[INFRA] Fix CircleCI workflows

.circleci/config.yml

@@ -4,6 +4,7 @@ jobs:
     docker:
       - image: circleci/python:3.8
     steps:
+      # checkout code to default ~/project
       - checkout
       - run:
           name: install dependencies
@@ -14,53 +15,56 @@ jobs:
           name: generate docs
           command: mkdocs build --clean --strict --verbose
       - persist_to_workspace:
-          root: .
+          # the mkdocs build outputs are in ~/project/site
+          root: ~/project
           paths: site
 
   linkchecker:
     docker:
       - image: yarikoptic/linkchecker:9.4.0.anchorfix1-1
     steps:
       - attach_workspace:
-          at: ~/build
+          # mkdocs build outputs will be in ~/project/site
+          at: ~/project
       - 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
+              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/[^/]*" \
+                ~/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
+            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
       - store_artifacts:
-          path: bids-spec.pdf
+          path: ~/project/pdf_build_src/bids-spec.pdf
 
   # Auto changelog collector
   github-changelog-generator:
@@ -69,84 +73,94 @@ 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
     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
     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 "bids.maintenance@gmail.com"
               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

DECISION-MAKING.md

@@ -86,7 +86,7 @@ and heavily depends on [GitHub Pull Request Review system](https://help.github.c
    Request (PR) to the Repository.
 1. Anyone can open a PR (this action is not limited to Contributors).
 1. PRs adding new Contributors must also add their GitHub names to the
-   [CODEOWNERS](CODEOWNERS) file.
+   [CODEOWNERS](./CODEOWNERS) file.
 1. A PR is eligible to be merged if and only if these conditions are met:
    1. The last commit is at least 5 working days old to allow the community to
       evaluate it.
@@ -138,7 +138,7 @@ and heavily depends on [GitHub Pull Request Review system](https://help.github.c
 1. To facilitate triage of incoming PR you can subscribe to
    notifications for new PRs proposing changes to specific files. To do this
    add your GitHub name next to the file you want to subscribe to in the
-   [CODEOWNERS](CODEOWNERS). This way you will be ask to review each relevant
+   [CODEOWNERS](./CODEOWNERS). This way you will be ask to review each relevant
    PR. Please mind that lack of your review will not prevent the PR from being
    merged so if you think the PR needs your attention, please review it
    promptly or request more time via Request changes.

src/99-appendices/03-hed.md

@@ -10,7 +10,7 @@ Each level of a hierarchical tag is delimited with a forward slash (`/`).
 A HED string contains one or more HED tags separated by commas (`,`).
 Parentheses (brackets, `()`) group tags and enable specification of multiple items
 and their attributes in a single **HED string** (see section 2.4 in
-[HED Tagging Strategy Guide](https://www.hedtags.org/downloads/HED%20Tagging%20Strategy%20Guide.pdf)).
+[HED Tagging Strategy Guide](https://www.hedtags.org/docs/HEDTaggingStrategyGuide.pdf)).
 For more information about HED and tools available to validate and match HED
 strings, please visit [www.hedtags.org](https://www.hedtags.org).
 Since dedicated fields already exist for the overall task classification in the