Merge remote-tracking branch 'origin/master' into rf-events

* origin/master: (278 commits) [FIX] Move ``_stim.<ext>`` specification within the Task Events module (bids-standard#1750) rm macros with missing metadata Update src/schema/objects/metadata.yaml Update src/schema/objects/metadata.yaml Update src/schema/objects/metadata.yaml [pre-commit.ci] pre-commit autoupdate Update src/common-principles.md Update src/common-principles.md Update src/common-principles.md Update src/common-principles.md fix: replace SHOULD with MUST in last changes (cc @effigies) Apply suggestions from code review Apply suggestions from code review Apply suggestions from code review fix: checking if chinese characters are accepted by pandoc Apply suggestions from code review Update src/common-principles.md Update src/schema/rules/checks/events.yaml fix: deduplicate prescriptions for columns in tsvgz Apply suggestions from code review ... Conflicts: mkdocs.yml - just redid changes found in prior diff but unifying for current indentation and use of ""
yarikoptic · Apr 13, 2024 · 3e9d605 · 3e9d605
2 parents 642484c + 943c20e
commit 3e9d605
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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
@@ -66,14 +67,16 @@ 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 +86,7 @@ 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
@@ -128,7 +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:
@@ -161,7 +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:
@@ -175,7 +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: |
@@ -194,7 +200,6 @@ jobs:
             fi
 
 workflows:
-  version: 2
   search_build:
     jobs:
       - build_docs

diff --git a/.codecov.yml b/.codecov.yml
@@ -1,3 +1,5 @@
 ignore:
-    - "*/*/tests/*"
-    - "**/tests/*"
+  - "*/*/tests/*"
+  - "**/tests/*"
+codecov:
+  token: 7e84a7fb-8f7e-45f5-8dcc-9f5219fa3855
diff --git a/.codespell_dict b/.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
diff --git a/.codespellrc b/.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,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
+# dictionary = .codespell_dict
 exclude-file = src/CHANGES.md
diff --git a/.github/workflows/redirect_circleci_artifacts.yml b/.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!
diff --git a/.github/workflows/schema_docs.yaml b/.github/workflows/schema_docs.yaml
diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
@@ -24,16 +24,16 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        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"
         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
@@ -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"]
+        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
@@ -104,10 +105,10 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        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