Merge branch 'master' into enh/metadata_statement

.circleci/config.yml

@@ -2,63 +2,90 @@ 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:
-          root: .
+          # the mkdocs build outputs are in ~/project/site
+          root: ~/project
           paths: site
+      - store_artifacts:
+          path: ~/project/site/
+          destination: dev_docs
 
   linkchecker:
     docker:
-      - image: yarikoptic/linkchecker:9.4.0.anchorfix1-1
+      - image: cimg/python:3.8
     steps:
+      # checkout code to default ~/project
+      - checkout
       - attach_workspace:
-          at: ~/build
+          # mkdocs build outputs will be in ~/project/site
+          at: ~/project
+      - run:
+          name: install linkchecker
+          command: |
+            python -m venv env
+            source env/bin/activate
+            python -m pip install --upgrade pip
+            python -m pip install linkchecker
       - run:
           name: check links
           command: |
-            if (! git log -1 --pretty=%b | grep REL:) ; then
-            chmod a+rX -R ~
-            linkchecker -t 1 ~/build/site/
-            # check external separately by pointing to all *html so no
-            # 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/[^/]*" \
-              ~/build/site/*html ~/build/site/*/*.html
+            source env/bin/activate
+            git status
+            if (! git log -1 --pretty=oneline | grep REL:) ; then
+              chmod a+rX -R ~
+              linkchecker -t 1 ~/project/site/
+              # check external separately by pointing to all *html so no
+              # 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://doi.org/.*' \
+                --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
+                ~/project/site/*html ~/project/site/*/*.html
             else
-            echo "Release PR - do nothing"
+              echo "Release PR - do nothing"
             fi
 
   build_docs_pdf:
-    working_directory: ~/bids-specification/pdf_build_src
     docker:
       - image: danteev/texlive:latest
     steps:
-      - checkout:
-          path: ~/bids-specification
+      # checkout code to default ~/project
+      - checkout
       - run:
           name: install dependencies
           command: |
-            python -m pip install --upgrade pip
-            pip install -r ../requirements.txt
+            apt-get update && apt install -y python3-pip
+            python3 -m pip install --upgrade pip
+            python3 -m pip install -r  ~/project/requirements.txt
       - run:
           name: install font that works with unicode emojis
           command: apt-get update && apt-get install -y fonts-symbola
       - run:
           name: generate pdf version docs
-          command: bash build_pdf.sh
+          command: |
+            cd ~/project/pdf_build_src
+            bash build_pdf.sh
+            mv ~/project/pdf_build_src/bids-spec.pdf ~/project/bids-spec.pdf
       - store_artifacts:
           path: bids-spec.pdf
 
@@ -69,84 +96,94 @@ jobs:
     steps:
       - setup_remote_docker:
           version: 18.06.0-ce
+      # checkout code to default ~/project
       - checkout
       - run:
           name: Build changelog
-          working_directory: ~/build
+          # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
           command: |
+            mkdir ~/changelog_build
+            git status
             if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
               github_changelog_generator \
                 --user bids-standard \
                 --project bids-specification \
                 --token ${CHANGE_TOKEN} \
-                --output ~/build/CHANGES.md \
-                --base ~/build/src/pregh-changes.md \
+                --output ~/changelog_build/CHANGES.md \
+                --base ~/project/src/pregh-changes.md \
                 --header-label "# Changelog" \
                 --no-issues \
                 --no-issues-wo-labels \
                 --no-filter-by-milestone \
                 --no-compare-link \
                 --pr-label "" \
                 --release-branch master
-              cat ~/build/CHANGES.md
-              mv ~/build/CHANGES.md ~/build/src/CHANGES.md
+              cat ~/changelog_build/CHANGES.md
             else
               echo "Commit or Release, do nothing"
             fi
       - persist_to_workspace:
-          root: .
-          paths: src
+          # raw generated changelog in ~/changelog_build/CHANGES.md
+          root: ~/.
+          paths: changelog_build
 
   # 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
       - attach_workspace:
-          at: ~/build
+          # the freshly built CHANGES.md will be in ~/changelog_build/CHANGES.md
+          at: ~/.
       - run:
           name: install remark and extensions
           command: npm install `cat npm-requirements.txt`
       - run:
           name: remark on autogenerated CHANGES.md
+          # format changelog, then use sed to change * to -, then lint changelog
           command: |
-            mkdir ~/project/src/tmp
+            git status
             if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-              cat ~/build/src/CHANGES.md
-              cp ~/build/src/CHANGES.md ~/project/src/tmp/CHANGES.md
-              npx remark ~/project/src/tmp/CHANGES.md --frail --rc-path .remarkrc
+              head -n 100 ~/changelog_build/CHANGES.md
+              npx remark-cli ~/changelog_build/CHANGES.md --rc-path ~/project/.remarkrc --output ~/changelog_build/CHANGES.md
+              head -n 100 ~/changelog_build/CHANGES.md
+              sed -i 's/*   /-   /' ~/changelog_build/CHANGES.md
+              head -n 100 ~/changelog_build/CHANGES.md
+              npx remark-cli ~/changelog_build/CHANGES.md --frail --rc-path ~/project/.remarkrc
             else
               echo "Commit or Release, do nothing"
-              touch ~/project/src/tmp/empty.txt
             fi
       - persist_to_workspace:
-          root: ~/project/src
-          paths: tmp
+          # fixed+linted changelog in ~/changelog_build/CHANGES.md
+          root: ~/.
+          paths: changelog_build
 
   # Push built changelog to repo
   Changelog-bot:
-    working_directory: ~/build
     docker:
-      - image: circleci/openjdk:8-jdk
+      - image: cimg/base:stable
     steps:
       - setup_remote_docker:
           version: 17.11.0-ce
+      # checkout code to default ~/project
       - checkout
       - attach_workspace:
-          at: ~/build
+          # fixed+linted changelog in ~/changelog_build/CHANGES.md
+          at: ~/.
       - deploy:
           name: Changelog deployment
-          working_directory: ~/build
+          # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
           command: |
             if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-              mv ~/build/tmp/CHANGES.md ~/build/src/CHANGES.md
+              mv ~/changelog_build/CHANGES.md ~/project/src/CHANGES.md
               merge_message=$(git log -1 | grep Merge | grep "pull")
               PR_number=$(echo $merge_message | cut -d ' ' -f 4)
               git config credential.helper 'cache --timeout=120'
               git config user.email "[email protected]"
               git config user.name "bids-maintenance"
-              git add ~/build/src/CHANGES.md
+              git add ~/project/src/CHANGES.md
               git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
               git push https://${CHANGE_TOKEN}@github.com/bids-standard/bids-specification.git master
             else
@@ -177,12 +214,4 @@ workflows:
           filters:
             branches:
               only: master
-      # Ensure that build_docs_pdf always runs last, so that we can use the CircleCI API link for the "latest" artifact
-      # https://circleci.com/api/v1.1/project/github/bids-standard/bids-specification/latest/artifacts/0/bids-spec.pdf?branch=master
-      - build_docs_pdf:
-          requires:
-            - build_docs
-            - linkchecker
-            - github-changelog-generator
-            - remark
-            - Changelog-bot
+      - build_docs_pdf

.gitattributes

@@ -0,0 +1,5 @@
+* text=auto
+*.png -text
+*.jpg -text
+*.webm -text
+tools/schemacode/schemacode/_version.py export-subst

.github/workflows/codespell.yml

@@ -0,0 +1,20 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: codespell-project/actions-codespell@master
+        with:
+          skip: js,*.svg
+          ignore_words_list: fo,te,als

.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

@@ -2,9 +2,9 @@
 # This action initially adopted from The Turing Way from in October 2020.
 # doi:10.5281/zenodo.3233853
 # https://github.com/alan-turing-institute/the-turing-way/blob/af98c94/.github/workflows/no-bad-latin.yml
-# 
+#
 # This action triggers the script tools/no-bad-latin.py to and will throw an error if any latin expression (like e.g. or i.e.) is detected:
-# 
+#
 #  This action will be triggered
 # -   on a push to master
 # -   on a PR to the master branch and will only check files that were modified in src
@@ -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/main.yml → .github/workflows/redirect_circleci_artifacts.yml

@@ -10,3 +10,4 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           artifact-path: 0/bids-spec.pdf
           circleci-jobs: build_docs_pdf
+          job-title: Check the rendered PDF version here!