Merge remote-tracking branch 'upstream/master' into extra_mri_metadata

bids-standard · Apr 11, 2024 · f3dd861 · f3dd861
2 parents f934160 + 83b12e9
commit f3dd861
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -192,6 +192,13 @@
             "login": "ali_khan",
             "name": "Ali Khan"
         },
+        {
+            "contributions": [
+                "tool"
+            ],
+            "login": "alizee_wickenheiser",
+            "name": "Alizee Wickenheiser"
+        },
         {
             "contributions": [
                 "userTesting"
@@ -443,6 +450,14 @@
             "login": "carlo_miniussi",
             "name": "Carlo Miniussi"
         },
+        {
+            "contributions": [
+                "data",
+                "tool"
+            ],
+            "login": "cecile_madjar",
+            "name": "Cecile Madjar"
+        },
         {
             "contributions": [
                 "doc"
@@ -1002,7 +1017,8 @@
                 "tool",
                 "eventOrganizing",
                 "fundingFinding",
-                "infra"
+                "infra",
+                "talk"
             ],
             "login": "francopestilli",
             "name": "Franco Pestilli",
@@ -1461,6 +1477,13 @@
             "name": "Jeanette Mumford",
             "profile": "https://jeanettemumford.org/"
         },
+        {
+            "contributions": [
+                "tool"
+            ],
+            "login": "jefferson_casimir",
+            "name": "Jefferson Casimir"
+        },
         {
             "contributions": [
                 "doc"
@@ -1799,6 +1822,13 @@
             "name": "Kurt Schilling",
             "profile": "https://github.com/schillkg"
         },
+        {
+            "contributions": [
+                "tool"
+            ],
+            "login": "laetitia_fesselier",
+            "name": "Laetitia Fesselier"
+        },
         {
             "contributions": [
                 "financial"
@@ -2728,6 +2758,17 @@
             "login": "stephan_bickel",
             "name": "Stephan Bickel"
         },
+        {
+            "contributions": [
+                "bug",
+                "code",
+                "question",
+                "tool",
+                "userTesting"
+            ],
+            "login": "smeisler",
+            "name": "Steven Meisler"
+        },
         {
             "avatar_url": "https://avatars.githubusercontent.com/u/11152799?v=4",
             "contributions": [
@@ -2987,6 +3028,14 @@
             "name": "Tristan Glatard",
             "profile": "https://github.com/glatard"
         },
+        {
+            "contributions": [
+                "data",
+                "tool"
+            ],
+            "login": "tyler_collins",
+            "name": "Tyler Collins"
+        },
         {
             "contributions": [
                 "doc"
@@ -3091,7 +3140,14 @@
                 "tool",
                 "question",
                 "bug",
-                "code"
+                "code",
+                "data",
+                "fundingFinding",
+                "ideas",
+                "plugin",
+                "review",
+                "userTesting",
+                "infra"
             ],
             "login": "yarikoptic",
             "name": "Yaroslav O. Halchenko",

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,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
-ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn
+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
@@ -86,8 +86,8 @@ jobs:
   validate_cff:
     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

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