Merge branch 'develop' into disjointset_optimize

.devcontainer/onCreate-conda.sh

@@ -8,6 +8,4 @@ conda init bash
 
 # Build sage
 conda run -n sage-dev ./bootstrap
-conda run -n sage-dev ./configure --with-python=/opt/conda/envs/sage-dev/bin/python --prefix=/opt/conda/envs/sage-dev
-conda run -n sage-dev pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup 
 conda run -n sage-dev pip install --no-build-isolation -v -v -e ./src

.github/workflows/ci-conda.yml

@@ -54,7 +54,7 @@ jobs:
           SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
 
       - name: Cache conda packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/conda_pkgs_dir
           key:
@@ -77,21 +77,16 @@ jobs:
           conda info
           conda list
 
-      - name: Configure
+      - name: Bootstrap
         shell: bash -l {0}
         continue-on-error: true
         run: |
           ./bootstrap
-          echo "::add-matcher::.github/workflows/configure-systempackage-problem-matcher.json"
-          ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX --enable-system-site-packages $(for pkg in $(./sage -package list :standard: --has-file spkg-configure.m4 --has-file distros/conda.txt --exclude rpy2); do echo --with-system-$pkg=force; done)
-          echo "::remove-matcher owner=configure-system-package-warning::"
-          echo "::remove-matcher owner=configure-system-package-error::"
 
       - name: Build
         shell: bash -l {0}
         run: |
           # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda.
-          pip install --no-build-isolation --no-deps -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
           pip install --no-build-isolation --no-deps --config-settings editable_mode=compat -v -v -e ./src
         env:
           SAGE_NUM_THREADS: 2

.github/workflows/dist.yml

@@ -116,7 +116,9 @@ jobs:
           - os: ubuntu-latest
             arch: i686
           - os: macos-latest
-            arch: auto
+            arch: x86_64
+          - os: macos-14
+            arch: arm64
     env:
       # SPKGs to install as system packages
       SPKGS: _bootstrap _prereq
@@ -141,6 +143,14 @@ jobs:
           name: dist
           path: dist
 
+      - uses: actions/setup-python@v5
+        # As of 2024-02-03, the macOS M1 runners do not have preinstalled python or pipx.
+        # Installing pipx follows the approach of https://github.com/pypa/cibuildwheel/pull/1743
+        id: python
+        with:
+          python-version: "3.8 - 3.12"
+          update-environment: false
+
       - name: Build platform wheels
         # We build the wheels from the sdists so that MANIFEST filtering becomes effective.
         # But we must run cibuildwheel with the unpacked source directory, not a tarball,
@@ -151,12 +161,13 @@ jobs:
         # This is unfortunately repeated for each of the packages that we build wheels for
         # because CIBW starts with a fresh container on each invocation.
         run: |
+          "${{ steps.python.outputs.python-path }}" -m pip install pipx
           export PATH=build/bin:$PATH
           export CIBW_BEFORE_ALL="( $(sage-print-system-package-command debian --yes --no-install-recommends install $(sage-get-system-packages debian $SPKGS)) || $(sage-print-system-package-command fedora --yes --no-install-recommends install $(sage-get-system-packages fedora $SPKGS | sed s/pkg-config/pkgconfig/)) || ( $(sage-print-system-package-command homebrew --yes --no-install-recommends install $(sage-get-system-packages homebrew $SPKGS)) || echo error ignored) ) && ./bootstrap && ./configure --enable-build-as-root && make -j4 V=0 $TARGETS_PRE"
           mkdir -p unpacked
           for pkg in sagemath-objects sagemath-categories; do
               (cd unpacked && tar xfz - ) < dist/$pkg*.tar.gz
-              pipx run cibuildwheel==2.16.2 unpacked/$pkg*
+              "${{ steps.python.outputs.python-path }}" -m pipx run cibuildwheel==2.17.0 unpacked/$pkg*
           done
 
       - uses: actions/upload-artifact@v3

.github/workflows/pr-labeler.yml

@@ -0,0 +1,39 @@
+# This action automatically labels Pull-Requests
+# based on files edited and no of lines changed.
+name: Size Labeler/Checker
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+      - review_requested
+      - edited
+jobs:
+  label-changes:
+    if: vars.SMALL_THRESHOLD && vars.MODERATE_THRESHOLD && vars.LARGE_THRESHOLD && github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Add labels based on size
+        run: |
+          git fetch origin $BASE_SHA
+          chmod a+x .github/workflows/set_labels_by_changes.sh
+          .github/workflows/set_labels_by_changes.sh
+        env:
+          BASE_SHA: ${{ github.base_ref }}
+          PR_BASE_SHA: ${{ github.event.pull_request.base.sha }}
+          PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          REPOSITORY: ${{ github.repository }}
+          PR_NUMBER: ${{ github.event.pull_request.number}}
+          SMALL_THRESHOLD: ${{ vars.SMALL_THRESHOLD }}
+          MODERATE_THRESHOLD: ${{ vars.MODERATE_THRESHOLD }}
+          LARGE_THRESHOLD: ${{ vars.LARGE_THRESHOLD }}

.github/workflows/set_labels_by_changes.sh

@@ -0,0 +1,67 @@
+#!/usr/bin/env bash
+
+echo 'set_labels_by_changes.sh called with environment:'
+echo "BASE SHA: $PR_BASE_SHA" 
+echo "HEAD SHA: $PR_HEAD_SHA" 
+echo "SMALL THRESHOLD $SMALL_THRESHOLD"
+echo "MODERATE THERESHOLD: $MODERATE_THRESHOLD"
+echo "LARGE THRESHOLD: $LARGE_THRESHOLD"
+
+# get all the changes made and changed files
+CHANGES=$(git diff --ignore-all-space $PR_BASE_SHA $PR_HEAD_SHA)
+
+# ignore blank lines
+CHANGES=$(echo "$CHANGES" | grep -vE '^[\+\-]\s*$')
+
+# ignore non necessary lines from git diff
+CHANGES=$(echo "$CHANGES" | grep -E '^[+\-]' | grep -vE '^\+\+\+|^\-\-\-')
+
+# count total no of lines
+CHANGES=$(echo "$CHANGES" | wc -l)
+
+echo "CHANGES MADE: $CHANGES"
+
+AUTH_HEADER="Authorization: Bearer $GITHUB_TOKEN"
+
+MINIMAL="v: minimal"
+SMALL="v: small"
+MODERATE="v: moderate"
+LARGE="v: large"
+
+DELETE_LABELS=("$MINIMAL" "$SMALL" "$MODERATE" "$LARGE")
+
+if [ "$CHANGES" -gt "$LARGE_THRESHOLD" ]; then
+    SIZE_LABEL="$LARGE"
+elif [ "$CHANGES" -gt "$MODERATE_THRESHOLD" ]; then
+    SIZE_LABEL="$MODERATE"
+elif [ "$CHANGES" -gt "$SMALL_THRESHOLD" ]; then
+    SIZE_LABEL="$SMALL"
+else
+    SIZE_LABEL="$MINIMAL"
+fi
+
+DELETE_LABELS=("${DELETE_LABELS[@]//${SIZE_LABEL}/}")
+
+# API for adding labels on the Pull Request 
+API_URL="https://api.github.com/repos/$REPOSITORY/issues/$PR_NUMBER/labels"
+
+echo "Adding label: ${SIZE_LABEL[@]}"
+for LABEL in "${SIZE_LABEL[@]}"; do
+    curl -X POST \
+        -H "$AUTH_HEADER" \
+        -H "Accept: application/vnd.github+json" \
+        -H "X-GitHub-Api-Version: 2022-11-28" \
+        -d "{\"labels\":[\"$LABEL\"]}" \
+        "$API_URL" >/dev/null
+done
+
+echo "Deleting Labels:"
+
+for DELETE_LABEL in "${DELETE_LABELS[@]}"; do
+    ENCODED_LABEL=$(echo "$DELETE_LABEL" | sed 's/ /%20/g')
+    curl -X DELETE \
+        -H "Accept: application/vnd.github+json" \
+        -H "$AUTH_HEADER" \
+        -H "X-GitHub-Api-Version: 2022-11-28" \
+        "$API_URL/$ENCODED_LABEL" >/dev/null
+done

.gitpod.yml

@@ -11,8 +11,6 @@ tasks:
       && conda config --append envs_dirs $(pwd)
       && conda activate $(pwd)/venv
       && ./bootstrap
-      && ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX
-      && pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
       && pip install --no-build-isolation -v -v -e ./src
     # Activate conda environment, set up Trac remote
     # RestructuredText extension recommends python extension, although we have already installed it

CITATION.cff

@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.4.beta3
+version: 10.4.beta4
 doi: 10.5281/zenodo.593563
-date-released: 2024-04-12
+date-released: 2024-04-27
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.4.beta3, Release Date: 2024-04-12
+SageMath version 10.4.beta4, Release Date: 2024-04-27

bootstrap

@@ -232,7 +232,8 @@ save () {
 	src/environment-optional-3.[89].yml src/environment-optional-3.1[0-9].yml \
 	src/Pipfile \
 	src/pyproject.toml \
-	src/requirements.txt
+	src/requirements.txt \
+	src/setup.cfg
 
     # Update version
     echo "$NEWCONFVERSION" >$PKG/package-version.txt

build/bin/sage-logger

@@ -63,15 +63,15 @@ fi
 
 timefile="$logdir/$logname.time"
 rm -f "$timefile"
-if /usr/bin/time -h -o /dev/null true; then
+if /usr/bin/time -h -o /dev/null true 2>/dev/null; then
     TIME="/usr/bin/time -h -o $timefile"
 else
     TIME=""
 fi
 
 report_time ()
 {
-    time=$(echo $(cat $timefile))
+    time=$(echo $(cat $timefile 2>/dev/null))
     case "$time" in
         *m*real*|*h*real*|*[1-9][0-9].*real*|*[1-9][0-9],*real*)
             # at least 10 seconds wall time

build/bin/write-dockerfile.sh

@@ -236,7 +236,7 @@ $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-
 $ADD config/config.rpath config/config.rpath
 $ADD src/doc/bootstrap src/doc/bootstrap
 $ADD src/bin src/bin
-$ADD src/Pipfile.m4 src/pyproject.toml.m4 src/requirements.txt.m4 src/VERSION.txt src/
+$ADD src/Pipfile.m4 src/pyproject.toml.m4 src/requirements.txt.m4 src/setup.cfg.m4 src/VERSION.txt src/
 $ADD m4 ./m4
 $ADD pkgs pkgs
 $ADD build ./build

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=b9d9a4bb2d949d8f6fffe63c77ff069d59ca6e8c
-md5=95f8a1d22f684e3f61019ae82111e639
-cksum=3352815196
+sha1=2d6779beb2e69f0f7bddc2edc44ad275442ffd29
+md5=789344e03a6b57ba1538c0c760449720
+cksum=3806733369

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-4dd66116b58babf05bb8e4b30282638e2c0b82c3
+0a7b2513287af1124a358c2494b8bef4668a1882

build/pkgs/gdb/dependencies

@@ -1,4 +1,4 @@
-mpfr zlib ncurses  xz | $(PYTHON)
+mpfr zlib ncurses | $(PYTHON) xz
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/gmp/dependencies

@@ -1,3 +1,3 @@
-xz
+| xz
 
 # xz is only needed to unpack the tarball when sage-bootstrap-python is Python < 3.3

build/pkgs/libgd/dependencies

@@ -1,4 +1,4 @@
-libpng xz
+libpng | xz
 
 # xz needed to unpack tarball when sage-bootstrap-python is Python < 3.3
 ----------

build/pkgs/onetbb/checksums.ini

@@ -1,5 +1,5 @@
 tarball=onetbb-VERSION.tar.gz
-sha1=b991f5d882aba2182871cfe011614cc43b92aa3c
-md5=ba4ecedc4949f673a34b35de738a72fc
-cksum=211900655
+sha1=740e86b703f42446ddde392b73a9db3dc0f5f4cd
+md5=b301151120b08a17e98dcdda6e4f6011
+cksum=3287903962
 upstream_url=https://github.com/oneapi-src/oneTBB/archive/refs/tags/vVERSION.tar.gz

build/pkgs/onetbb/package-version.txt

@@ -1 +1 @@
-2021.9.0
+2021.11.0

build/pkgs/papilo/checksums.ini

@@ -1,5 +1,5 @@
 tarball=papilo-VERSION.tar.gz
-sha1=85d599ac9936aa1ddf687e04273b995522909de5
-md5=c41f5aa615ffc9914f8ca924947aa8cb
-cksum=1535425476
+sha1=069f64ff25cfb08c9b2a416d1d215bd5b907c877
+md5=d58b7c991ac1c4a863de92a404409ca8
+cksum=1552180280
 upstream_url=https://github.com/scipopt/papilo/archive/refs/tags/vVERSION.tar.gz

build/pkgs/papilo/package-version.txt

@@ -1 +1 @@
-2.1.1
+2.2.0