Merge branch 'sagemath:develop' into lazy-species

mantepse · Oct 13, 2024 · 5db564d · 5db564d
2 parents 8058889 + 7726cd9
commit 5db564d
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diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh
@@ -35,7 +35,7 @@ STRIP_COMMENTS="sed s/#.*//;"
 SAGE_ROOT=.
 export PATH="$SAGE_ROOT"/build/bin:$PATH
 SYSTEM_PACKAGES=$EXTRA_SYSTEM_PACKAGES
-SYSTEM_CONFIGURE_ARGS="--enable-option-checking "
+SYSTEM_CONFIGURE_ARGS=" --enable-option-checking"
 for SPKG in $(sage-package list --has-file=spkg-configure.m4 $SAGE_PACKAGE_LIST_ARGS) $EXTRA_SAGE_PACKAGES; do
     SYSTEM_PACKAGE=$(sage-get-system-packages $SYSTEM $SPKG)
     if [ -n "${SYSTEM_PACKAGE}" ]; then
@@ -45,13 +45,20 @@ for SPKG in $(sage-package list --has-file=spkg-configure.m4 $SAGE_PACKAGE_LIST_
             # shell-quote package if necessary
             SYSTEM_PACKAGES+=$(printf " %q" "$a")
         done
-        SYSTEM_CONFIGURE_ARGS+="--with-system-${SPKG}=${WITH_SYSTEM_SPKG} "
+        # Check if SPKG is not a dummy package
+        if [[ $SPKG != _* ]]; then
+            SYSTEM_CONFIGURE_ARGS+=" --with-system-${SPKG}=${WITH_SYSTEM_SPKG}"
+        fi
     fi
 done
 echo "# Automatically generated by SAGE_ROOT/.ci/write-dockerfile.sh"
 echo "# the :comments: separate the generated file into sections"
 echo "# to simplify writing scripts that customize this file"
-ADD="ADD $__CHOWN"
+if [ -z "$__CHOWN" ]; then
+  ADD="ADD"
+else
+  ADD="ADD $__CHOWN"
+fi
 RUN=RUN
 cat <<EOF
 ARG BASE_IMAGE=$(eval echo "${FULL_BASE_IMAGE_AND_TAG}")
@@ -86,10 +93,7 @@ case $SYSTEM in
                 # we remove the unminimize binary here after it has done its job.
                 #
                 cat <<EOF
-RUN if command -v unminimize > /dev/null; then  \
-        (yes | unminimize) || echo "(ignored)"; \
-        rm -f "\$(command -v unminimize)";       \
-    fi
+RUN if command -v unminimize > /dev/null; then (yes | unminimize) || echo "(ignored)"; rm -f "\$(command -v unminimize)"; fi
 EOF
                 if [ -n "$DIST_UPGRADE" ]; then
                     cat <<EOF
@@ -254,10 +258,10 @@ case ${DOCKER_BUILDKIT-0} in
         # With buildkit we cannot retrieve failed builds.
         # So we do not allow the main step of a build stage to fail.
         # Instead we record the exit code in the file STATUS.
-        THEN_SAVE_STATUS='; echo $? > STATUS'
+        THEN_SAVE_STATUS=' ; echo $? > STATUS'
         # ... and at the beginning of the next build stage,
         # we check the status and exit with an error status.
-        CHECK_STATUS_THEN='STATUS=$(cat STATUS 2>/dev/null); case "$STATUS" in ""|0) ;; *) exit $STATUS;; esac; '
+        CHECK_STATUS_THEN=' STATUS=$(cat STATUS 2>/dev/null); case "$STATUS" in ""|0) ;; *) exit $STATUS;; esac;'
 esac
 
 if [ -n "$GITHUB_ACTIONS" ]; then
@@ -281,38 +285,37 @@ $ADD pkgs /new/pkgs
 $ADD build /new/build
 $ADD .upstream.d /new/.upstream.d
 ADD .ci /.ci
-RUN if [ -d /sage ]; then                                               \
-        echo "### Incremental build from \$(cat /sage/VERSION.txt)" &&  \
-        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /sage/.gitignore && \
-        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /new/.gitignore && \
-        if ! (cd /new && /.ci/retrofit-worktree.sh worktree-image /sage); then \
-            echo "retrofit-worktree.sh failed, falling back to replacing /sage"; \
-            for a in local logs; do                                     \
-                if [ -d /sage/\$a ]; then mv /sage/\$a /new/; fi;       \
-            done;                                                       \
-            rm -rf /sage;                                               \
-            mv /new /sage;                                              \
-        fi;                                                             \
-    else                                                                \
-        mv /new /sage;                                                  \
+RUN if [ -d /sage ]; then \\
+        echo "### Incremental build from \$(cat /sage/VERSION.txt)" && \\
+        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /sage/.gitignore && \\
+        printf '/src/*\n!/src/doc/bootstrap\n!/src/bin\n!/src/*.m4\n!/src/*.toml\n!/src/VERSION.txt\n' >> /new/.gitignore && \\
+        if ! (cd /new && /.ci/retrofit-worktree.sh worktree-image /sage); then \\
+            echo "retrofit-worktree.sh failed, falling back to replacing /sage"; \\
+            for a in local logs; do \\
+                if [ -d /sage/\$a ]; then mv /sage/\$a /new/; fi; \\
+            done; \\
+            rm -rf /sage; \\
+            mv /new /sage; \\
+        fi; \\
+    else \\
+        mv /new /sage; \\
     fi
 WORKDIR /sage
-
 ARG BOOTSTRAP="${BOOTSTRAP-./bootstrap}"
-$RUN sh -x -c "\${BOOTSTRAP}" $ENDRUN $THEN_SAVE_STATUS
+$RUN sh -x -c "\${BOOTSTRAP}"$ENDRUN$THEN_SAVE_STATUS
 
 FROM bootstrapped AS configured
 #:configuring:
-RUN $CHECK_STATUS_THEN mkdir -p logs/pkgs; rm -f config.log; ln -s logs/pkgs/config.log config.log
+RUN$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}"
 EOF
 if [ ${WITH_SYSTEM_SPKG} = "force" ]; then
     cat <<EOF
-$RUN ./configure $SYSTEM_CONFIGURE_ARGS \${CONFIGURE_ARGS} || (echo "::group::config.log"; cat config.log; echo "::endgroup::"; echo "********** configuring without forcing ***********"; ./configure \${CONFIGURE_ARGS}; echo "::group::config.log"; cat config.log; echo "::endgroup::"; exit 1) $ENDRUN $THEN_SAVE_STATUS
+$RUN ./configure $SYSTEM_CONFIGURE_ARGS \${CONFIGURE_ARGS} || (echo "::group::config.log"; cat config.log; echo "::endgroup::"; echo "********** configuring without forcing ***********"; ./configure \${CONFIGURE_ARGS}; echo "::group::config.log"; cat config.log; echo "::endgroup::"; exit 1)$ENDRUN$THEN_SAVE_STATUS
 EOF
 else
     cat <<EOF
-$RUN ./configure $SYSTEM_CONFIGURE_ARGS \${CONFIGURE_ARGS} || (echo "::group::config.log"; cat config.log; echo "::endgroup::"; exit 1) $ENDRUN $THEN_SAVE_STATUS
+$RUN ./configure $SYSTEM_CONFIGURE_ARGS \${CONFIGURE_ARGS} || (echo "::group::config.log"; cat config.log; echo "::endgroup::"; exit 1)$ENDRUN$THEN_SAVE_STATUS
 EOF
 fi
 cat <<EOF
@@ -325,7 +328,7 @@ ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
 ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
 #:toolchain:
-$RUN $CHECK_STATUS_THEN make \${USE_MAKEFLAGS} base-toolchain $ENDRUN $THEN_SAVE_STATUS
+$RUN$CHECK_STATUS_THEN make \${USE_MAKEFLAGS} base-toolchain$ENDRUN$THEN_SAVE_STATUS
 
 FROM with-base-toolchain AS with-targets-pre
 ARG NUMPROC=8
@@ -335,7 +338,7 @@ ENV SAGE_CHECK=warn
 ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
 #:make:
 ARG TARGETS_PRE="all-sage-local"
-$RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_PRE} $ENDRUN $THEN_SAVE_STATUS
+$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
 ARG NUMPROC=8
@@ -345,19 +348,18 @@ ENV SAGE_CHECK=warn
 ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
 $ADD .gitignore /new/.gitignore
 $ADD src /new/src
-RUN cd /new && rm -rf .git && \
-    if /.ci/retrofit-worktree.sh worktree-pre /sage; then \
-        cd /sage && touch configure build/make/Makefile; \
-    else \
-        echo "retrofit-worktree.sh failed, falling back to replacing /sage/src"; \
-        rm -rf /sage/src;                                    \
-        mv src /sage/src;                                    \
-        cd /sage && ./bootstrap && ./config.status;          \
-    fi; \
+RUN cd /new && rm -rf .git && \\
+    if /.ci/retrofit-worktree.sh worktree-pre /sage; then \\
+        cd /sage && touch configure build/make/Makefile; \\
+    else \\
+        echo "retrofit-worktree.sh failed, falling back to replacing /sage/src"; \\
+        rm -rf /sage/src; \\
+        mv src /sage/src; \\
+        cd /sage && ./bootstrap && ./config.status; \\
+    fi; \\
     cd /sage && rm -rf .git; rm -rf /new || echo "(error ignored)"
-
 ARG TARGETS="build"
-$RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS} $ENDRUN $THEN_SAVE_STATUS
+$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
 ARG NUMPROC=8
@@ -366,7 +368,7 @@ ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
 ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
 ARG TARGETS_OPTIONAL="ptest"
-$RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_OPTIONAL} || echo "(error ignored)" $ENDRUN $THEN_SAVE_STATUS
+$RUN$CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_OPTIONAL} || echo "(error ignored)"$ENDRUN$THEN_SAVE_STATUS
 
 #:end:
 EOF
diff --git a/.github/sync_labels.py b/.github/sync_labels.py
@@ -609,7 +609,7 @@ def actor_valid(self):
         for com in coms:
             for auth in com['authors']:
                 login = auth['login']
-                if not login in authors:
+                if login not in authors:
                     if not self.is_this_bot(login) and login != author:
                         debug('PR %s has recent commit by %s' % (self._issue, login))
                         authors.append(login)
@@ -746,7 +746,7 @@ def add_label(self, label):
         r"""
         Add the given label to the issue or PR.
         """
-        if not label in self.get_labels():
+        if label not in self.get_labels():
             self.edit(label, '--add-label')
             info('Add label to %s: %s' % (self._issue, label))
 

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -97,9 +97,11 @@ jobs:
           remove-haskell:       true
           remove-codeql:        true
           remove-docker-images: true
+
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
+
       - name: Get changed files and packages
         id: changed-files
         uses: tj-actions/changed-files@v45
@@ -110,26 +112,47 @@ jobs:
               - 'build/pkgs/*/spkg-configure.m4'
             pkgs:
               - 'build/pkgs/**'
+              - '!build/pkgs/_**'
+              - '!build/pkgs/configure/**'
               - '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 "$SPKG-ensure"; fi; done | sort -u))
+          uninstall_targets=$(echo $(
+            for a in '' ${{ steps.changed-files.outputs.configures_all_changed_files }}; do
+              # Extract package name from the file path and append '-uninstall'
+              echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'
+            done | sort -u  # Sort and ensure uniqueness
+          ))
+          build_targets=$(echo $(
+            for a in '' ${{ steps.changed-files.outputs.pkgs_all_changed_files }}; do
+              # Extract package name, replace '-' with '_', and strip extra parts from the path
+              SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;')
+              # Check if key files exist in the package directory
+              if [ -f "build/pkgs/$SPKG/checksums.ini" ] || \
+                 [ -f "build/pkgs/$SPKG/requirements.txt" ] || \
+                 [ -f "build/pkgs/$SPKG/spkg-install" ]; then
+                echo "$SPKG-ensure"  # add the "$SPKG-ensure" target
+              fi
+            done | sort -u  # Sort and ensure uniqueness
+          ))
           if [ -n "$uninstall_targets" ]; then
-              echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+            echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
           else
-              echo "build_targets=$build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+            echo "build_targets=$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
@@ -140,13 +163,15 @@ jobs:
           else
             sage-package metrics :all:
           fi
+
       - name: Install test prerequisites
         # From docker.yml
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
           sudo apt-get clean
           df -h
+
       - name: Merge CI fixes from sagemath/sage
         # From docker.yml
         # This step needs to happen after the commit sha is put in DOCKER_TAG
@@ -254,16 +279,19 @@ jobs:
           remove-haskell:       true
           remove-codeql:        true
           remove-docker-images: true
+
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
+
       - name: Install test prerequisites
         # From docker.yml
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
           sudo apt-get clean
           df -h
+
       - name: Merge CI fixes from sagemath/sage
         # From docker.yml
         # This step needs to happen after the commit sha is put in DOCKER_TAG
@@ -352,16 +380,19 @@ jobs:
           remove-haskell:       true
           remove-codeql:        true
           remove-docker-images: true
+
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
+
       - name: Install test prerequisites
         # From docker.yml
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
           sudo apt-get clean
           df -h
+
       - name: Merge CI fixes from sagemath/sage
         # From docker.yml
         # This step needs to happen after the commit sha is put in DOCKER_TAG
@@ -469,16 +500,19 @@ jobs:
           remove-haskell:       true
           remove-codeql:        true
           remove-docker-images: true
+
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
+
       - name: Install test prerequisites
         # From docker.yml
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
           sudo apt-get clean
           df -h
+
       - name: Merge CI fixes from sagemath/sage
         # From docker.yml
         # This step needs to happen after the commit sha is put in DOCKER_TAG

diff --git a/CITATION.cff b/CITATION.cff
@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.5.beta6
+version: 10.5.beta7
 doi: 10.5281/zenodo.8042260
-date-released: 2024-09-29
+date-released: 2024-10-12
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 10.5.beta6, Release Date: 2024-09-29
+SageMath version 10.5.beta7, Release Date: 2024-10-12
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
@@ -1,3 +1,3 @@
 tarball=configure-VERSION.tar.gz
-sha1=140d921780212198287a0d626b8c9655d4408f7a
-sha256=4f82ec8bdb67c4dffd43daddd5160e8f9c624f6a5cf16c4128bfab2e5ddca459
+sha1=978eb775a20fea3ed9b88f0d67ecd84a3d9cd6ea
+sha256=c3987bb0f8aca81e112a17d8904ef2353a706159d43250305dc2bcac4ca2e33a
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-2b4fe39e420df022d34a67fbc820252618e15f83
+4326d0d9422011034a230ab3c1445fafeb2ac444
diff --git a/build/pkgs/pari/spkg-configure.m4 b/build/pkgs/pari/spkg-configure.m4
@@ -1,7 +1,8 @@
 SAGE_SPKG_CONFIGURE([pari], [
   dnl See gp_version below on how the version is computed from MAJV.MINV.PATCHV
   m4_pushdef([SAGE_PARI_MINVER],["134916"])dnl this version and higher allowed
-  m4_pushdef([SAGE_PARI_MAXVER],["999999"])dnl this version and higher not allowed
+  dnl Do not allow Pari 2.17 or later, see #38769:
+  m4_pushdef([SAGE_PARI_MAXVER],["135424"])dnl this version and higher not allowed
   SAGE_SPKG_DEPCHECK([gmp readline], [
     AC_PATH_PROG([GP], [gp])
     if test x$GP = x; then dnl GP test

diff --git a/build/pkgs/r/spkg-configure.m4 b/build/pkgs/r/spkg-configure.m4
diff --git a/build/pkgs/r_jupyter/dependencies b/build/pkgs/r_jupyter/dependencies
@@ -1 +1,5 @@
-notebook r
+notebook rpy2
+
+----------
+R is the real dependency. But SPKG r is a dummy package, and does not install R.
+Since SPKG rpy2 checks for the system R, we put rpy2 as a dependency instead.
diff --git a/build/pkgs/rpy2/dependencies b/build/pkgs/rpy2/dependencies
@@ -1,4 +1,4 @@
- r cffi tzlocal pytz jinja2 | $(PYTHON_TOOLCHAIN) pycparser $(PYTHON)
+cffi tzlocal pytz jinja2 | $(PYTHON_TOOLCHAIN) pycparser $(PYTHON)
 
 ----------
 All lines of this file are ignored except the first.