Merge branch 'jupyter_sphinx_optional' into binary_wheels

sagemath · Aug 4, 2024 · fdc5453 · fdc5453
2 parents bce80f9 + 93a2b83
commit fdc5453
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diff --git a/.ci/create-changes-html.sh b/.ci/create-changes-html.sh
@@ -8,8 +8,6 @@ fi
 BASE_DOC_COMMIT="$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
@@ -19,31 +17,34 @@ 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);
   });
 });
 });
@@ -54,39 +55,51 @@ echo '<body>' >> CHANGES.html
 (cd $DOC_REPOSITORY && git diff $BASE_DOC_COMMIT -- "*.html") > diff.txt
 python3 - << EOF
 import os, re, html
+from itertools import chain
 with open('diff.txt', 'r') as f:
     diff_text = f.read()
 diff_blocks = re.split(r'^(?=diff --git)', diff_text, flags=re.MULTILINE)
 out_blocks = []
 for block in diff_blocks:
     match = re.search(r'^diff --git a/(.*) b/\1', block, flags=re.MULTILINE)
     if match:
-        doc = match.group(1)
-        file_path = os.path.join('$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('<'):
+                    span = int(search_result.group(4))
+                    for i in chain(range(line_number, line_number + span), range(line_number - 1, -1, -1)):
+                        if content[i].startswith('<') and not content[i].startswith('</'):
                             count += 1
                             content[i] = f'<span id="hunk{count}" style="visibility: hidden;"></span>' + content[i]
+                            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)

diff --git a/.ci/set_labels_by_changes.sh b/.ci/set_labels_by_changes.sh
diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh
@@ -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
 $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-conda configure.ac sage .homebrew-build-env tox.ini Pipfile.m4 .gitignore /new/
@@ -295,7 +301,7 @@ WORKDIR /sage
 ARG BOOTSTRAP="${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"

diff --git a/.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/devcontainer.json b/.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/devcontainer.json
diff --git a/.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/portability-Dockerfile b/.devcontainer/portability-centos-7-devtoolset-gcc_11-minimal/portability-Dockerfile
diff --git a/.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/devcontainer.json b/.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/devcontainer.json
diff --git a/.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/portability-Dockerfile b/.devcontainer/portability-centos-7-devtoolset-gcc_11-standard/portability-Dockerfile
diff --git a/.github/workflows/ci-conda-known-test-failures.json b/.github/workflows/ci-conda-known-test-failures.json
@@ -53,6 +53,12 @@
     "sage.rings.function_field.drinfeld_modules.morphism": {
         "failed": "unreported random failure seen in https://github.com/sagemath/sage/actions/runs/6840502530/job/18599835766#step:11:10107"
     },
+    "sage.rings.number_field.galois_group": {
+        "failed": "unreported failure on macOS (sort order) in GaloisGroup_v2.artin_symbol, https://github.com/sagemath/sage/actions/runs/9525536510/job/26259809272?pr=37998"
+    },
+    "sage.rings.number_field.number_field": {
+        "failed": "unreported failure on macOS (sort order) in NumberField_absolute.[optimized_]subfields, https://github.com/sagemath/sage/actions/runs/9525536510/job/26259809272?pr=37998"
+    },
     "sage.rings.polynomial.multi_polynomial_ideal": {
         "failed": true
     },
@@ -65,6 +71,9 @@
     "sage.rings.polynomial.skew_polynomial_finite_field": {
         "failed": true
     },
+    "sage.rings.qqbar": {
+        "failed": "unreported failure on macOS seen in https://github.com/sagemath/sage/actions/runs/9525536510/job/26259809272?pr=37998"
+    },
     "sage.schemes.elliptic_curves.descent_two_isogeny": {
         "failed": "random segfault (macOS) https://github.com/sagemath/sage/issues/36949"
     },