Merge branch 'develop' into fix-is-valid-lex-BFS-order-undirected

vbraun · Jul 22, 2024 · 03cbae8 · 03cbae8
2 parents 73c6e1c + b6c1456
commit 03cbae8
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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
@@ -19,7 +17,9 @@ 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 => {

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"
     },

diff --git a/.github/workflows/ci-conda.yml b/.github/workflows/ci-conda.yml
@@ -18,15 +18,16 @@ concurrency:
 jobs:
   test:
     name: Conda
-    runs-on: ${{ matrix.os }}-latest
+    runs-on: ${{ matrix.os }}
 
     strategy:
+      fail-fast: false
       matrix:
         # On pushes to tags or branches, test the whole matrix.
         os: >-
           ${{ github.event_name == 'pull_request'
-                && fromJson('["ubuntu"]')
-                || fromJson('["ubuntu", "macos"]') }}
+                && fromJson('["ubuntu-latest"]')
+                || fromJson('["ubuntu-latest", "macos-latest", "macos-13"]') }}
         python: >-
           ${{ github.event_name == 'pull_request'
                 && fromJson('["3.9"]')
@@ -35,12 +36,12 @@ jobs:
         # environment: [environment, environment-optional]
         conda-env: [environment]
         # On pull requests, only test two jobs:
-        # Ubuntu with Python 3.9, macOS with Python 3.11.
+        # Ubuntu with Python 3.9, macOS (arm64) with Python 3.11.
         # Build & Test currently uses Python 3.10 (on ubuntu-jammy).
         # Together, they cover the supported minor Python versions.
         include: >-
           ${{ github.event_name == 'pull_request'
-                && fromJson('[{"os": "macos", "python": "3.11", "conda-env": "environment"}]')
+                && fromJson('[{"os": "macos-latest", "python": "3.11", "conda-env": "environment"}]')
                 || fromJson('[]') }}
 
     steps:
@@ -69,7 +70,7 @@ jobs:
           channels: conda-forge
           channel-priority: true
           activate-environment: sage
-          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}-${{ startsWith(matrix.os, 'macos') && 'macos' || 'linux' }}.yml
+          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}-${{ startsWith(matrix.os, 'macos') && (startsWith(runner.arch, 'ARM') && 'macos' || 'macos-x86_64') || 'linux' }}.yml
 
       - name: Print Conda environment
         shell: bash -l {0}
@@ -89,8 +90,8 @@ jobs:
           # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda.
           pip install --no-build-isolation --no-deps --config-settings editable_mode=compat -v -v -e ./src
         env:
-          SAGE_NUM_THREADS: 2
-        
+          SAGE_NUM_THREADS: 5
+
       - name: Verify dependencies
         if: success() || failure()
         shell: bash -l {0}

diff --git a/.github/workflows/conda-lock-update.py b/.github/workflows/conda-lock-update.py
@@ -11,8 +11,8 @@
 platforms = {
     "linux-64": "linux",
     "linux-aarch64": "linux-aarch64",
-    "osx-64": "macos",
-    "osx-arm64": "macos-arm64"
+    "osx-64": "macos-x86_64",
+    "osx-arm64": "macos"
     #"win-64": "win",
 }
 pythons = ["3.9", "3.10", "3.11"]

diff --git a/.github/workflows/doc-build-pdf.yml b/.github/workflows/doc-build-pdf.yml
@@ -30,7 +30,7 @@ env:
   EXTRA_CONFIGURE_ARGS:   --enable-fat-binary
 
 jobs:
-  build-docs-pdf:
+  build-doc-pdf:
     runs-on: ubuntu-latest
     services:
       # https://docs.docker.com/build/ci/github-actions/local-registry/
@@ -110,7 +110,9 @@ jobs:
                      --workdir $(pwd) \
                      ${{ env.BUILD_IMAGE }} /bin/sh
 
-      # Docs
+      #
+      # On PRs and pushes to branches
+      #
 
       - name: Update system packages
         id: packages
@@ -122,29 +124,27 @@ jobs:
           eval $(sage-print-system-package-command auto --spkg --yes --no-install-recommends install git texlive texlive_luatex free_fonts xindy)
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
-      - name: Build docs (PDF)
+      - name: Build doc (PDF)
         id: docbuild
         if: (success() || failure()) && steps.packages.outcome == 'success'
         run: |
           export MAKE="make -j5 --output-sync=recurse" SAGE_NUM_THREADS=5
           make doc-clean doc-uninstall; make sagemath_doc_html-build-deps sagemath_doc_pdf-no-deps
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
-      - name: Copy docs
+      - name: Copy doc
         id: copy
         if: (success() || failure()) && steps.docbuild.outcome == 'success'
         run: |
-          # For some reason the deploy step below cannot find /sage/...
-          # So copy everything from there to local folder
-          mkdir -p ./docs
-          cp -r -L /sage/local/share/doc/sage/pdf ./docs
+          mkdir -p ./doc
+          # We copy everything to a local folder
+          docker cp BUILD:/sage/local/share/doc/sage/pdf doc
           # Zip everything for increased performance
-          zip -r docs-pdf.zip docs
-        shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
+          zip -r doc-pdf.zip doc
 
-      - name: Upload docs
+      - name: Upload doc
         if: (success() || failure()) && steps.copy.outcome == 'success'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: docs-pdf
-          path: docs-pdf.zip
+          name: doc-pdf
+          path: doc-pdf.zip
diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml
@@ -4,8 +4,15 @@ on:
   pull_request:
   merge_group:
   push:
+    tags:
+      # Match all release tags including beta, rc
+      - '[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.beta[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+.beta[0-9]+'
+      - '[0-9]+.[0-9]+.rc[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+.rc[0-9]+'
     branches:
-      - master
       - develop
   workflow_dispatch:
     # Allow to run manually
@@ -34,7 +41,7 @@ env:
   EXTRA_CONFIGURE_ARGS:   --enable-fat-binary
 
 jobs:
-  build-docs:
+  build-doc:
     runs-on: ubuntu-latest
     services:
       # https://docs.docker.com/build/ci/github-actions/local-registry/
@@ -114,38 +121,50 @@ jobs:
                      --workdir $(pwd) \
                      ${{ env.BUILD_IMAGE }} /bin/sh
 
-      # Docs
+      #
+      # On PRs and pushes to develop
+      #
 
-      - name: Store old docs
+      - name: Store old doc
         id: worktree
-        if: (success() || failure()) && steps.container.outcome == 'success'
+        if: (success() || failure()) && steps.container.outcome == 'success' && !startsWith(github.ref, 'refs/tags/')
         run: |
           git config --global --add safe.directory $(pwd)
           git config --global user.email "ci-sage@example.com"
           git config --global user.name "Build documentation workflow"
-          # mathjax path in old doc (regex)
-          mathjax_path_from="[-./A-Za-z_]*/tex-chtml[.]js?v=[0-9a-f]*"
-          # mathjax path in new doc
-          mathjax_path_to=$(docker exec -e SAGE_USE_CDNS=yes BUILD /sage/sage -python -c "from sage_docbuild.conf import mathjax_path; print(mathjax_path)")
-          new_version=$(docker exec BUILD cat src/VERSION.txt)
-          mkdir -p docs/
-          docker cp BUILD:/sage/local/share/doc/sage/html docs/
-          # Wipe out chronic diffs of old doc against new doc
-          (cd docs && \
-           find . -name "*.html" | xargs sed -i -e '/class="sidebar-brand-text"/ s/Sage [0-9a-z.]* /Sage '"$new_version"' /' \
-                                                -e '/<link rel="stylesheet"/ s/?v=[0-9a-f]*"/"/' \
-                                                -e 's;'"$mathjax_path_from"';'"$mathjax_path_to"';' \
-                                                -e '\;<script type="application/vnd\.jupyter\.widget-state+json">;,\;</script>; d')
-          # Create git repo from old doc
-          (cd docs && \
-           git init && \
-           (echo "*.svg binary"; echo "*.pdf binary") >> .gitattributes && \
-           (echo ".buildinfo"; echo '*.inv'; echo '.git*'; echo '*.svg'; echo '*.pdf'; echo '*.png'; echo 'searchindex.js') > .gitignore; \
-           git add -A && git commit --quiet -m "old")
-
-      - name: Build docs
+          mkdir -p doc
+          # Check if we are on PR
+          PR_NUMBER=""
+          if [[ -n "$GITHUB_REF" ]]; then
+            if [[ "$GITHUB_REF" =~ refs/pull/([0-9]+)/merge ]]; then
+              PR_NUMBER="${BASH_REMATCH[1]}"
+            fi
+          fi
+          # If so, then prepare to create CHANGES.html
+          if [[ -n "$PR_NUMBER" ]]; then
+            # mathjax path in old doc (regex)
+            mathjax_path_from="[-./A-Za-z_]*/tex-chtml[.]js?v=[0-9a-f]*"
+            # mathjax path in new doc
+            mathjax_path_to=$(docker exec -e SAGE_USE_CDNS=yes BUILD /sage/sage -python -c "from sage_docbuild.conf import mathjax_path; print(mathjax_path)")
+            new_version=$(docker exec BUILD cat src/VERSION.txt)
+            docker cp BUILD:/sage/local/share/doc/sage/html doc/
+            # Wipe out chronic diffs between old doc and new doc
+            (cd doc && \
+             find . -name "*.html" | xargs sed -i -e '/class="sidebar-brand-text"/ s/Sage [0-9a-z.]* /Sage '"$new_version"' /' \
+                                                  -e '/<link rel="stylesheet"/ s/?v=[0-9a-f]*"/"/' \
+                                                  -e 's;'"$mathjax_path_from"';'"$mathjax_path_to"';' \
+                                                  -e '\;<script type="application/vnd\.jupyter\.widget-state+json">;,\;</script>; d')
+            # Create git repo from old doc
+            (cd doc && \
+             git init && \
+             (echo "*.svg binary"; echo "*.pdf binary") >> .gitattributes && \
+             (echo ".buildinfo"; echo '*.inv'; echo '.git*'; echo '*.svg'; echo '*.pdf'; echo '*.png'; echo 'searchindex.js') > .gitignore; \
+             git add -A && git commit --quiet -m 'old')
+          fi
+
+      - name: Build doc
         id: docbuild
-        if: (success() || failure()) && steps.worktree.outcome == 'success'
+        if: (success() || failure()) && steps.worktree.outcome == 'success' && !startsWith(github.ref, 'refs/tags/')
         # Always non-incremental because of the concern that
         # incremental docbuild may introduce broken links (inter-file references) though build succeeds
         run: |
@@ -157,50 +176,57 @@ jobs:
           ./config.status && make sagemath_doc_html-no-deps
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
-      - name: Copy docs
+      - name: Copy doc
         id: copy
         if: (success() || failure()) && steps.docbuild.outcome == 'success'
         run: |
           set -ex
           # We copy everything to a local folder
-          docker cp BUILD:/sage/local/share/doc/sage/html docs
-          docker cp BUILD:/sage/local/share/doc/sage/index.html docs
-          (cd docs && git commit -a -m 'new')
-          # Wipe out chronic diffs of new doc against old doc
-          (cd docs && \
-           find . -name "*.html" | xargs sed -i -e '/This is documentation for/ s/ built with GitHub PR .*. Doc/. Doc/' \
-                                                -e '/<link rel="stylesheet"/ s/?v=[0-9a-f]*"/"/')
-          .ci/create-changes-html.sh $(cd docs && git rev-parse HEAD^) docs
-          # Restore the new doc from changes by "wipe out"
-          (cd docs && git checkout -f)
-          (cd docs && rm -rf .git)
-          mv CHANGES.html docs
-          # We also need to replace the symlinks because netlify is not following them
-          # CHECK IF STILL NEEDED
-          #cp -r -L $DOC_DIR ./docs
+          docker cp --follow-link BUILD:/sage/local/share/doc/sage/html doc
+          docker cp --follow-link BUILD:/sage/local/share/doc/sage/index.html doc
+          # Check if we are on PR
+          PR_NUMBER=""
+          if [[ -n "$GITHUB_REF" ]]; then
+            if [[ "$GITHUB_REF" =~ refs/pull/([0-9]+)/merge ]]; then
+              PR_NUMBER="${BASH_REMATCH[1]}"
+            fi
+          fi
+          # If so, then create CHANGES.html
+          if [[ -n "$PR_NUMBER" ]]; then
+            (cd doc && git commit -a -m 'new')
+            # Wipe out chronic diffs of new doc against old doc before creating CHANGES.html
+            (cd doc && \
+             find . -name "*.html" | xargs sed -i -e '/This is documentation/ s/ built with GitHub PR .* for development/ for development/' \
+                                                  -e '/<link rel="stylesheet"/ s/?v=[0-9a-f]*"/"/' \
+                                                  -e '\;<script type="application/vnd\.jupyter\.widget-state+json">;,\;</script>; d' \
+             && git commit -a -m 'wipe-out')
+            # Since HEAD is at commit 'wipe-out', HEAD~1 is commit 'new' (new doc), HEAD~2 is commit 'old' (old doc)
+            .ci/create-changes-html.sh $(cd doc && git rev-parse HEAD~2) doc
+            # Restore the new doc with changes made in create-changes-html.sh but dropping changes by "wipe out"
+            (cd doc && git stash -q && git checkout -q -f HEAD~1 && git stash pop -q)
+            # Sometimes rm -rf .git errors out because of some diehard hidden files
+            # So we simply move it out of the doc directory
+            (cd doc && mv .git ../git && mv .gitattributes ../gitattributes)
+            mv CHANGES.html doc
+          fi
           # Zip everything for increased performance
-          zip -r docs.zip docs
+          zip -r doc.zip doc
 
-      - name: Upload docs
+      - name: Upload doc
         id: upload
         if: (success() || failure()) && steps.copy.outcome == 'success'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: docs
-          path: docs.zip
+          name: doc
+          path: doc.zip
 
-      - name: Save space
-        id: savespace
-        if: (success() || failure()) && steps.upload.outcome == 'success' && github.repository == 'sagemath/sage' && github.ref == 'refs/heads/develop'
-        run: |
-          set -ex
-          # Save space on runner device before we start to build livedoc
-          rm -rf docs/
-          rm -f docs.zip
+      #
+      # On release tags: live doc and wheels
+      #
 
       - name: Build live doc
         id: buildlivedoc
-        if: (success() || failure()) && steps.savespace.outcome == 'success'
+        if: (success() || failure()) && startsWith(github.ref, 'refs/tags/')
         run: |
           export MAKE="make -j5 --output-sync=recurse" SAGE_NUM_THREADS=5
           export PATH="build/bin:$PATH"
@@ -222,12 +248,12 @@ jobs:
           # We copy everything to a local folder
           docker cp --follow-link BUILD:/sage/local/share/doc/sage/html livedoc
           docker cp --follow-link BUILD:/sage/local/share/doc/sage/pdf livedoc
-          docker cp BUILD:/sage/local/share/doc/sage/index.html livedoc
+          docker cp --follow-link BUILD:/sage/local/share/doc/sage/index.html livedoc
           zip -r livedoc.zip livedoc
 
       - name: Upload live doc
         if: (success() || failure()) && steps.copylivedoc.outcome == 'success'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: livedoc
           path: livedoc.zip