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Merge remote-tracking branch 'origin/bep-016' into bvec_reference_axes
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Lestropie committed Jun 5, 2024
2 parents b093ac1 + d56816d commit bda570f
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122 changes: 0 additions & 122 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -93,133 +93,11 @@ jobs:
- store_artifacts:
path: bids-spec.pdf

# Automatically generate a changelog since migration from Google Docs to GitHub
github_changelog_generator:
docker:
- image: ferrarimarco/github-changelog-generator:1.14.3
steps:
- setup_remote_docker:
version: 18.06.0-ce
# checkout code to default ~/project
- checkout
- run:
name: Build changelog
# $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
command: |
mkdir ~/changelog_build
git status
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
github_changelog_generator \
--exclude-tags-regex "^(?!v).*?$" \
--user bids-standard \
--project bids-specification \
--token ${CHANGE_TOKEN} \
--output ~/changelog_build/CHANGES.md \
--base ~/project/src/pregh-changes.md \
--header-label "# Changelog" \
--release-branch master \
--no-issues \
--no-filter-by-milestone \
--no-compare-link \
--pr-label "" \
--enhancement-label "" \
--bugs-label "" \
--exclude-labels "exclude-from-changelog"
cat ~/changelog_build/CHANGES.md
else
echo "Commit or Release, do nothing"
fi
- persist_to_workspace:
# raw generated changelog in ~/changelog_build/CHANGES.md
root: ~/.
paths:
- changelog_build

# Lint and fix the auto generated changes.md file
lint_generated_changelog:
docker:
- image: cimg/node:lts
steps:
# checkout code to default ~/project
- checkout
- attach_workspace:
# 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: |
git status
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
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"
fi
- persist_to_workspace:
# linted and fixed changelog in ~/changelog_build/CHANGES.md
root: ~/.
paths:
- changelog_build

# Push built changelog to repo
commit_generated_changelog:
docker:
- image: cimg/base:stable
steps:
- setup_remote_docker:
version: 17.11.0-ce
# checkout code to default ~/project
- checkout
- attach_workspace:
# fixed+linted changelog in ~/changelog_build/CHANGES.md
at: ~/.
- run:
name: Changelog deployment
# $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
command: |
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
mv ~/changelog_build/CHANGES.md ~/project/src/CHANGES.md
merge_message=$(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 ~/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
echo "Commit or Release, do nothing"
fi
workflows:
search_build:
jobs:
- build_docs
- check_links:
requires:
- build_docs
- github_changelog_generator:
filters:
branches:
only: master
- lint_generated_changelog:
requires:
- github_changelog_generator
filters:
branches:
only: master
- commit_generated_changelog:
requires:
- lint_generated_changelog
filters:
branches:
only: master
- build_docs_pdf
57 changes: 41 additions & 16 deletions .github/pull_request_template.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,27 +2,52 @@

See the [CONTRIBUTING](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md) guide. Specifically:

- Please keep the title of your Pull Request (PR) short but informative - it will
appear in the changelog.
- Please keep the title of your Pull Request (PR) short but informative - it will appear in the changelog.
- If you do **not** want a PR to appear in the changelog, it must receive the `exclude-from-changelog` label.
- Please ensure your name is credited on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors) and add your name with the type of contribution.

- Please ensure your name is credited
on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors)
and add your name with the type of contribution.
For assistance, please tag @bids-standard/maintainers.

- Use one of the following prefixes in the title of your PR:
- `[ENH]` - enhancement of the specification that adds a new feature or
support for a new data type
- `[ENH]` - enhancement of the specification that adds a new feature or support for a new data type
- `[FIX]` - fix of a typo or language clarification
- `[INFRA]` - changes to the infrastructure automating the specification
release (for example building HTML docs)
- `[INFRA]` - changes to the infrastructure automating the specification release (for example building HTML docs)
- `[SCHEMA]` - changes to the BIDS schema and/or related code
- `[MISC]` - everything else including changes to the file listing
contributors
- If you are opening a PR to obtain early feedback, but the changes
are not ready to be merged (also known as a "Work in Progress" PR), please
use a [Draft PR](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
- After opening the PR, our continuous integration services will automatically check your contribution for formatting errors and render a preview of the BIDS specification with your changes.
- `[MISC]` - everything else including changes to the file listing contributors

- If you are opening a PR to obtain early feedback,
but the changes are not ready to be merged (also known as a "Work in Progress" PR),
please use a [Draft PR](https://github.blog/2019-02-14-introducing-draft-pull-requests/).

- After opening the PR, our continuous integration services will automatically check your contribution
for formatting errors and render a preview of the BIDS specification with your changes.
To see the checks and preview, scroll down and click on the `show all checks` link.
From the list, select the `Details` link of the `ci/circleci: build_docs artifact` check to see the preview of the BIDS specification.
- If you are updating the schema *and* you need to subsequently make changes to the bidsschematools code (validation, tests, rendering), this means your PR probably introduces a compatibility breaking change and you should increment the minor version (the second number) in `bids-specification/src/schema/SCHEMA_VERSION`.
From the list:
- select the `Details` link of the `docs/readthedocs.org:bids-specification` check to see the HTML preview of the BIDS specification.
- select the `Details` link of the `Check the rendered PDF version here! ` check to see the PDF preview of the BIDS specification.

- If you are updating the schema *and* you need to subsequently make changes to the bidsschematools code (validation, tests, rendering),
this means your PR probably introduces a compatibility breaking change
and you should increment the minor version (the second number) in `bids-specification/src/schema/SCHEMA_VERSION`.

- If you are opening a PR for a BIDS extension proposal (BEP),
make sure that your top message contains the following notes

> [!Note]
>
> **We meet regularly to discuss this BEP**
>
> Next meeting: **insert date** on **URL to join**
>
> Communication channel on github repo / matrix / slack / discord : **insert URL to join**
>
> [!Tip]
>
> [**HTML preview of this BEP**](insert URL to HTML preview once available)
>
--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---
130 changes: 130 additions & 0 deletions .github/workflows/changelog_generator.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,130 @@
---
name: GitHub_Changelog_Generator

on:
push:
branches: ["master"]

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

jobs:
github_changelog_generator:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Ruby
uses: ruby/setup-ruby@v1
with:
ruby-version: '3.2'
- name: Install dependencies
run: |
gem install github_changelog_generator
- name: Check version
run: |
github_changelog_generator --version
- name: Build changelog
run: |
mkdir ~/changelog_build
github_changelog_generator \
--exclude-tags-regex "^(?!v).*?$" \
--user bids-standard \
--project bids-specification \
--token ${{ secrets.GITHUB_TOKEN }} \
--output ~/changelog_build/CHANGES.md \
--header-label "# Changelog" \
--release-branch master \
--no-issues \
--no-filter-by-milestone \
--no-compare-link \
--pr-label "" \
--enhancement-label "" \
--bugs-label "" \
--exclude-labels "exclude-from-changelog"
- name: Append changelog from pre-GitHub times
run: |
cat ${{ github.workspace }}/src/pregh-changes.md >> ~/changelog_build/CHANGES.md
- name: Remove the inserted advert from the file
run: |
sed -i '/This Changelog was automatically generated by/d' ~/changelog_build/CHANGES.md
- name: Print out complete changelog
run: |
cat ~/changelog_build/CHANGES.md
- name: Archive changelog
uses: actions/upload-artifact@v4
with:
name: changelog_pre_lint
path: |
~/changelog_build/CHANGES.md
lint_generated_changelog:
needs: github_changelog_generator
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Download previously build changelog
uses: actions/download-artifact@v4
with:
name: changelog_pre_lint
path: ~/changelog_build
- name: Set up Node
uses: actions/setup-node@v4
with:
node-version: 20
- name: Install remark and extensions
run: |
npm install `cat npm-requirements.txt`
- name: Remark on autogenerated CHANGES.md
# first remove empty lines
# then run remark to re-organize
# replace remark's bullet list "*" with "-"
# final run of remark to check everything passes now
run: |
head -n 25 ~/changelog_build/CHANGES.md
sed -i '/^$/d' ~/changelog_build/CHANGES.md
echo $'\n------------------------------\n'
head -n 25 ~/changelog_build/CHANGES.md
npx remark ~/changelog_build/CHANGES.md --rc-path ${{ github.workspace }}/.remarkrc --output ~/changelog_build/CHANGES.md --quiet
echo $'\n------------------------------\n'
head -n 25 ~/changelog_build/CHANGES.md
sed -i 's/^* /- /' ~/changelog_build/CHANGES.md
echo $'\n------------------------------\n'
head -n 25 ~/changelog_build/CHANGES.md
npx remark ~/changelog_build/CHANGES.md --rc-path ${{ github.workspace }}/.remarkrc --frail --quiet --no-stdout
- name: Archive linted changelog
uses: actions/upload-artifact@v4
with:
name: changelog_post_lint
path: |
~/changelog_build/CHANGES.md
commit_generated_changelog:
permissions:
# Give the default GITHUB_TOKEN write permission to commit and push the
# added or changed files to the repository.
contents: write
needs: lint_generated_changelog
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Download previously build changelog
uses: actions/download-artifact@v4
with:
name: changelog_post_lint
path: ~/changelog_build
- name: Changelog deployment
run: |
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
mv ~/changelog_build/CHANGES.md ${{ github.workspace }}/src/CHANGES.md
merge_message=$(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 ${{ github.workspace }}/src/CHANGES.md
git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
git push https://${{ secrets.GITHUB_TOKEN }}@github.com/bids-standard/bids-specification.git master
else
echo "Did not detect a "Merge commit" to master, or detected a Release ... doing nothing."
fi
6 changes: 3 additions & 3 deletions .github/workflows/schemacode_ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ jobs:
- name: "Install build dependencies"
run: pip install --upgrade build twine
- name: "Install test dependencies on tag"
run: pip install --upgrade pytest pyyaml pandas tabulate markdown-it-py pyparsing
run: pip install --upgrade tools/schemacode[test]
if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
- name: "Build archive on tag"
run: pytest tools/schemacode/bidsschematools -k make_archive
Expand Down Expand Up @@ -117,8 +117,8 @@ jobs:
with:
user: __token__
password: ${{ secrets.TEST_PYPI_API_TOKEN }}
repository_url: https://test.pypi.org/legacy/
skip_existing: true
repository-url: https://test.pypi.org/legacy/
skip-existing: true
- name: "Upload to PyPI (on tags)"
if: startsWith(github.ref, 'refs/tags/schema-')
uses: pypa/gh-action-pypi-publish@release/v1
Expand Down
26 changes: 26 additions & 0 deletions .github/workflows/shellcheck.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
---
name: Shellcheck

on:
push:
branches: [master]
pull_request:
branches: [master]

permissions:
contents: read

jobs:
shellcheck:
name: Check shell scripts
runs-on: ubuntu-latest

steps:
- name: Checkout
uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt update && sudo apt install -y shellcheck
- name: shellcheck
run: |
git grep -l '^#\( *shellcheck \|!\(/bin/\|/usr/bin/env \)\(sh\|bash\|dash\|ksh\)\)' | xargs shellcheck
2 changes: 1 addition & 1 deletion .github/workflows/validation.yml
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ jobs:
- uses: actions/checkout@v4
- uses: actions/setup-node@v4
with:
node-version: 14
node-version: 22
- name: Install dependencies
run: npm install `cat npm-requirements.txt`
- name: Run style checks
Expand Down
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