Merge branch 'develop' into thesis

kryzar · Aug 1, 2024 · 0ce7a96 · 0ce7a96
2 parents 760514c + 79c047c
commit 0ce7a96
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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/.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"
@@ -353,7 +359,7 @@ RUN cd /new && rm -rf .git && \
 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/.devcontainer/portability-centos-stream-8-python3.9-minimal/devcontainer.json b/.devcontainer/portability-centos-stream-8-python3.9-minimal/devcontainer.json
diff --git a/.devcontainer/portability-centos-stream-8-python3.9-minimal/portability-Dockerfile b/.devcontainer/portability-centos-stream-8-python3.9-minimal/portability-Dockerfile
diff --git a/.devcontainer/portability-centos-stream-8-python3.9-standard/devcontainer.json b/.devcontainer/portability-centos-stream-8-python3.9-standard/devcontainer.json
diff --git a/.devcontainer/portability-centos-stream-8-python3.9-standard/portability-Dockerfile b/.devcontainer/portability-centos-stream-8-python3.9-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"
     },

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/ci-linux.yml b/.github/workflows/ci-linux.yml
@@ -118,7 +118,6 @@ jobs:
          "linuxmint-21.2",
          "fedora-38",
          "fedora-39",
-         "centos-stream-8-python3.9",
          "centos-stream-9-python3.9",
          "almalinux-8-python3.9",
          "gentoo-python3.10",

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"]