *.js,*.svg,*.eps,.git
-ignore-words-list = fo,te,als
-builtin = clear,rare
-dictionary = .codespell_dict
+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
+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
+# dictionary = .codespell_dict
 exclude-file = src/CHANGES.md

.github/labeler.yml

@@ -0,0 +1,27 @@
+# labeler "full" schema
+# https://github.com/marketplace/actions/auto-labeler
+
+# enable labeler on issues, prs, or both.
+enable:
+  issues: false
+  prs: true
+# comments object allows you to specify a different message for issues and prs
+
+comments:
+  prs: |
+    I have applied any labels matching special text in your title and description.
+
+    Please review the labels and make any necessary changes.
+
+# Labels is an object where:
+# - keys are labels
+# - values are objects of { include: [ pattern ], exclude: [ pattern ] }
+#    - pattern must be a valid regex, and is applied globally to
+#      title + description of issues and/or prs (see enabled config above)
+#    - 'include' patterns will associate a label if any of these patterns match
+#    - 'exclude' patterns will ignore this label if any of these patterns match
+labels:
+  exclude-from-changelog:
+    include:
+      - 'pre-commit\.ci'
+    exclude: []

.github/workflows/labeler.yml

@@ -0,0 +1,21 @@
+name: "Label PRs"
+# See https://github.com/marketplace/actions/auto-labeler
+
+on:
+
+  pull_request_target:
+    types: [opened]
+
+jobs:
+
+  labeler:
+    runs-on: ubuntu-latest
+
+    if: github.repository_owner == 'bids-standard'
+
+    steps:
+    - name: Check Labels
+      id: labeler
+      uses: jimschubert/labeler-action@v2
+      with:
+        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.github/workflows/redirect_circleci_artifacts.yml

@@ -2,14 +2,17 @@ on: [status]
 
 jobs:
   circleci_artifacts_redirector_job:
-    if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs_pdf') }}"
     runs-on: ubuntu-latest
+    if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs_pdf') }}"
+    permissions:
+      statuses: write
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step
         uses: larsoner/circleci-artifacts-redirector-action@master
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+          api-token: ${{ secrets.CIRCLECI_TOKEN }}
           artifact-path: 0/bids-spec.pdf
           circleci-jobs: build_docs_pdf
           job-title: Check the rendered PDF version here!

.github/workflows/schemacode_ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -33,7 +33,7 @@ jobs:
       - name: "Install build dependencies"
         run: pip install --upgrade build twine
       - name: "Install test dependencies on tag"
-        run: pip install --upgrade pytest pyyaml pandas tabulate markdown-it-py
+        run: pip install --upgrade pytest pyyaml pandas tabulate markdown-it-py pyparsing
         if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
       - name: "Build archive on tag"
         run: pytest tools/schemacode/bidsschematools -k make_archive
@@ -56,7 +56,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         include:
           - os: macos-latest
             python-version: 3
@@ -104,7 +104,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     steps:
       - name: "Fetch packages"
         uses: actions/download-artifact@v3

.github/workflows/validation.yml

@@ -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@v3
+    - uses: actions/setup-python@v4
+      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

.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: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,27 +13,53 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.7.0
     hooks:
       - id: black
+        files: ^tools/(?!schemacode)
+        args: ["--verbose"]
+      - id: black
+        name: "black bidsschematools"
         files: tools/schemacode
-        args: [--verbose]
+        args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
   - repo: https://github.com/pyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
-        files: tools/
+        files: ^tools/(?!schemacode)
+        args: ["--profile", "black"]
+      - id: isort
+        name: "isort bidsschematools"
+        files: tools/schemacode
+        args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.2
+    rev: v3.0.0
     hooks:
       - id: prettier
         files: src/schema/.*/.*\.yaml
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.2.5
     hooks:
       - id: codespell
+        args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.4.1
+    hooks:
+      - id: mypy
+        # Sync with project.optional-dependencies.typing
+        additional_dependencies:
+          - click
+          - markdown-it-py
+          - importlib_resources
+          - pandas-stubs
+          - pyparsing
+          - pytest
+          - types-PyYAML
+          - types-tabulate
+        args: ["tools/schemacode/bidsschematools"]
+        pass_filenames: false