Merge branch 'master' into define_entity

Resolves bids-standard#947 against:
- bids-standard#962 (21b7725)
- bids-standard#1044 (d9eeb6d)
- bids-standard#867 (5fe26e1)
- bids-standard#998 (e47283a)

Conflicts:
	src/02-common-principles.md
	src/schema/README.md
	src/schema/objects/entities.yaml
	src/schema/objects/metadata.yaml

.circleci/config.yml

@@ -2,26 +2,34 @@ version: 2
 jobs:
   build_docs:
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.8
     steps:
       # checkout code to default ~/project
       - checkout
       - run:
           name: install dependencies
           command: |
+            python -m venv env
+            source env/bin/activate
             python -m pip install --upgrade pip
             pip install -r requirements.txt
+            pip install -e ~/project/tools/schemacode/
       - run:
           name: generate docs
-          command: mkdocs build --clean --strict --verbose
+          command: |
+            source env/bin/activate
+            mkdocs build --clean --strict --verbose
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
           paths: site
+      - store_artifacts:
+          path: ~/project/site/
+          destination: dev_docs
 
   linkchecker:
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.8
     steps:
       # checkout code to default ~/project
       - checkout
@@ -31,11 +39,14 @@ jobs:
       - run:
           name: install linkchecker
           command: |
-            python -m ensurepip
+            python -m venv env
+            source env/bin/activate
+            python -m pip install --upgrade pip
             python -m pip install linkchecker
       - run:
           name: check links
           command: |
+            source env/bin/activate
             git status
             if (! git log -1 --pretty=oneline | grep REL:) ; then
               chmod a+rX -R ~
@@ -44,9 +55,11 @@ jobs:
               # failures for local file:/// -- yoh found no better way,
               linkchecker -t 1 --check-extern \
                 --ignore-url 'file:///.*' \
-                --ignore-url https://fonts.gstatic.com \
-                --ignore-url "https://github.com/bids-standard/bids-specification/(pull|tree)/.*" \
-                --ignore-url "https://github.com/[^/]*" \
+                --ignore-url 'https://fonts.gstatic.com' \
+                --ignore-url 'https://github.com/bids-standard/bids-specification/(pull|tree)/.*' \
+                --ignore-url 'https://github.com/[^/]*' \
+                --ignore-url 'https://doi.org/.*' \
+                --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"
@@ -117,7 +130,7 @@ jobs:
   # Run remark on the auto generated changes.md file
   remark:
     docker:
-      - image: node:latest
+      - image: cimg/node:lts
     steps:
       # checkout code to default ~/project
       - checkout
@@ -150,7 +163,7 @@ jobs:
   # Push built changelog to repo
   Changelog-bot:
     docker:
-      - image: circleci/openjdk:8-jdk
+      - image: cimg/base:stable
     steps:
       - setup_remote_docker:
           version: 17.11.0-ce

.gitattributes

@@ -2,3 +2,4 @@
 *.png -text
 *.jpg -text
 *.webm -text
+tools/schemacode/schemacode/_version.py export-subst

.github/workflows/codespell.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: codespell-project/actions-codespell@master
         with:
           skip: js,*.svg

.github/workflows/markdown_style.yml

@@ -6,7 +6,7 @@ jobs:
   markdown-style:
     runs-on : ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Setup NodeJS
       uses: actions/setup-node@v2
       with:

.github/workflows/no-bad-latin.yml

@@ -31,10 +31,10 @@ jobs:
     # This section collects together the steps involved in running the test
     steps:
     # Checkout the repository. Relies on another GH-Action.
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     # Set up the Python version. Relies on another GH-Action.
     - name: Setup Python 3.7
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v3
       with:
         python-version: 3.7
     # Install Python dependencies

.github/workflows/schemacode_ci.yml

@@ -0,0 +1,94 @@
+name: "schemacode_ci"
+
+on:
+  push:
+    branches:
+      - "master"
+    paths:
+      - "tools/schemacode/**"
+      - "src/schema/**"
+  pull_request:
+    branches:
+      - "*"
+    paths:
+      - "tools/schemacode/**"
+      - "src/schema/**"
+
+jobs:
+  check_skip:
+    runs-on: ubuntu-latest
+    outputs:
+      skip: ${{ steps.result_step.outputs.ci-skip }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - id: result_step
+        uses: mstachniuk/ci-skip@master
+        with:
+          commit-filter: "[skip ci];[ci skip];[skip github]"
+          commit-filter-separator: ";"
+
+  run_tests:
+    needs: check_skip
+    if: ${{ needs.check_skip.outputs.skip == 'false' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+            python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+    name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v3
+        with:
+            python-version: ${{ matrix.python-version }}
+
+      - name: "Display Python version"
+        shell: bash {0}
+        run: python -c "import sys; print(sys.version)"
+
+      - name: "Install the schemacode package"
+        shell: bash {0}
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install -e ./tools/schemacode[tests]
+
+      - name: "Run tests"
+        shell: bash {0}
+        run: |
+          python -m pytest --pyargs schemacode --cov=schemacode ./tools/schemacode/
+
+      - name: "Upload coverage to CodeCov"
+        uses: codecov/codecov-action@v1
+        if: success()
+
+  flake8-lint:
+    runs-on: ubuntu-latest
+    name: Lint schemacode
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python environment
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.7"
+
+      - name: "Install the schemacode package"
+        shell: bash {0}
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install -e ./tools/schemacode[tests]
+
+      - name: "Run flake8"
+        working-directory: ./tools/schemacode/
+        shell: bash {0}
+        run: |
+          flake8 .

.github/workflows/yml_lint.yml

@@ -6,9 +6,9 @@ jobs:
   yml-lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
     - name: Install dependencies

.gitignore

@@ -2,6 +2,7 @@ site/
 .DS_Store
 .idea
 venvs
+.vscode/
 
 pdf_build_src/bids-spec.pdf
 pdf_build_src/bids-spec_pandoc_log.json

BIDS_logo/README.md

@@ -1,11 +1,21 @@
-The BIDS logo originates from a [design competition](https://en.99designs.de/logo-design/contests/design-brain-imaging-data-standard-logo-916110).
+# BIDS logo
+
+The BIDS logo originates from a
+[design competition](https://en.99designs.de/logo-design/contests/design-brain-imaging-data-standard-logo-916110).
 
 See the related discussion here: https://github.com/bids-standard/bids-specification/issues/216
 
-The sources of the animated version of the logo can be found at
+All static versions of the logo are shared under a CC BY 4.0 license, see
+[LICENSE](../LICENSE)
+in the root of the repository.
+
+The animated version of the logo is shared under a CC BY-SA 4.0 license,
+copyright Adina Wagner,
+please see the source:
 [github.com/adswa/animated-bids-logo](https://github.com/adswa/animated-bids-logo).
 
 # Files
+
 - Standard formats
     - `BIDS_logo.jpg`
     - Transparent background

CODEOWNERS

@@ -18,3 +18,7 @@
 /src/05-derivatives/05-functional-derivatives.md @effigies
 /src/05-derivatives/06-diffusion-derivatives.md @francopestilli @oesteban @Lestropie
 /src/99-appendices/06-meg-file-formats.md @monkeyman192
+
+# The schema
+/src/schema/ @tsalo @erdalkaraca
+/tools/schemacode/ @tsalo @erdalkaraca