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Merge branch 'develop' into pr-lattice
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‎.ci/create-changes-html.sh

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#!/bin/sh
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if [ $# != 2 ]; then
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echo >&2 "usage: $0 BASE_DOC_COMMIT DOC_REPO"
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echo >&2 "creates CHANGES.html in the current directory"
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echo >&2 "for the diffs of DOC_REPO against BASE_DOC_COMMIT"
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exit 1
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fi
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BASE_DOC_COMMIT="$1"
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DOC_REPOSITORY="$2"
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# Wipe out chronic diffs between old doc and new doc
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(cd $DOC_REPOSITORY && find . -name "*.html" | xargs sed -i -e '\;<script type="application/vnd\.jupyter\.widget-state+json">;,\;</script>; d')
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# Create CHANGES.html
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echo '<html>' > CHANGES.html
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echo '<head>' >> CHANGES.html
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echo '<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/styles/default.min.css">' >> CHANGES.html
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echo '<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/highlight.min.js"></script>' >> CHANGES.html
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echo '<script>hljs.highlightAll();</script>' >> CHANGES.html
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cat >> CHANGES.html << EOF
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<script>
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document.addEventListener('DOMContentLoaded', () => {
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const diffSite = 'https://pianomister.github.io/diffsite'
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const baseDocURL = 'https://sagemath-tobias.netlify.app'
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const diffParagraphs = document.querySelectorAll('p.diff');
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diffParagraphs.forEach(paragraph => {
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const rootURL = window.location.origin;
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const docAnchor = paragraph.querySelector('a'); // first "a" element
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const url = new URL(docAnchor.href);
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const path = url.pathname;
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const anchor = document.createElement('a');
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anchor.href = diffSite + '/?url1=' + rootURL + path + '&url2=' + baseDocURL + path;
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anchor.textContent = 'compare with the base';
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anchor.setAttribute('target', '_blank');
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paragraph.appendChild(anchor);
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paragraph.innerHTML += '&nbsp;';
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const hunkAnchors = paragraph.querySelectorAll('a.hunk');
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hunkAnchors.forEach(hunkAnchor => {
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const url = new URL(hunkAnchor.href);
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const path = url.pathname;
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const pathHash = path + url.hash.replace('#', '%23');
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const anchor = document.createElement('a');
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anchor.href = diffSite + '/?url1=' + rootURL + pathHash + '&url2=' + baseDocURL + path;
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anchor.textContent = hunkAnchor.textContent;
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anchor.setAttribute('target', '_blank');
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paragraph.appendChild(anchor);
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paragraph.innerHTML += '&nbsp;';
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});
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});
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});
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</script>
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EOF
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echo '</head>' >> CHANGES.html
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echo '<body>' >> CHANGES.html
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(cd $DOC_REPOSITORY && git diff $BASE_DOC_COMMIT -- *.html) > diff.txt
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python3 - << EOF
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import os, re, html
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with open('diff.txt', 'r') as f:
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diff_text = f.read()
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diff_blocks = re.split(r'^(?=diff --git)', diff_text, flags=re.MULTILINE)
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out_blocks = []
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for block in diff_blocks:
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match = re.search(r'^diff --git a/(.*) b/\1', block, flags=re.MULTILINE)
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if match:
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doc = match.group(1)
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file_path = os.path.join('$DOC_REPOSITORY', doc)
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try:
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with open(file_path, 'r') as file:
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content = file.readlines()
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except FileNotFoundError:
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content = []
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count = 0
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for line in block.splitlines():
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if line.startswith('@@ -'):
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search_result = re.search(r'@@ -(\d+),(\d+) \+(\d+),(\d+)', line)
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if search_result:
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line_number = int(search_result.group(3))
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for i in range(line_number - 1, -1, -1):
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if content[i].startswith('<'):
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count += 1
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content[i] = f'<span id="hunk{count}" style="visibility: hidden;"></span>' + content[i]
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break
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if content:
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with open(file_path, 'w') as file:
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file.writelines(content)
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path = 'html/' + doc
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hunks = '&nbsp;'.join(f'<a href="{path}#hunk{i+1}" class="hunk" target="_blank">#{i + 1}</a>' for i in range(count))
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out_blocks.append(f'<p class="diff"><a href="{path}">{doc}</a>&nbsp;' + hunks + '&emsp;</p>'
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+ '\n<pre><code class="language-diff">'
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+ html.escape(block).strip() + '</code></pre>')
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output_text = '\n'.join(out_blocks)
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with open('diff.html', 'w') as f:
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f.write(output_text)
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EOF
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cat diff.html >> CHANGES.html
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echo '</body>' >> CHANGES.html
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echo '</html>' >> CHANGES.html
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rm diff.txt diff.html

‎.ci/describe-system.sh

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This file was deleted.

‎.ci/merge-fixes.sh

Lines changed: 79 additions & 33 deletions
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#!/bin/sh
2-
# Merge open PRs from sagemath/sage labeled "blocker".
3-
REPO="sagemath/sage"
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GH="gh -R $REPO"
5-
PRs="$($GH pr list --label "p: blocker / 1" --json number --jq '.[].number')"
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if [ -z "$PRs" ]; then
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echo 'Nothing to do: Found no open PRs with "blocker" status.'
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else
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echo "Found PRs: " $PRs
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export GIT_AUTHOR_NAME="ci-sage workflow"
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export GIT_AUTHOR_EMAIL="[email protected]"
12-
export GIT_COMMITTER_NAME="$GIT_AUTHOR_NAME"
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export GIT_COMMITTER_EMAIL="$GIT_AUTHOR_EMAIL"
14-
git tag -f test_base
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git commit -q -m "Uncommitted changes" --no-allow-empty -a
16-
for a in $PRs; do
17-
echo "::group::Merging PR https://github.com/$REPO/pull/$a"
18-
git tag -f test_head
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$GH pr checkout -b pr-$a $a
20-
git fetch --unshallow --all
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git checkout -q test_head
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if git merge --no-edit --squash -q pr-$a; then
23-
echo "::endgroup::"
24-
if git commit -q -m "Merge https://github.com/$REPO/pull/$a" -a --no-allow-empty; then
25-
echo "Merged #$a"
2+
# Apply open PRs labeled "blocker" from sagemath/sage as patches.
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# This script is invoked by various workflows in .github/workflows
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#
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# The repository variable SAGE_CI_FIXES_FROM_REPOS can be set
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# to customize this for CI runs in forks:
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#
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# - If set to a whitespace-separated list of repositories, use them instead of sagemath/sage.
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# - If set to "none", do not apply any PRs.
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#
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# https://docs.github.com/en/actions/learn-github-actions/variables#creating-configuration-variables-for-a-repository
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export GIT_AUTHOR_NAME="ci-sage workflow"
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export GIT_AUTHOR_EMAIL="[email protected]"
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export GIT_COMMITTER_NAME="$GIT_AUTHOR_NAME"
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export GIT_COMMITTER_EMAIL="$GIT_AUTHOR_EMAIL"
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mkdir -p upstream
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for REPO in ${SAGE_CI_FIXES_FROM_REPOSITORIES:-sagemath/sage}; do
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case $REPO in
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none)
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echo "Nothing to do for 'none' in SAGE_CI_FIXES_FROM_REPOSITORIES"
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;;
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*/*)
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echo "Getting open PRs with 'blocker' status from https://github.com/$REPO/pulls?q=is%3Aopen+label%3A%22p%3A+blocker+%2F+1%22"
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GH="gh -R $REPO"
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REPO_FILE="upstream/ci-fixes-${REPO%%/*}-${REPO##*/}"
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PRs="$($GH pr list --label "p: blocker / 1" --json number --jq '.[].number' | tee $REPO_FILE)"
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date -u +"%Y-%m-%dT%H:%M:%SZ" > $REPO_FILE.date # Record the date, for future reference
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if [ -z "$PRs" ]; then
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echo "Nothing to do: Found no open PRs with 'blocker' status in $REPO."
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else
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echo "Empty, skipped"
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echo "Found open PRs with 'blocker' status in $REPO: $(echo $PRs)"
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git tag -f test_base
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git commit -q -m "Uncommitted changes" --no-allow-empty -a
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for a in $PRs; do
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# We used to pull the branch and merge it (after unshallowing), but when run on PRs that are
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# based on older releases, it has the side effect of updating to this release,
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# which may be confusing.
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#
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# Here, we obtain the "git am"-able patch of the PR branch.
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# This also makes it unnecessary to unshallow the repository.
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#
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# Considered alternative: Use https://github.com/$REPO/pull/$a.diff,
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# which squashes everything into one diff without commit metadata.
44+
PULL_URL="https://github.com/$REPO/pull/$a"
45+
PULL_FILE="$REPO_FILE-$a"
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PATH=build/bin:$PATH build/bin/sage-download-file --quiet "$PULL_URL.patch" $PULL_FILE.patch
47+
date -u +"%Y-%m-%dT%H:%M:%SZ" > $PULL_FILE.date # Record the date, for future reference
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LAST_SHA=$(sed -n -E '/^From [0-9a-f]{40}/s/^From ([0-9a-f]{40}).*/\1/p' $PULL_FILE.patch | tail -n 1)
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COMMITS_URL="https://github.com/$REPO/commits/$LAST_SHA"
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echo "::group::Applying PR $PULL_URL @ $COMMITS_URL as a patch"
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export GIT_COMMITTER_NAME="$GIT_AUTHOR_NAME applying $PULL_URL @ $COMMITS_URL"
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if git am --signoff --empty=keep < $PULL_FILE.patch; then
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echo "---- Applied patch --------------------------------------------------------------------------------"
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cat $PULL_FILE.patch
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echo "--------------------------------------------------------------------8<-----------------------------"
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echo "::endgroup::"
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elif git am --abort \
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&& if git fetch --unshallow --all > /dev/null 2>&1; then echo "Unshallowed"; fi \
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&& echo "Retrying with 3-way merge" \
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&& git am --empty=keep --3way < $PULL_FILE.patch; then
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echo "---- Applied patch --------------------------------------------------------------------------------"
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cat $PULL_FILE.patch
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echo "--------------------------------------------------------------------8<-----------------------------"
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echo "::endgroup::"
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else
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echo "---- Failure applying patch -----------------------------------------------------------------------"
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git am --signoff --show-current-patch=diff
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echo "--------------------------------------------------------------------8<-----------------------------"
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echo "::endgroup::"
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echo "Failure applying $PULL_URL as a patch, resetting"
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git am --signoff --abort
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fi
73+
done
2874
fi
29-
else
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echo "::endgroup::"
31-
echo "Failure merging #$a, resetting"
32-
git reset --hard
33-
fi
34-
done
35-
git log test_base..HEAD
36-
fi
75+
;;
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*)
77+
echo "Repository variable SAGE_CI_FIXES_FROM_REPOSITORIES, if set, should be a whitespace-separated list of repositories or 'none'"
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echo "Got: $SAGE_CI_FIXES_FROM_REPOSITORIES"
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exit 1
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;;
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esac
82+
done

‎.ci/protect-secrets.sh

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This file was deleted.

‎.ci/retrofit-worktree.sh

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#!/bin/sh
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if [ $# != 2 ]; then
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echo >&2 "usage: $0 WORKTREE_NAME WORKTREE_DIRECTORY"
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echo >&2 "Ensures that the current working directory is a git repository,"
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echo >&2 "then makes WORKTREE_DIRECTORY a git worktree named WORKTREE_NAME."
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fi
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WORKTREE_NAME="$1"
8+
WORKTREE_DIRECTORY="$2"
9+
10+
export GIT_AUTHOR_NAME="ci-sage workflow"
11+
export GIT_AUTHOR_EMAIL="[email protected]"
12+
export GIT_COMMITTER_NAME="$GIT_AUTHOR_NAME"
13+
export GIT_COMMITTER_EMAIL="$GIT_AUTHOR_EMAIL"
14+
15+
# Set globally for other parts of the workflow
16+
git config --global user.name "$GIT_AUTHOR_NAME"
17+
git config --global user.email "$GIT_AUTHOR_EMAIL"
18+
19+
set -ex
20+
21+
# If actions/checkout downloaded our source tree using the GitHub REST API
22+
# instead of with git (because do not have git installed in our image),
23+
# we first make the source tree a repo.
24+
if [ ! -d .git ]; then git init && git add -A && git commit --quiet -m "new"; fi
25+
26+
# Tag this state of the source tree "new". This is what we want to build and test.
27+
git tag -f new
28+
29+
# Our container image contains a source tree in $WORKTREE_DIRECTORY with a full build of Sage.
30+
# But $WORKTREE_DIRECTORY is not a git repository.
31+
# We make $WORKTREE_DIRECTORY a worktree whose index is at tag "new".
32+
# We then commit the current sources and set the tag "old". (This keeps all mtimes unchanged.)
33+
# Then we update worktree and index with "git reset --hard new".
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# (This keeps mtimes of unchanged files unchanged and mtimes of changed files newer than unchanged files.)
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# Finally we reset the index to "old". (This keeps all mtimes unchanged.)
36+
# The changed files now show up as uncommitted changes.
37+
# The final "git add -N" makes sure that files that were added in "new" do not show
38+
# as untracked files, which would be removed by "git clean -fx".
39+
git worktree add --detach $WORKTREE_NAME
40+
rm -rf $WORKTREE_DIRECTORY/.git && mv $WORKTREE_NAME/.git $WORKTREE_DIRECTORY/
41+
rm -rf $WORKTREE_NAME && ln -s $WORKTREE_DIRECTORY $WORKTREE_NAME
42+
if [ ! -f $WORKTREE_NAME/.gitignore ]; then cp .gitignore $WORKTREE_NAME/; fi
43+
(cd $WORKTREE_NAME && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset --quiet old && git add -N . && git status)

‎.devcontainer/onCreate-conda.sh

Lines changed: 1 addition & 1 deletion
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@@ -4,7 +4,7 @@ set -e
44
# Create conda environment
55
./bootstrap-conda
66
conda install mamba -n base -c conda-forge -y
7-
mamba env create --file src/environment-dev.yml || mamba env update --file src/environment-dev.yml
7+
mamba env create --file src/environment-dev-3.11.yml || mamba env update --file src/environment-dev-3.11.yml
88
conda init bash
99

1010
# Build sage

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