diff --git a/.ci/retrofit-worktree.sh b/.ci/retrofit-worktree.sh index eba1b674ecb..4c283f7ff4a 100755 --- a/.ci/retrofit-worktree.sh +++ b/.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. diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh index 67ef594729c..3a4ae5b152d 100755 --- a/.ci/write-dockerfile.sh +++ b/.ci/write-dockerfile.sh @@ -264,6 +264,7 @@ cat <> $GITHUB_OUTPUT + else + echo "build_targets=$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 diff --git a/.github/workflows/ci-linux-incremental.yml b/.github/workflows/ci-linux-incremental.yml index 88a31a5ce42..ce468ff3a42 100644 --- a/.github/workflows/ci-linux-incremental.yml +++ b/.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: >- diff --git a/.github/workflows/doc-build-pdf.yml b/.github/workflows/doc-build-pdf.yml index d4cc6ebc6ca..2eac8e17ffc 100644 --- a/.github/workflows/doc-build-pdf.yml +++ b/.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 $(sage-print-system-package-command auto update) @@ -119,6 +124,7 @@ jobs: - name: Build docs (PDF) id: docbuild + if: (success() || failure()) && steps.packages.outcome == 'success' run: | export MAKE="make -j5 --output-sync=recurse" SAGE_NUM_THREADS=5 make doc-clean doc-uninstall; make sagemath_doc_html-build-deps sagemath_doc_pdf-no-deps diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml index 4d0420874b8..f47dac38d57 100644 --- a/.github/workflows/doc-build.yml +++ b/.github/workflows/doc-build.yml @@ -105,6 +105,9 @@ jobs: TARGETS=ci-build-with-fallback - name: Start container + id: container + # Try to continue when "exporting to GitHub Actions Cache" failed with timeout + if: (success() || failure()) run: | docker run --name BUILD -dit \ --mount type=bind,src=$(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 "ci-sage@example.com" @@ -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: | diff --git a/build/pkgs/tdlib/SPKG.rst b/build/pkgs/tdlib/SPKG.rst index ebcdd1213e0..9f4c30a3d01 100644 --- a/build/pkgs/tdlib/SPKG.rst +++ b/build/pkgs/tdlib/SPKG.rst @@ -1,32 +1,23 @@ -tdlib: Algorithms for computing tree decompositions -=================================================== +tdlib: Algorithms for computing tree decompositions of graphs +============================================================= Description ----------- -Providing algorithms concerning treedecompositions +This library, now known as treedec, +provides algorithms concerning tree decompositions. -website: https://github.com/freetdi/tdlib License ------- -GNU General Public License v2 - - -SPKG Maintainers ----------------- - -Lukas Larisch (lukas.larisch@kaust.edu.sa) +- GNU General Public License v2 +- GNU General Public License v3 Upstream Contact ---------------- -- Lukas Larisch (lukas.larisch@kaust.edu.sa) -- git-repo: https://github.com/freetdi/tdlib - -Dependencies ------------- - -- None +- https://gitlab.com/freetdi/treedec +- https://github.com/freetdi/tdlib +- https://github.com/felix-salfelder diff --git a/build/pkgs/tdlib/checksums.ini b/build/pkgs/tdlib/checksums.ini index 6f3275ad092..36ade31259e 100644 --- a/build/pkgs/tdlib/checksums.ini +++ b/build/pkgs/tdlib/checksums.ini @@ -1,3 +1,4 @@ -tarball=tdlib-VERSION.tar.gz -sha1=8e200d0e3ac009030f3ada6658d20717e433220f -sha256=5a40375e738e9e6dbd37f53e54deb1efa6b58f154d83b7bfeaee9f47d47b444b +tarball=treedec-VERSION.tar.gz +sha1=355930ce66a14afed89d32ead280bfdd801d53d7 +sha256=16f9683af4c33e3e79fe36439cb4bb4b63216ad88d59f5dc00dd3fb9256aa4ae +upstream_url=https://www.algok.uni-bamberg.de/treedec/treedec-VERSION.tar.gz diff --git a/build/pkgs/tdlib/dependencies b/build/pkgs/tdlib/dependencies new file mode 100644 index 00000000000..d568ea3cf53 --- /dev/null +++ b/build/pkgs/tdlib/dependencies @@ -0,0 +1 @@ +boost_cropped diff --git a/build/pkgs/tdlib/package-version.txt b/build/pkgs/tdlib/package-version.txt index af2629893df..998ed53f13a 100644 --- a/build/pkgs/tdlib/package-version.txt +++ b/build/pkgs/tdlib/package-version.txt @@ -1 +1 @@ -0.3.1.p0 +0.9.3.p0 diff --git a/build/pkgs/tdlib/patches/0001-src-exact_cutset.hpp-Suppress-incomplete-message.patch b/build/pkgs/tdlib/patches/0001-src-exact_cutset.hpp-Suppress-incomplete-message.patch new file mode 100644 index 00000000000..9369b84d496 --- /dev/null +++ b/build/pkgs/tdlib/patches/0001-src-exact_cutset.hpp-Suppress-incomplete-message.patch @@ -0,0 +1,25 @@ +From f9bea896a49ef909aeb910c140661ab06b3b6a0b Mon Sep 17 00:00:00 2001 +From: Matthias Koeppe +Date: Fri, 7 Jun 2024 12:21:28 -0700 +Subject: [PATCH] src/exact_cutset.hpp: Suppress 'incomplete' message + +--- + src/exact_cutset.hpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/exact_cutset.hpp b/src/exact_cutset.hpp +index 782bb96..2caa7bd 100755 +--- a/src/exact_cutset.hpp ++++ b/src/exact_cutset.hpp +@@ -994,7 +994,7 @@ bool exact_cutset::try_it(T_t &T, unsigned bagsize) + }else{ + // incomplete(); //no// + // messes up random tests, send to cerr instead +- std::cerr << "incomplete ../../src/exact_cutset.hpp:978:try_it\n"; ++ // std::cerr << "incomplete ../../src/exact_cutset.hpp:978:try_it\n"; + } + + typename boost::graph_traits::vertex_iterator vIt, vEnd; +-- +2.42.0 + diff --git a/build/pkgs/tdlib/spkg-install.in b/build/pkgs/tdlib/spkg-install.in index 9ee5b9f1566..09c5e4899a0 100644 --- a/build/pkgs/tdlib/spkg-install.in +++ b/build/pkgs/tdlib/spkg-install.in @@ -1,5 +1,5 @@ cd src -sdh_configure +sdh_configure --with-python=no sdh_make sdh_make_install -j1 diff --git a/src/sage/graphs/graph_decompositions/sage_tdlib.cpp b/src/sage/graphs/graph_decompositions/sage_tdlib.cpp index 3644edf6ac7..886859e8d74 100644 --- a/src/sage/graphs/graph_decompositions/sage_tdlib.cpp +++ b/src/sage/graphs/graph_decompositions/sage_tdlib.cpp @@ -4,8 +4,8 @@ #include #include -#include "tdlib/TD_combinations.hpp" -#include "tdlib/TD_misc.hpp" +#include +#include #ifndef TD_STRUCT_VERTEX #define TD_STRUCT_VERTEX @@ -18,13 +18,6 @@ struct Vertex{ typedef boost::adjacency_list TD_graph_t; -struct bag{ - std::set bag; -}; - -typedef boost::adjacency_list TD_tree_dec_t; - - void make_tdlib_graph(TD_graph_t &G, std::vector &V, std::vector &E){ unsigned int max = 0; for(unsigned int i = 0; i < V.size(); i++)