Merge branch 'sagemath_standard_pyproject_toml' into distribution_dir…

…ectives

.ci/create-changes-html.sh

@@ -19,8 +19,8 @@ echo '<script>hljs.highlightAll();</script>' >> CHANGES.html
 cat >> CHANGES.html << EOF
 <script>
 document.addEventListener('DOMContentLoaded', () => {
+const baseDocURL = 'https://sagemath.netlify.app'
 const diffSite = 'https://pianomister.github.io/diffsite'
-const baseDocURL = 'https://sagemath-tobias.netlify.app'
 const diffParagraphs = document.querySelectorAll('p.diff');
 diffParagraphs.forEach(paragraph => {
   const rootURL = window.location.origin;

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.beta1
+version: 10.4.beta2
 doi: 10.5281/zenodo.593563
-date-released: 2024-03-31
+date-released: 2024-04-08
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

Makefile

@@ -78,14 +78,6 @@ reconfigure:
 	        exit 1; \
 	fi
 
-# This is used to monitor progress towards Python 3 and prevent
-# regressions. Should be removed after the full switch to python3.
-#
-# As of Sage 9.0: keep the build target for backward compatibility,
-# but it just runs "make".
-buildbot-python3:
-	$(MAKE)
-
 # Preemptively download all source tarballs of normal packages.
 download:
 	export SAGE_ROOT=$$(pwd) && \
@@ -343,15 +335,15 @@ CONFIGURE_DEPENDENCIES =							\
 	build/pkgs/*/spkg-configure.m4						\
 	build/pkgs/*/type build/pkgs/*/SPKG.rst					\
 	build/pkgs/*/checksums.ini build/pkgs/*/requirements.txt		\
-	build/pkgs/*/install-requires.txt build/pkgs/*/package-version.txt	\
+	build/pkgs/*/version_requirements.txt build/pkgs/*/package-version.txt	\
 	build/pkgs/*/spkg-install build/pkgs/*/spkg-install.in
 
 # SPKG_INFO_DEPENDENCIES is the list of files that influence the run of 'sage-spkg-info' and hence
 # the generation of the files generated in 'src/doc' by 'src/doc/bootstrap'.
 SPKG_INFO_DEPENDENCIES =							\
 	build/pkgs/*/type build/pkgs/*/SPKG.rst					\
 	build/pkgs/*/requirements.txt						\
-	build/pkgs/*/install-requires.txt build/pkgs/*/package-version.txt	\
+	build/pkgs/*/version_requirements.txt build/pkgs/*/package-version.txt	\
 	build/pkgs/*/distros/*.txt
 
 configure: bootstrap src/doc/bootstrap $(CONFIGURE_DEPENDENCIES) $(SPKG_INFO_DEPENDENCIES)
@@ -376,5 +368,5 @@ list:
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \
-	buildbot-python3 list \
+	list \
 	doc-clean clean sagelib-clean build-clean

README.md

@@ -52,7 +52,7 @@ obtaining Sage from a package manager, using a container image, or using
 Sage in the cloud.
 
 **This README contains self-contained instructions for building Sage from source.**
-It assumes that you have already cloned the git repository or downloaded the
+This requires you to clone the git repository (as described in this README) or download the
 [sources](https://www.sagemath.org/download-source.html) in the form
 of a tarball.
 
@@ -123,7 +123,7 @@ read the following step-by-step instructions for building Sage.
 The instructions cover all of Linux, macOS, and WSL.
 
 More details, providing a background for these instructions, can be found
-in the [section "Install from Source Code"](https://doc.sagemath.org/html/en/installation/source.html).
+in the section [Install from Source Code](https://doc.sagemath.org/html/en/installation/source.html)
 in the Installation Guide.
 
 
@@ -424,9 +424,9 @@ in the Installation Guide.
         $ sudo ln -s $(./sage -sh -c 'ls $SAGE_ROOT/venv/bin/sage') /usr/local/bin
 
 21. Optional: Set up SageMath as a Jupyter kernel in an existing Jupyter notebook
-    or JupyterLab installation, as described in [section
-    "Launching SageMath"](https://doc.sagemath.org/html/en/installation/launching.html)
-    in the Sage Installation Manual.
+    or JupyterLab installation, as described in the section
+    [Launching SageMath](https://doc.sagemath.org/html/en/installation/launching.html)
+    in the Sage Installation Guide.
 
 Alternative Installation using PyPI
 ---------------

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.4.beta1, Release Date: 2024-03-31
+SageMath version 10.4.beta2, Release Date: 2024-04-08

bootstrap

@@ -105,7 +105,7 @@ EOF
             SPKG_TREE_VAR="$(sed "s/#.*//;" "$DIR/trees.txt")"
         else
             SPKG_TREE_VAR=SAGE_LOCAL
-            if test -f "$DIR/requirements.txt" -o -f "$DIR/install-requires.txt"; then
+            if test -f "$DIR/requirements.txt" -o -f "$DIR/version_requirements.txt"; then
                 # A Python package
                 SPKG_TREE_VAR=SAGE_VENV
                 echo "define(>>>SPKG_INSTALL_REQUIRES_${pkgname}<<<, >>>$(echo $(sage-get-system-packages install-requires ${pkgname}))<<<)dnl" >> m4/sage_spkg_versions.m4

bootstrap-conda

@@ -132,11 +132,11 @@ echo >&2 $0:$LINENO: generate conda environment files
     (
         echo >&4 "  - pip:"
         echo >&5 "  - pip:"
-        for PKG_BASE in $(sage-package list :standard: :optional: --has-file requirements.txt --no-file distros/conda.txt --no-file src; sage-package list :standard: :optional: --has-file install-requires.txt --no-file requirements.txt --no-file distros/conda.txt --no-file src); do
+        for PKG_BASE in $(sage-package list :standard: :optional: --has-file requirements.txt --no-file distros/conda.txt --no-file src; sage-package list :standard: :optional: --has-file version_requirements.txt --no-file requirements.txt --no-file distros/conda.txt --no-file src); do
             PKG_SCRIPTS=build/pkgs/$PKG_BASE
             SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
             if [ ! -f $SYSTEM_PACKAGES_FILE ]; then
-                SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/install-requires.txt
+                SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/version_requirements.txt
             fi
             PKG_TYPE=$(cat $PKG_SCRIPTS/type)
             if grep -q SAGERUNTIME $PKG_SCRIPTS/dependencies $PKG_SCRIPTS/dependencies_order_only 2>/dev/null; then

build/bin/sage-dist-helpers

@@ -323,8 +323,13 @@ sdh_store_wheel() {
         wheel_basename="${wheel##*/}"
         distname="${wheel_basename%%-*}"
         # Record name and wheel file location
+        if [ -n "$SAGE_DESTDIR" ]; then
+            echo "Staged wheel file, staged ${SAGE_SPKG_SCRIPTS}/${PKG_BASE}/spkg-requirements.txt"
+        else
+            echo "Copied wheel file, wrote ${SAGE_SPKG_SCRIPTS}/${PKG_BASE}/spkg-requirements.txt"
+        fi
         mkdir -p ${SAGE_DESTDIR}${SAGE_SPKG_SCRIPTS}/${PKG_BASE}
-        echo "${distname} @ file://${wheel}" >> ${SAGE_DESTDIR}${SAGE_SPKG_SCRIPTS}/${PKG_BASE}/spkg-requirements.txt
+        echo "${distname} @ file://${wheel}" >> "${SAGE_DESTDIR}${SAGE_SPKG_SCRIPTS}/${PKG_BASE}/spkg-requirements.txt"
     fi
     wheel="${SAGE_DESTDIR}${wheel}"
 }
@@ -392,7 +397,7 @@ sdh_actually_pip_install_wheel() {
     # of sage-conf, sage-setup, etc.) bump the version number, we need to
     # override this behavior.  The pip install option --force-reinstall does too
     # much -- it also reinstalls all dependencies, which we do not want.
-    $sudo sage-pip-uninstall "$distname"
+    $sudo sage-pip-uninstall "$distname" 2>&1 | sed '/^WARNING: Skipping .* as it is not installed./d'
     if [ $? -ne 0 ]; then
         echo "(ignoring error)" >&2
     fi

build/bin/sage-get-system-packages

@@ -14,21 +14,21 @@ fi
 
 case "$SYSTEM" in
     install-requires)
-        # Collect install-requires.txt (falling back to requirements.txt) and output it in the format
-        # needed by setup.cfg [options] install_requires=
-        SYSTEM_PACKAGES_FILE_NAMES="install-requires.txt requirements.txt"
+        # Collect version_requirements.txt (falling back to requirements.txt) and output it in the format
+        # needed by setup.cfg [options] version_requirements=
+        SYSTEM_PACKAGES_FILE_NAMES="version_requirements.txt requirements.txt"
         STRIP_COMMENTS="sed s/#.*//;/^[[:space:]]*$/d;"
         COLLECT=
         ;;
     install-requires-toml)
-        # Collect install-requires.txt (falling back to requirements.txt) and output it in the format
+        # Collect version_requirements.txt (falling back to requirements.txt) and output it in the format
         # needed by pyproject.toml [build-system] requires=
-        SYSTEM_PACKAGES_FILE_NAMES="install-requires.txt requirements.txt"
+        SYSTEM_PACKAGES_FILE_NAMES="version_requirements.txt requirements.txt"
         STRIP_COMMENTS="sed s/#.*//;/^[[:space:]]*$/d;s/^/'/;s/$/',/;"
         COLLECT=
         ;;
     pip)
-        SYSTEM_PACKAGES_FILE_NAMES="requirements.txt install-requires.txt"
+        SYSTEM_PACKAGES_FILE_NAMES="requirements.txt version_requirements.txt"
         STRIP_COMMENTS='sed s/#.*//;s/[[:space:]]//g;'
         COLLECT=echo
         ;;

build/bin/sage-logger

@@ -61,6 +61,25 @@ else
     SED=cat
 fi
 
+timefile="$logdir/$logname.time"
+rm -f "$timefile"
+if /usr/bin/time -h -o /dev/null true; then
+    TIME="/usr/bin/time -h -o $timefile"
+else
+    TIME=""
+fi
+
+report_time ()
+{
+    time=$(echo $(cat $timefile))
+    case "$time" in
+        *m*real*|*h*real*|*[1-9][0-9].*real*|*[1-9][0-9],*real*)
+            # at least 10 seconds wall time
+            echo "$time"
+            ;;
+    esac
+}
+
 mkdir -p "$logdir"
 
 # Do all logging of child processes with V=1 to ensure that no
@@ -75,22 +94,30 @@ if [ -n "$SAGE_SILENT_BUILD" -a ${use_prefix} = true ]; then
     # Silent build.
     # Similar to https://www.gnu.org/software/automake/manual/html_node/Automake-Silent-Rules.html#Automake-Silent-Rules
     echo "[$logname] installing. Log file: $logfile"
-    ( exec>> $logfile 2>&1 ; eval "$cmd" )
+    ( exec>> $logfile 2>&1 ; $TIME sh -c "$cmd"; status=$?;
+      [ -r $timefile ] && cat $timefile; exit $status )
     status=$?
     if [[ $status != 0 ]]; then
         echo "  [$logname] error installing, exit status $status. End of log file:"
         tail -n 120 "$logfile" | sed "/Please email sage-devel/,$ d;s;^;  [$logname]   ;" >&2
         echo "  [$logname] Full log file: $logfile"
     else
-        echo "  [$logname] successfully installed."
+        time=$(report_time)
+        if [ -n "$time" ]; then
+            echo "  [$logname] successfully installed ($time)."
+        else
+            echo "  [$logname] successfully installed."
+        fi
     fi
     exit $status
 else
     # Redirect stdout and stderr to a subprocess running tee.
     # We trap SIGINT such that SIGINT interrupts the main process being
     # run, not the logging.
 
-    ( exec 2>&1; eval "$cmd" ) | \
+    ( exec 2>&1;
+      $TIME sh -c "$cmd"; status=$?; report_time;
+      exit $status ) | \
         ( trap '' SIGINT; if [ -n "$GITHUB_ACTIONS" -a -n "$prefix" ]; then echo "::group::${logname}"; fi; tee -a "$logfile" | $SED; if [ -n "$GITHUB_ACTIONS" -a -n "$prefix" ]; then echo "::endgroup::"; fi )
 
     pipestatus=(${PIPESTATUS[*]})