sagemathgh-37819: igraph: Update to 0.10.12, fix spkg-check; `pytho…

…n_igraph`: Update to 0.11.5, remove spkg-install workarounds

    
<!-- ^ Please provide a concise and informative title. -->
<!-- ^ Don't put issue numbers in the title, do this in the PR
description below. -->
<!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method
to calculate 1 + 2". -->
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<!-- v If this PR resolves an open issue, please link to it here. For
example, "Fixes sagemath#12345". -->

### 📝 Checklist

- https://github.com/igraph/python-igraph/blob/main/CHANGELOG.md

Increasing the lower bound for system `cmake` to 3.18. This will cause
system cmake on ubuntu-focal to be rejected, so cmake will be built from
source on this platform. https://repology.org/project/cmake/versions

<!-- Put an `x` in all the boxes that apply. -->

- [x] The title is concise and informative.
- [ ] The description explains in detail what this PR is about.
- [ ] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation and checked the documentation
preview.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on. For example,
-->
<!-- - sagemath#12345: short description why this is a dependency -->
<!-- - sagemath#34567: ... -->

- sagemath#38144 (merged here for testing)
    
URL: sagemath#37819
Reported by: Matthias Köppe
Reviewer(s): David Coudert

.ci/retrofit-worktree.sh

@@ -23,9 +23,10 @@ set -x
 # If actions/checkout downloaded our source tree using the GitHub REST API
 # instead of with git (because do not have git installed in our image),
 # we first make the source tree a repo.
-if [ ! -d .git ]; then git init && git add -A && git commit --quiet -m "new"; fi
+if [ ! -d .git ]; then git init; fi
 
-# Tag this state of the source tree "new". This is what we want to build and test.
+# Commit and tag this state of the source tree "new". This is what we want to build and test.
+git add -A && git commit --quiet --allow-empty -m "new"
 git tag -f new
 
 # Our container image contains a source tree in $WORKTREE_DIRECTORY with a full build of Sage.

.ci/write-dockerfile.sh

@@ -264,6 +264,7 @@ cat <<EOF
 
 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/
 $ADD config/config.rpath /new/config/config.rpath
 $ADD src/doc/bootstrap /new/src/doc/bootstrap
@@ -338,7 +339,6 @@ ENV SAGE_CHECK=warn
 ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
 $ADD .gitignore /new/.gitignore
 $ADD src /new/src
-ADD .ci /.ci
 RUN cd /new && rm -rf .git && \
     if /.ci/retrofit-worktree.sh worktree-pre /sage; then \
         cd /sage && touch configure build/make/Makefile; \
@@ -347,7 +347,8 @@ RUN cd /new && rm -rf .git && \
         rm -rf /sage/src;                                    \
         mv src /sage/src;                                    \
         cd /sage && ./bootstrap && ./config.status;          \
-    fi
+    fi; \
+    cd /sage && rm -rf /new .git
 
 ARG TARGETS="build"
 $RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS} $ENDRUN $THEN_SAVE_STATUS

.github/workflows/build.yml

@@ -78,6 +78,8 @@ env:
 jobs:
   test-new:
     runs-on: ubuntu-latest
+    outputs:
+      build_targets:     ${{ steps.build-targets.outputs.build_targets }}
     services:
       # https://docs.docker.com/build/ci/github-actions/local-registry/
       registry:
@@ -98,6 +100,46 @@ jobs:
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
+      - name: Get changed files and packages
+        id: changed-files
+        uses: tj-actions/changed-files@v44
+        with:
+          # File extensions for doctests per sage.doctest.control.skipfile
+          files_yaml: |
+            configures:
+              - 'build/pkgs/*/spkg-configure.m4'
+            pkgs:
+              - 'build/pkgs/**'
+              - 'pkgs/**'
+            doctests:
+              - 'src/**/*.{py,pyx,pxd,pxi,sage,spyx,rst,tex}'
+              - '!src/{setup,conftest*}.py'
+      - name: Determine targets to build
+        id: build-targets
+        run: |
+          uninstall_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))
+          build_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))
+          if [ -n "$uninstall_targets" ]; then
+              echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          else
+              echo "build_targets=$build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          fi
+          cat $GITHUB_OUTPUT
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.base_ref }}
+          path: worktree-base
+        if: github.base_ref && steps.changed-files.outputs.pkgs_all_changed_files
+      - name: Compute metrics
+        run: |
+          export PATH=build/bin:$PATH
+          if [ -d worktree-base ]; then
+            (echo "# $GITHUB_BASE_REF"; SAGE_ROOT=worktree-base sage-package metrics :all:) > base-metrics.txt
+            (echo "# $GITHUB_REF"; sage-package metrics :all:) > metrics.txt
+            diff --color=always --width=100 --side-by-side --left-column base-metrics.txt metrics.txt || true
+          else
+            sage-package metrics :all:
+          fi
       - name: Install test prerequisites
         # From docker.yml
         run: |
@@ -142,7 +184,7 @@ jobs:
           # more reliable than "load", for which we observed random failure
           # conditions in which the built image could not be found.
           #
-          push:       true
+          push:       ${{ steps.changed-files.outputs.doctests_all_changed_files && true || false }}
           load:       false
           context:    .
           tags:       ${{ env.BUILD_IMAGE }}
@@ -153,9 +195,12 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ steps.build-targets.outputs.build_targets }}
 
       - name: Start container
+        id: container
+        # Try to continue when "exporting to GitHub Actions Cache" failed with timeout
+        if: (success() || failure()) && steps.changed-files.outputs.doctests_all_changed_files
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -165,6 +210,7 @@ jobs:
       # Testing
 
       - name: Check that all modules can be imported
+        if: (success() || failure()) && steps.container.outcome == 'success' && steps.changed-files.outputs.doctests_all_changed_files
         run: |
           # Increase the length of the lines in the "short summary"
           export COLUMNS=120
@@ -175,20 +221,12 @@ jobs:
           ./sage -python -m pytest -c tox.ini -qq --doctest --collect-only || true
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
-      - name: Get changed files
-        id: changed-files
-        uses: tj-actions/changed-files@v44
-        with:
-          # File extensions per sage.doctest.control.skipfile
-          files: src/**/*.{py,pyx,pxd,pxi,sage,spyx,rst,tex}
-          files_ignore: src/{setup,conftest*}.py
-
       - name: Test changed files (sage -t --new)
-        if: steps.changed-files.outputs.all_changed_files
+        if: (success() || failure()) && steps.container.outcome == 'success' && steps.changed-files.outputs.doctests_all_changed_files
         run: |
           export MAKE="make -j2 --output-sync=recurse" SAGE_NUM_THREADS=4
           # https://github.com/tj-actions/changed-files?tab=readme-ov-file#outputs-
-          ./sage -t --long --format github -p4 ${{ steps.changed-files.outputs.all_changed_files }}
+          ./sage -t --long --format github -p4 ${{ steps.changed-files.outputs.doctests_all_changed_files }}
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
   test-mod:
@@ -266,9 +304,11 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ needs.test-new.outputs.build_targets }}
 
       - name: Start container
+        id: container
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -278,6 +318,7 @@ jobs:
       # Testing
 
       - name: Test modularized distributions
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           export MAKE="make -j2 --output-sync=recurse" SAGE_NUM_THREADS=4
           make V=0 tox-ensure && make ${{ matrix.targets }}
@@ -361,10 +402,11 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ needs.test-new.outputs.build_targets }}
 
       - name: Start container
         id: container
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -374,6 +416,7 @@ jobs:
       # Testing
 
       - name: Test all files (sage -t --long ${{ matrix.tests }})
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           mkdir .coverage
           rm -rf /sage/.coverage
@@ -473,10 +516,11 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ needs.test-new.outputs.build_targets }}
 
       - name: Start container
         id: container
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -490,8 +534,10 @@ jobs:
         with:
           path: .coverage
           pattern: coverage-*
+        if: (success() || failure()) && steps.container.outcome == 'success'
 
       - name: Coverage report
+        if: (success() || failure()) && steps.container.outcome == 'success'
         # Using --omit to avoid "CoverageWarning: Couldn't parse '/tmp/tmp06qizzie/tmp_ldpu46ob.py': No source for code"
         run: |
           rm -rf /sage/.coverage
@@ -505,6 +551,7 @@ jobs:
         shell: sh .ci/docker-exec-script.sh BUILD . {0}
 
       - name: Upload coverage to codecov
+        if: (success() || failure()) && steps.container.outcome == 'success'
         uses: codecov/codecov-action@v4
         with:
           directory: .coverage/coverage-report

.github/workflows/ci-linux-incremental.yml

@@ -41,12 +41,11 @@ jobs:
     runs-on: ubuntu-latest
     name: List changed packages
     outputs:
-      uninstall_targets: ${{ steps.build-targets.outputs.uninstall_targets }}
       build_targets:     ${{ steps.build-targets.outputs.build_targets }}
     steps:
       - uses: actions/checkout@v4
       - name: Get all packages that have changed
-        id: changed-packages
+        id: changed-files
         uses: tj-actions/changed-files@v44
         with:
           files_yaml: |
@@ -58,14 +57,19 @@ jobs:
       - name: Determine targets to build
         id: build-targets
         run: |
-          echo "uninstall_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))" >> $GITHUB_OUTPUT
-          echo "build_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))" >> $GITHUB_OUTPUT
+          uninstall_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))
+          build_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))
+          if [ -n "$uninstall_targets" ]; then
+              echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          else
+              echo "build_targets=$build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          fi
           cat $GITHUB_OUTPUT
       - uses: actions/checkout@v4
         with:
           ref: ${{ github.base_ref }}
           path: worktree-base
-        if: github.base_ref
+        if: github.base_ref && steps.changed-files.outputs.pkgs_all_changed_files
       - name: Compute metrics
         run: |
           export PATH=build/bin:$PATH
@@ -88,15 +92,14 @@ jobs:
       from_docker_target: "with-targets"
       from_docker_tag: "dev"
       docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      targets: "${{needs.changed_files.outputs.build_targets}} doc-html ptest-nodoc"
       tox_system_factors: >-
         ["ubuntu-focal",
-         "ubuntu-jammy",
-         "ubuntu-mantic",
+         "ubuntu-noble",
          "debian-bullseye",
          "debian-bookworm",
          "fedora-30",
-         "fedora-38",
+         "fedora-40",
          "gentoo-python3.11",
          "debian-bullseye-i386"]
       tox_packages_factors: >-
@@ -107,14 +110,6 @@ jobs:
 
   site:
     needs: [changed_files]
-    if: |
-      github.event_name != 'pull_request' ||
-      ((github.event.action != 'labeled' &&
-         (contains(github.event.pull_request.labels.*.name, 'c: packages: standard') ||
-          contains(github.event.pull_request.labels.*.name, 'c: packages: optional'))) ||
-       (github.event.action == 'labeled' &&
-         (github.event.label.name == 'c: packages: optional' ||
-          github.event.label.name == 'c: packages: standard')))
     uses: ./.github/workflows/docker.yml
     with:
       # Build incrementally from published Docker image
@@ -124,7 +119,7 @@ jobs:
       from_docker_target: "with-targets"
       from_docker_tag: "dev"
       docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      targets: "${{needs.changed_files.outputs.build_targets}} doc-html ptest-nodoc"
       # Only test systems with a usable system python (>= 3.9)
       # with only a small number of test failures as of 10.2.rc0
       tox_system_factors: >-

.github/workflows/doc-build-pdf.yml

@@ -101,6 +101,9 @@ jobs:
             TARGETS=ci-build-with-fallback
 
       - name: Start container
+        id: container
+        # Try to continue when "exporting to GitHub Actions Cache" failed with timeout
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -110,6 +113,8 @@ jobs:
       # Docs
 
       - name: Update system packages
+        id: packages
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           export PATH="build/bin:$PATH"
           eval $(sage-print-system-package-command auto update)
@@ -119,6 +124,7 @@ jobs:
 
       - name: Build docs (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

.github/workflows/doc-build.yml

@@ -105,6 +105,9 @@ jobs:
             TARGETS=ci-build-with-fallback
 
       - name: Start container
+        id: container
+        # Try to continue when "exporting to GitHub Actions Cache" failed with timeout
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -115,6 +118,7 @@ jobs:
 
       - name: Store old docs
         id: worktree
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           git config --global --add safe.directory $(pwd)
           git config --global user.email "[email protected]"
@@ -140,6 +144,7 @@ jobs:
 
       - name: Build docs
         id: docbuild
+        if: (success() || failure()) && steps.worktree.outcome == 'success'
         # Always non-incremental because of the concern that
         # incremental docbuild may introduce broken links (inter-file references) though build succeeds
         run: |

build/bin/sage-dist-helpers

@@ -247,9 +247,10 @@ sdh_pip_install() {
                 install_options="$install_options $1"
                 ;;
             -C|--config-settings)
-                build_options="$build_options --config-setting"
                 shift
-                build_options="$build_options $1"
+                # Per 'python -m build --help', options which begin with a hyphen
+                # must be in the form of "--config-setting=--opt(=value)" or "-C--opt(=value)"
+                build_options="$build_options --config-setting=$1"
                 ;;
             *)
                 break

build/pkgs/cmake/spkg-configure.m4

@@ -1,5 +1,5 @@
 SAGE_SPKG_CONFIGURE([cmake], [dnl
-        AC_CACHE_CHECK([for cmake >= 3.11], [ac_cv_path_CMAKE], [dnl
+        AC_CACHE_CHECK([for cmake >= 3.18], [ac_cv_path_CMAKE], [dnl
         dnl Do not accept cmake installed via https://pypi.org/project/cmake/
         dnl in the default user scheme; it will not work in our venv because
         dnl we set PYTHONUSERBASE in sage-env.
@@ -8,7 +8,7 @@ SAGE_SPKG_CONFIGURE([cmake], [dnl
                 cmake_version=`$ac_path_CMAKE --version 2>&1 \
                     | $SED -n -e 's/cmake version *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'`
                 AS_IF([test -n "$cmake_version"], [dnl
-                    AX_COMPARE_VERSION([$cmake_version], [ge], [3.11], [dnl
+                    AX_COMPARE_VERSION([$cmake_version], [ge], [3.18], [dnl
                         ac_cv_path_CMAKE="$ac_path_CMAKE"
                         ac_path_CMAKE_found=:
                     ])

build/pkgs/igraph/checksums.ini

@@ -1,4 +1,4 @@
 tarball=igraph-VERSION.tar.gz
-sha1=40efbd2adf3c1cc0a2bb3e14f4c7898d053f1fe4
-sha256=ac5fa94ae6fd1eace651e4b235e99c056479a5c5d0d641aed30240ac33b19403
+sha1=3789f61beac1f1231f8c3832102dcb2720f2a0c9
+sha256=b011f7f9f38a3e59924cc9ff652e6d33105fa03fcaf3792f47d752626a0a4625
 upstream_url=https://github.com/igraph/igraph/releases/download/VERSION/igraph-VERSION.tar.gz

build/pkgs/igraph/package-version.txt

@@ -1 +1 @@
-0.10.8
+0.10.12

build/pkgs/igraph/spkg-check.in

@@ -1,2 +1,3 @@
 cd src
-$MAKE check
+cd build
+sdh_make_check