sagemath
diff --git a/‎.ci/create-changes-html.sh‎
Lines changed: 50 additions & 28 deletions b/‎.ci/create-changes-html.sh‎
Lines changed: 50 additions & 28 deletions
diff --git a/‎.ci/retrofit-worktree.sh‎
Lines changed: 1 addition & 1 deletion b/‎.ci/retrofit-worktree.sh‎
Lines changed: 1 addition & 1 deletion
diff --git a/‎.ci/set_labels_by_changes.sh‎
Lines changed: 0 additions & 71 deletions b/‎.ci/set_labels_by_changes.sh‎
Lines changed: 0 additions & 71 deletions
diff --git a/‎.ci/write-dockerfile.sh‎
Lines changed: 17 additions & 11 deletions b/‎.ci/write-dockerfile.sh‎
Lines changed: 17 additions & 11 deletions
diff --git a/‎.devcontainer/portability-centos-stream-9-python3.9-minimal/devcontainer.json‎ renamed to ‎.devcontainer/portability-centos-stream-9-minimal/devcontainer.json‎
Lines changed: 2 additions & 2 deletions b/‎.devcontainer/portability-centos-stream-9-python3.9-minimal/devcontainer.json‎ renamed to ‎.devcontainer/portability-centos-stream-9-minimal/devcontainer.json‎
Lines changed: 2 additions & 2 deletions
diff --git a/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/portability-Dockerfile‎ renamed to ‎.devcontainer/portability-centos-stream-9-minimal/portability-Dockerfile‎ b/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/portability-Dockerfile‎ renamed to ‎.devcontainer/portability-centos-stream-9-minimal/portability-Dockerfile‎
diff --git a/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/devcontainer.json‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-minimal/devcontainer.json‎
Lines changed: 2 additions & 2 deletions b/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/devcontainer.json‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-minimal/devcontainer.json‎
Lines changed: 2 additions & 2 deletions
diff --git a/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/portability-Dockerfile‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-minimal/portability-Dockerfile‎ b/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/portability-Dockerfile‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-minimal/portability-Dockerfile‎
diff --git a/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/devcontainer.json‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-standard/devcontainer.json‎
Lines changed: 2 additions & 2 deletions b/‎.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/devcontainer.json‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-standard/devcontainer.json‎
Lines changed: 2 additions & 2 deletions
diff --git a/‎.devcontainer/portability-centos-stream-9-python3.9-minimal/portability-Dockerfile‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-standard/portability-Dockerfile‎ b/‎.devcontainer/portability-centos-stream-9-python3.9-minimal/portability-Dockerfile‎ renamed to ‎.devcontainer/portability-centos-stream-9-python3.12-standard/portability-Dockerfile‎
@@ -1,15 +1,14 @@
 #!/bin/sh
 if [ $# != 2 ]; then
-    echo >&2 "usage: $0 BASE_DOC_COMMIT DOC_REPO"
-    echo >&2 "creates CHANGES.html in the current directory"
-    echo >&2 "for the diffs of DOC_REPO against BASE_DOC_COMMIT"
+    echo >&2 "Usage: $0 DIFF_TEXT DOC_REPO"
+    echo >&2 "This script generates a CHANGES.html file in the current directory"
+    echo >&2 "and adds anchor targets in the documents within DOC_REPO"
+    echo >&2 "based on the diff hunks in the DIFF_TEXT file."
     exit 1
 fi
-BASE_DOC_COMMIT="$1"
+DIFF_TEXT="$1"
 DOC_REPOSITORY="$2"
 
-# Wipe out chronic diffs between old doc and new doc
-(cd $DOC_REPOSITORY && find . -name "*.html" | xargs sed -i -e '\;<script type="application/vnd\.jupyter\.widget-state+json">;,\;</script>; d')
 # Create CHANGES.html
 echo '<html>' > CHANGES.html
 echo '<head>' >> CHANGES.html
@@ -19,79 +18,102 @@ echo '<script>hljs.highlightAll();</script>' >> CHANGES.html
 cat >> CHANGES.html << EOF
 <script>
 document.addEventListener('DOMContentLoaded', () => {
-const baseDocURL = 'https://sagemath.netlify.app'
+// This URL is hardcoded in the file .github/workflows/doc-publish.yml.
+// See NETLIFY_ALIAS of the "Deploy to Netlify" step.
+const baseDocURL = 'https://doc-develop--sagemath.netlify.app'
 const diffSite = 'https://pianomister.github.io/diffsite'
 const diffParagraphs = document.querySelectorAll('p.diff');
 diffParagraphs.forEach(paragraph => {
   const rootURL = window.location.origin;
-  const docAnchor = paragraph.querySelector('a');  // first "a" element
+  const docAnchor = paragraph.querySelector('a');
   const url = new URL(docAnchor.href);
   const path = url.pathname;
   const anchor = document.createElement('a');
   anchor.href = diffSite + '/?url1=' + rootURL + path + '&url2=' + baseDocURL + path;
   anchor.textContent = 'compare with the base';
   anchor.setAttribute('target', '_blank');
+  paragraph.innerHTML += '&nbsp;&nbsp;';
   paragraph.appendChild(anchor);
-  paragraph.innerHTML += '&nbsp;';
-  const hunkAnchors = paragraph.querySelectorAll('a.hunk');
-  hunkAnchors.forEach(hunkAnchor => {
+  const hunks = paragraph.parentNode.querySelectorAll('p.hunk');
+  hunks.forEach(hunk => {
+    const hunkAnchor = hunk.querySelector('a');
     const url = new URL(hunkAnchor.href);
     const path = url.pathname;
     const pathHash = path + url.hash.replace('#', '%23');
     const anchor = document.createElement('a');
     anchor.href = diffSite + '/?url1=' + rootURL + pathHash + '&url2=' + baseDocURL + path;
-    anchor.textContent = hunkAnchor.textContent;
+    anchor.textContent = 'compare with the base';
     anchor.setAttribute('target', '_blank');
-    paragraph.appendChild(anchor);
-    paragraph.innerHTML += '&nbsp;';
+    hunk.innerHTML += '&nbsp;&nbsp;';
+    hunk.appendChild(anchor);
   });
 });
 });
 </script>
 EOF
 echo '</head>' >> CHANGES.html
 echo '<body>' >> CHANGES.html
-(cd $DOC_REPOSITORY && git diff $BASE_DOC_COMMIT -- "*.html") > diff.txt
 python3 - << EOF
 import os, re, html
-with open('diff.txt', 'r') as f:
+from itertools import chain
+with open('$DIFF_TEXT', 'r') as f:
     diff_text = f.read()
 diff_blocks = re.split(r'^(?=diff --git)', diff_text, flags=re.MULTILINE)
 out_blocks = []
 for block in diff_blocks:
     match = re.search(r'^diff --git a/(.*) b/\1', block, flags=re.MULTILINE)
     if match:
-        doc = match.group(1)
-        file_path = os.path.join('$DOC_REPOSITORY', doc)
+        path = match.group(1)
+        file_path = os.path.join('$DOC_REPOSITORY', path)
         try:
             with open(file_path, 'r') as file:
                 content = file.readlines()
         except FileNotFoundError:
             content = []
         count = 0
+        hunks = []
+        hunk_lines = []
+        in_hunk = False
         for line in block.splitlines():
             if line.startswith('@@ -'):
+                if hunk_lines:
+                    hunks.append('<pre><code class="language-diff">'
+                                 + html.escape('\n'.join(hunk_lines)).strip()
+                                 + '</code></pre>')
+                    hunk_lines = []
                 search_result = re.search(r'@@ -(\d+),(\d+) \+(\d+),(\d+)', line)
                 if search_result:
-                    line_number = int(search_result.group(3))
-                    for i in range(line_number - 1, -1, -1):
-                        if content[i].startswith('<'):
+                    line_number = int(search_result.group(3)) - 1
+                    span = int(search_result.group(4))
+                    for i in chain(range(line_number, line_number + span), range(line_number - 1, -1, -1)):
+                        try:
+                            ln = content[i]
+                        except IndexError:
+                            continue
+                        for idx, char in enumerate(ln):
+                            if not char.isspace():
+                                break
+                        else:
+                            idx = len(ln)
+                        if ln.startswith('<', idx) and not ln.startswith('</', idx):
                             count += 1
-                            content[i] = f'<span id="hunk{count}" style="visibility: hidden;"></span>' + content[i]
+                            content[i] = ln[:idx] + f'<span id="hunk{count}" style="visibility: hidden;"></span>' + ln[idx:]
+                            hunks.append(f'<p class="hunk"><a href="{path}#hunk{count}" class="hunk" target="_blank">hunk #{count}</a></p>')
                             break
+            hunk_lines.append(line)
+        if hunk_lines:
+            hunks.append('<pre><code class="language-diff">'
+                          + html.escape('\n'.join(hunk_lines)).strip()
+                          + '</code></pre>')
         if content:
             with open(file_path, 'w') as file:
                 file.writelines(content)
-        path = doc
-        hunks = '&nbsp;'.join(f'<a href="{path}#hunk{i+1}" class="hunk" target="_blank">#{i + 1}</a>' for i in range(count))
-        out_blocks.append(f'<p class="diff"><a href="{path}">{doc}</a>&nbsp;' + hunks + '&emsp;</p>'
-                            + '\n<pre><code class="language-diff">'
-                            + html.escape(block).strip() + '</code></pre>')
+        out_blocks.append(f'<div class="diff"><p class="diff"><a href="{path}">{path}</a></p>\n' + '\n'.join(hunks) + '\n</div>')
 output_text = '\n'.join(out_blocks)
 with open('diff.html', 'w') as f:
     f.write(output_text)
 EOF
 cat diff.html >> CHANGES.html
 echo '</body>' >> CHANGES.html
 echo '</html>' >> CHANGES.html
-rm diff.txt diff.html
+rm diff.html
@@ -43,4 +43,4 @@ git worktree add --detach $WORKTREE_NAME
 rm -rf $WORKTREE_DIRECTORY/.git && mv $WORKTREE_NAME/.git $WORKTREE_DIRECTORY/
 rm -rf $WORKTREE_NAME && ln -s $WORKTREE_DIRECTORY $WORKTREE_NAME
 if [ ! -f $WORKTREE_NAME/.gitignore ]; then cp .gitignore $WORKTREE_NAME/; fi
-(cd $WORKTREE_NAME && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git checkout new && git status)
+(cd $WORKTREE_NAME && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git checkout -f new && git clean -fd && git status)
@@ -55,7 +55,7 @@ ADD="ADD $__CHOWN"
 RUN=RUN
 cat <<EOF
 ARG BASE_IMAGE=$(eval echo "${FULL_BASE_IMAGE_AND_TAG}")
-FROM \${BASE_IMAGE} as with-system-packages
+FROM \${BASE_IMAGE} AS with-system-packages
 EOF
 case $SYSTEM in
     debian*|ubuntu*)
@@ -199,7 +199,7 @@ EOF
     *)
         cat <<EOF
 ARG BASE_IMAGE
-FROM \${BASE_IMAGE} as with-system-packages
+FROM \${BASE_IMAGE} AS with-system-packages
 EOF
         INSTALL=$(sage-print-system-package-command $SYSTEM install " ")
         ;;
@@ -260,9 +260,15 @@ case ${DOCKER_BUILDKIT-0} in
         CHECK_STATUS_THEN='STATUS=$(cat STATUS 2>/dev/null); case "$STATUS" in ""|0) ;; *) exit $STATUS;; esac; '
 esac
 
+if [ -n "$GITHUB_ACTIONS" ]; then
+    cat <<EOF
+ENV GITHUB_ACTIONS=1
+EOF
+fi
+
 cat <<EOF
 
-FROM with-system-packages as bootstrapped
+FROM with-system-packages AS bootstrapped
 #:bootstrapping:
 RUN rm -rf /new /sage/.git
 $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-conda configure.ac sage .homebrew-build-env tox.ini Pipfile.m4 .gitignore /new/
@@ -277,8 +283,8 @@ $ADD .upstream.d /new/.upstream.d
 ADD .ci /.ci
 RUN if [ -d /sage ]; then                                               \
         echo "### Incremental build from \$(cat /sage/VERSION.txt)" &&  \
-        printf '/src\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /sage/.gitignore && \
-        printf '/src\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /new/.gitignore && \
+        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /sage/.gitignore && \
+        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /new/.gitignore && \
         if ! (cd /new && /.ci/retrofit-worktree.sh worktree-image /sage); then \
             echo "retrofit-worktree.sh failed, falling back to replacing /sage"; \
             for a in local logs; do                                     \
@@ -295,7 +301,7 @@ WORKDIR /sage
 ARG BOOTSTRAP="${BOOTSTRAP-./bootstrap}"
 $RUN sh -x -c "\${BOOTSTRAP}" $ENDRUN $THEN_SAVE_STATUS
 
-FROM bootstrapped as configured
+FROM bootstrapped AS configured
 #:configuring:
 RUN $CHECK_STATUS_THEN mkdir -p logs/pkgs; rm -f config.log; ln -s logs/pkgs/config.log config.log
 ARG CONFIGURE_ARGS="${CONFIGURE_ARGS:---enable-build-as-root}"
@@ -311,7 +317,7 @@ EOF
 fi
 cat <<EOF
 
-FROM configured as with-base-toolchain
+FROM configured AS with-base-toolchain
 # We first compile base-toolchain because otherwise lots of packages are missing their dependency on 'patch'
 ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
@@ -321,7 +327,7 @@ ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!
 #:toolchain:
 $RUN $CHECK_STATUS_THEN make \${USE_MAKEFLAGS} base-toolchain $ENDRUN $THEN_SAVE_STATUS
 
-FROM with-base-toolchain as with-targets-pre
+FROM with-base-toolchain AS with-targets-pre
 ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
@@ -331,7 +337,7 @@ ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!
 ARG TARGETS_PRE="all-sage-local"
 $RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_PRE} $ENDRUN $THEN_SAVE_STATUS
 
-FROM with-targets-pre as with-targets
+FROM with-targets-pre AS with-targets
 ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
@@ -348,12 +354,12 @@ RUN cd /new && rm -rf .git && \
         mv src /sage/src;                                    \
         cd /sage && ./bootstrap && ./config.status;          \
     fi; \
-    cd /sage && rm -rf /new .git
+    cd /sage && rm -rf .git; rm -rf /new || echo "(error ignored)"
 
 ARG TARGETS="build"
 $RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS} $ENDRUN $THEN_SAVE_STATUS
 
-FROM with-targets as with-targets-optional
+FROM with-targets AS with-targets-optional
 ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "centos-stream-9-python3.9-minimal (≥ 8-core)",
+    "name": "centos-stream-9-minimal (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "centos-stream-9-python3.9",
+            "SYSTEM_FACTOR": "centos-stream-9",
             "PACKAGE_FACTOR": "minimal",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"
 
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "centos-7-devtoolset-gcc_11-minimal (≥ 8-core)",
+    "name": "centos-stream-9-python3.12-minimal (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "centos-7-devtoolset-gcc_11",
+            "SYSTEM_FACTOR": "centos-stream-9-python3.12",
             "PACKAGE_FACTOR": "minimal",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"
 
@@ -3,12 +3,12 @@
 //      from .devcontainer/portability-devcontainer.json.in
 // See https://aka.ms/devcontainer.json for format details.
 {
-    "name": "centos-7-devtoolset-gcc_11-standard (≥ 8-core)",
+    "name": "centos-stream-9-python3.12-standard (≥ 8-core)",
     "build": {
         "dockerfile": "portability-Dockerfile",
         // See tox.ini for definitions
         "args": {
-            "SYSTEM_FACTOR": "centos-7-devtoolset-gcc_11",
+            "SYSTEM_FACTOR": "centos-stream-9-python3.12",
             "PACKAGE_FACTOR": "standard",
             "DOCKER_TARGET": "with-targets",
             "DOCKER_TAG": "dev"