Merge branch 'develop' into magma_series_rings

Author: fchapoton

.ci/create-changes-html.sh

@@ -16,6 +16,12 @@ echo '<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highli
 echo '<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/highlight.min.js"></script>' >> CHANGES.html
 echo '<script>hljs.highlightAll();</script>' >> CHANGES.html
 cat >> CHANGES.html << EOF
+<style>
+  p.diff a:first-child {
+    font-weight: bold;
+    font-size: x-large;
+  }
+</style>
 <script>
 document.addEventListener('DOMContentLoaded', () => {
 // This URL is hardcoded in the file .github/workflows/doc-publish.yml.

.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 "$GITHUB_ACTIONS" ]; then
@@ -271,48 +275,47 @@ cat <<EOF
 FROM with-system-packages AS bootstrapped
 #:bootstrapping:
 RUN rm -rf /new /sage/.git
-$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 Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap configure.ac sage .homebrew-build-env tox.ini .gitignore /new/
 $ADD config/config.rpath /new/config/config.rpath
 $ADD src/doc/bootstrap /new/src/doc/bootstrap
 $ADD src/bin /new/src/bin
-$ADD src/Pipfile.m4 src/pyproject.toml src/requirements.txt.m4 src/setup.cfg.m4 src/VERSION.txt /new/src/
+$ADD src/pyproject.toml src/requirements.txt.m4 src/setup.cfg.m4 src/VERSION.txt /new/src/
 $ADD m4 /new/m4
 $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$THEN_SAVE_STATUS
 EOF
 fi
 cat <<EOF
@@ -323,50 +326,49 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 #:toolchain:
-$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
 ENV MAKE="make -j\${NUMPROC}"
 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"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!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
 ENV MAKE="make -j\${NUMPROC}"
 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"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!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
 ENV MAKE="make -j\${NUMPROC}"
 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"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!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

.codecov.yml

@@ -17,3 +17,4 @@ coverage:
         target: auto
         threshold: 0%
         base: auto
+        informational: true

.devcontainer/onCreate-conda.sh

@@ -2,10 +2,12 @@
 set -e
 
 # Create conda environment
-conda install mamba -n base -c conda-forge -y
-mamba env create --file src/environment-dev-3.11-linux.yml || mamba env update --file src/environment-dev-3.11-linux.yml
+conda config --env --add channels conda-forge
+conda config --env --set channel_priority strict
+conda update -y --all --override-channels -c conda-forge
+conda install mamba=1 -n base -y
+mamba env create -y --file environment-3.11-linux.yml || mamba env update -y --file environment-3.11-linux.yml
 conda init bash
 
 # Build sage
-conda run -n sage-dev ./bootstrap
-conda run -n sage-dev pip install --no-build-isolation -v -v -e ./src
+conda run -n sage-dev pip install --no-build-isolation -v -v -e .

.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))