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autoupdate.yml
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name: Autoupdate
on:
schedule:
- cron: "0 4 * * 1"
push:
branches: [main]
workflow_dispatch:
jobs:
build:
env:
python-version: '3.11'
strategy:
fail-fast: false
matrix:
include:
- upstream_repo_owner: bgruening
upstream_repo_name: galaxytools
upstream_repo_branch: master
upstream_repo_dir: .
- upstream_repo_owner: galaxycomputationalchemistry
upstream_repo_name: galaxy-tools-compchem
upstream_repo_branch: master
upstream_repo_dir: .
- upstream_repo_owner: galaxyproject
upstream_repo_name: iwc
upstream_repo_branch: main
upstream_repo_dir: workflows/
- upstream_repo_owner: galaxyproject
upstream_repo_name: tools-iuc
upstream_repo_branch: main
upstream_repo_dir: tools/
- upstream_repo_owner: lldelisle
upstream_repo_name: tools-lldelisle
upstream_repo_branch: master
upstream_repo_dir: tools/
runs-on: ubuntu-latest
steps:
- name: Checkout this repo
uses: actions/checkout@v4
with:
path: autoupdate
- name: Checkout our fork of ${{ matrix.upstream_repo_name }}
uses: actions/checkout@v4
with:
repository: planemo-autoupdate/${{ matrix.upstream_repo_name }}
token: ${{ secrets.PAT }} # So we can push to it
path: tools_repo
fetch-depth: 0 # So we can checkout other branches
- uses: actions/setup-python@v4
with:
python-version: ${{ env.python-version }}
- name: Cache pip dir
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: cache-${{ env.python-version }}
- name: Install planemo
run: |
# pip3 install https://github.com/galaxyproject/planemo/archive/refs/heads/master.zip
pip3 install planemo
- name: Set git credentials
run: |
git config --global user.email "[email protected]"
git config --global user.name "planemo-autoupdate"
- name: Pull from upstream tool repo and push to our fork
run: |
git remote add upstream "https://github.com/${{ matrix.upstream_repo_owner }}/${{ matrix.upstream_repo_name }}"
git pull upstream "${{ matrix.upstream_repo_branch}}"
git push origin "${{ matrix.upstream_repo_branch}}"
working-directory: ./tools_repo
- name: Ensure skip_list file exists
run: touch "${{ matrix.upstream_repo_owner }}_${{ matrix.upstream_repo_name }}_skip_list"
working-directory: ./autoupdate
- name: Run a multi-line script
env:
GITHUB_TOKEN: ${{ secrets.PAT }}
run: |
errors=""
REPOS=$(planemo ci_find_repos "${{ matrix.upstream_repo_dir }}")
for REPO in $REPOS; do
echo $REPO
# First try to update
echo "Running autoupdate command..."
cd "$REPO"
# This may fail
planemo autoupdate . --skiplist "${{ github.workspace }}/autoupdate/${{ matrix.upstream_repo_owner }}_${{ matrix.upstream_repo_name }}_skip_list" > "${{ github.workspace }}/autoupdate.log" || errors="${errors}\nCannot autoupdate $REPO"
rm -f tool_test_output.* tools.yml
cd -
# Check if it changed something
if git diff --quiet; then
echo "nothing has been updated"
continue
fi
# Get the PR title and change the CHANGELOG.md for workflows
git status
case $REPO in
workflows/*)
TITLE=$(python3 "${{ github.workspace }}/autoupdate/pr_text_iwc.py" --repo "$REPO" --log "${{ github.workspace }}/autoupdate.log" --out "${{ github.workspace }}/body.txt" --changelog "$REPO/CHANGELOG.md")
FILE_TO_CHECK=${REPO}/CHANGELOG.md
;;
*)
TITLE=$(python3 "${{ github.workspace }}/autoupdate/pr_text.py" --repo "$REPO" --log "${{ github.workspace }}/autoupdate.log" --shed "$REPO/.shed.yml" --out "${{ github.workspace }}/body.txt")
FILE_TO_CHECK=
;;
esac
# Check if there is a branch/PR that already exists
# We cannot use the -A option of `gh pr list` because the PR author changes with the Personal Access Token used,
# so we filter on the 3rd output field (headRefName, i.e. remote_repository:branch).
if gh_pr_list_out=$(gh pr list --search "head:$REPO" | grep -P "^\d+\t[^\t]+\tplanemo-autoupdate:$REPO\t"); then
OLD_TITLE=$(echo "$gh_pr_list_out" | cut -f 2)
PR_EXISTS=1
PR_NUMBER=$(echo "$gh_pr_list_out" | cut -f 1)
PR_STATUS="OPENED"
echo "PR exists and is opened"
DIFF_BRANCH="origin/$REPO"
else
# Check if a closed PR exists with the same title
if gh_pr_list_out=$(gh pr list --search "is:closed is:unmerged '$TITLE' in:title" | grep -P "^\d+\t[^\t]+\tplanemo-autoupdate:" | head -n 1); then
echo "Found a closed PR with title: $TITLE"
OLD_TITLE=$(echo "$gh_pr_list_out" | cut -f 2)
PR_EXISTS=1
PR_NUMBER=$(echo "$gh_pr_list_out" | cut -f 1)
PR_STATUS="CLOSED"
if [ "$(git branch -a --list "origin/$REPO")" != "" ]; then
# The branch still exists and the PR should be reopened only if there is a new change
DIFF_BRANCH="origin/$REPO"
else
# The branch does not exists anymore so any change should reopen the PR
DIFF_BRANCH="upstream/${{ matrix.upstream_repo_branch }}"
fi
else
OLD_TITLE=
PR_EXISTS=0
PR_NUMBER=
PR_STATUS=
if [ "$(git branch -a --list "origin/$REPO")" != "" ]; then
echo "Branch exists without an open PR - deleting"
git push origin --delete "$REPO"
fi
DIFF_BRANCH="upstream/${{ matrix.upstream_repo_branch }}"
fi
fi
if ! git diff $DIFF_BRANCH --quiet $FILE_TO_CHECK; then
echo "There are changes"
if [ "$PR_EXISTS" -eq 1 ]; then
# Check if the last commit of the existing branch was manual
LAST_AUTHOR=$(git log -1 --pretty=format:'%an' $DIFF_BRANCH)
if [ "$LAST_AUTHOR" != "planemo-autoupdate" ]; then
# There were manual commits we do not do anything
gh pr comment "$PR_NUMBER" --body "There are new updates, if you want to integrate them, close the PR and delete branch."
# clean up for the next repo
git checkout -- .
continue
fi
fi
echo "Creating branch and checking out"
git checkout -b "$REPO" "upstream/${{ matrix.upstream_repo_branch }}"
echo "Adding..."
git add .
echo "Committing..."
git commit -m "$TITLE"
echo "Push branch to our fork"
git push --force --set-upstream origin "$REPO"
if [ "$PR_EXISTS" -eq 1 ]; then
# just need to update PR title
if [[ $OLD_TITLE == *\) ]]; then
# older PRs
NEW_TITLE="$OLD_TITLE $(echo "$TITLE" | cut -f 6,7 -d ' ')"
else # newer PRs
NEW_TITLE="$(echo "$OLD_TITLE" | cut --complement -f 7 -d ' ') $(echo "$TITLE" | cut -f 7 -d ' ')"
fi
if [ "$NEW_TITLE" != "$OLD_TITLE" ]; then
# This may fail if for example the PR was opened by someone else like
# https://github.com/bgruening/galaxytools/pull/1353
gh pr edit "$PR_NUMBER" -t "$NEW_TITLE" || errors="${errors}\nCannot change title of PR $PR_NUMBER for $REPO"
fi
# If the PR is closed, we need to reopen it.
if [ "$PR_STATUS" = "CLOSED" ]; then
# This may fail
gh pr reopen "$PR_NUMBER" || errors="${errors}\nCannot reopen PR $PR_NUMBER for $REPO"
fi
# Comment on the PR
gh pr comment "$PR_NUMBER" --body "There are new updates, they have been integrated to the PR, check the file diff."
else # we need to create a PR
echo "Creating a PR..."
gh pr create --base "${{ matrix.upstream_repo_branch }}" --head "planemo-autoupdate:$REPO" --title "$TITLE" --repo "${{ matrix.upstream_repo_owner}}/${{ matrix.upstream_repo_name }}" --body-file "${{ github.workspace }}/body.txt"
fi
else
echo "No changes compared to $DIFF_BRANCH"
# clean up for the next repo
git checkout -- .
fi
done
if [ ! -z "$errors" ]; then
echo "ERRORS OCCURED DURING AUTOUPDATE:"
echo -e $errors
exit 1
fi
working-directory: ./tools_repo