Merge branch 'master' into Clarify-Parametric-structural-MR-images

.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",

.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

.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

.github/workflows/schemacode_ci.yml

@@ -27,7 +27,7 @@ jobs:
         python-version: ["3.11"]
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@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/
@@ -56,7 +56,7 @@ 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
@@ -67,15 +67,16 @@ jobs:
       - 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/
@@ -132,9 +133,9 @@ jobs:
       - 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
@@ -160,10 +161,10 @@ jobs:
         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

.github/workflows/validation.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: 14
       - name: Install dependencies
@@ -37,7 +37,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Install dependencies
@@ -50,7 +50,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - run: python -m pip install --upgrade flake8 black isort[colors]
@@ -64,7 +64,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Install dependencies
@@ -87,7 +87,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: 3
     - name: Install dependencies

.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: 23.9.1
+    rev: 24.2.0
     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: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.3
+    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: v1.5.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing