Modularization of sagelib: Distributions sagemath-{brial,combinat,eclib,flint,gap,giac,glpk,graphs,groups,homfly,lcalc,libbraiding,libecm,linbox,modules,mpmath,ntl,pari,plot,polyhedra,schemes,singular,standard-no-symbolics,symbolics}

.ci/write-dockerfile.sh

@@ -279,7 +279,7 @@ $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-
 $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/Pipfile.m4 src/pyproject.toml src/requirements.txt.m4 src/VERSION.txt /new/src/
 $ADD m4 /new/m4
 $ADD pkgs /new/pkgs
 $ADD build /new/build

.github/workflows/dist.yml

@@ -181,7 +181,7 @@ jobs:
       # SPKGs to install as system packages
       SPKGS: _bootstrap _prereq
       # Non-Python packages to install as spkgs
-      TARGETS_PRE: gmp mpfr mpc bliss coxeter3 mcqd meataxe sirocco boost_cropped tdlib
+      TARGETS_PRE: gmp mpfr mpc bliss coxeter3 mcqd meataxe sirocco boost_cropped tdlib brial
       CIBW_BUILD: "*${{ matrix.build }}*"
       # Disable building PyPy wheels on all platforms
       CIBW_SKIP: "pp*"
@@ -255,6 +255,10 @@ jobs:
         run: |
           "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*bliss*
 
+      - name: sagemath-brial
+        run: |
+          "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*brial*
+
       - name: sagemath-coxeter3
         run: |
           "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*coxeter3*
@@ -263,6 +267,13 @@ jobs:
         run: |
           "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*mcqd*
 
+      - name: sagemath-tdlib
+        run: |
+          case "${{ matrix.arch }}" in
+              sagemath*tdlib:i686) ;;  # broken - boost-related
+              *) "${{ steps.python.outputs.python-path }}" -m cibuildwheel unpacked/sagemath*tdlib*
+          esac
+
       - uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.os }}-${{ matrix.build }}-${{ matrix.arch }}-wheels

.github/workflows/docker.yml

@@ -28,6 +28,7 @@ on:
            "debian-bullseye",
            "debian-bookworm",
            "debian-trixie",
+           "debian-trixie-python3.12",
            "debian-sid",
            "linuxmint-20.1",
            "linuxmint-20.2",
@@ -45,6 +46,7 @@ on:
            "fedora-36",
            "fedora-37",
            "fedora-38",
+           "fedora-38-python3.12",
            "fedora-39",
            "fedora-40",
            "fedora-41",
@@ -58,8 +60,10 @@ on:
            "archlinux-latest",
            "opensuse-15.5-gcc_11-python3.11",
            "opensuse-tumbleweed-python3.10",
-           "opensuse-tumbleweed",
+           "opensuse-tumbleweed-python3.11",
+           "opensuse-tumbleweed-python3.12",
            "conda-forge-python3.11",
+           "conda-forge",
            "ubuntu-bionic-gcc_8-i386",
            "debian-bullseye-i386",
           ]

.github/workflows/doctest-problem-matcher.json

@@ -0,0 +1,17 @@
+{
+    "problemMatcher": [
+        {
+            "owner": "doctest-failure",
+            "severity": "error",
+            "pattern": [
+                {
+                    "regexp": "^(\\[(\\S*)-[0-9.a-z]\\] )?File \"(\\S*)\", line ([0-9]*), in (\\S*)\\s*$(\\[(\\S*)-[0-9.a-z]\\] )?^(Failed example):",
+                    "code": 2,
+                    "file": 3,
+                    "line": 4,
+                    "message": 7,
+                }
+            ]
+        }
+    ]
+}

.gitignore

@@ -52,9 +52,10 @@
 /src/environment-optional-3.11.yml
 
 /src/setup.cfg
-/src/requirements.txt
+/src/requirements*.txt
 /src/Pipfile
 /src/Pipfile.lock
+/src/pyproject.toml
 /Pipfile
 /Pipfile.lock
 
@@ -185,28 +186,20 @@ __pycache__/
 build/temp.*/
 build/bin/sage-build-env-config
 
-# Generated files in build
-build/pkgs/cypari/version_requirements.txt
-build/pkgs/cysignals/version_requirements.txt
-build/pkgs/cython/version_requirements.txt
-build/pkgs/gmpy2/version_requirements.txt
-build/pkgs/jupyter_core/version_requirements.txt
-build/pkgs/memory_allocator/version_requirements.txt
-build/pkgs/numpy/version_requirements.txt
-build/pkgs/pkgconfig/version_requirements.txt
-build/pkgs/pplpy/version_requirements.txt
-build/pkgs/setuptools/version_requirements.txt
-build/pkgs/wheel/version_requirements.txt
+# Vendored on sdist/install
+/src/sage/libs/mpmath/_vendor/mpmath*
 
 # Generated files in the top-level source trees
 /pkgs/*/build
+/pkgs/*/cython_debug
 /pkgs/*/dist
 /pkgs/*/MANIFEST
 /pkgs/*/*.egg-info
 /pkgs/*/.tox
 /pkgs/*/venv*
 /pkgs/*/.venv*
 
+/pkgs/sage-conf/pyproject.toml
 /pkgs/sage-conf_pypi/sage_root/config.log
 /pkgs/sage-conf_pypi/sage_root/config.status
 /pkgs/sage-conf_pypi/sage_root/local/
@@ -219,6 +212,7 @@ build/pkgs/wheel/version_requirements.txt
 
 /pkgs/sagemath-objects/setup.cfg
 /pkgs/sagemath-bliss/setup.cfg
+/pkgs/sagemath-brial/setup.cfg
 /pkgs/sagemath-coxeter3/setup.cfg
 /pkgs/sagemath-mcqd/setup.cfg
 /pkgs/sagemath-meataxe/setup.cfg
@@ -227,8 +221,36 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-categories/setup.cfg
 /pkgs/sagemath-environment/setup.cfg
 /pkgs/sagemath-repl/setup.cfg
+/pkgs/sagemath-polyhedra/setup.cfg
+/pkgs/sagemath-combinat/setup.cfg
+/pkgs/sagemath-graphs/setup.cfg
+/pkgs/sagemath-groups/setup.cfg
+/pkgs/sagemath-modules/setup.cfg
+/pkgs/sagemath-schemes/setup.cfg
+/pkgs/sagemath-plot/setup.cfg
+/pkgs/sagemath-symbolics/setup.cfg
+/pkgs/sagemath-standard-no-symbolics/setup.cfg
+/pkgs/sagemath-flint/setup.cfg
+/pkgs/sagemath-gap/setup.cfg
+/pkgs/sagemath-giac/setup.cfg
+/pkgs/sagemath-glpk/setup.cfg
+/pkgs/sagemath-homfly/setup.cfg
+/pkgs/sagemath-linbox/setup.cfg
+/pkgs/sagemath-mpmath/setup.cfg
+/pkgs/sagemath-ntl/setup.cfg
+/pkgs/sagemath-pari/setup.cfg
+/pkgs/sagemath-singular/setup.cfg
+/pkgs/sagemath-brial/setup.cfg
+/pkgs/sagemath-eclib/setup.cfg
+/pkgs/sagemath-lcalc/setup.cfg
+/pkgs/sagemath-libbraiding/setup.cfg
+/pkgs/sagemath-libecm/setup.cfg
+
+/pkgs/*/pyproject.toml
+
 /pkgs/sagemath-objects/pyproject.toml
 /pkgs/sagemath-bliss/pyproject.toml
+/pkgs/sagemath-brial/pyproject.toml
 /pkgs/sagemath-coxeter3/pyproject.toml
 /pkgs/sagemath-mcqd/pyproject.toml
 /pkgs/sagemath-meataxe/pyproject.toml
@@ -239,6 +261,7 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-repl/pyproject.toml
 /pkgs/sagemath-objects/requirements*.txt
 /pkgs/sagemath-bliss/requirements*.txt
+/pkgs/sagemath-brial/requirements*.txt
 /pkgs/sagemath-coxeter3/requirements*.txt
 /pkgs/sagemath-mcqd/requirements*.txt
 /pkgs/sagemath-meataxe/requirements*.txt
@@ -247,7 +270,43 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/sagemath-categories/requirements*.txt
 /pkgs/sagemath-environment/requirements*.txt
 /pkgs/sagemath-repl/requirements*.txt
+/pkgs/sagemath-polyhedra/requirements*.txt
+/pkgs/sagemath-combinat/requirements*.txt
+/pkgs/sagemath-graphs/requirements*.txt
+/pkgs/sagemath-groups/requirements*.txt
+/pkgs/sagemath-modules/requirements*.txt
+/pkgs/sagemath-plot/requirements*.txt
+/pkgs/sagemath-schemes/requirements*.txt
+/pkgs/sagemath-symbolics/requirements*.txt
+/pkgs/sagemath-standard-no-symbolics/requirements*.txt
+/pkgs/sagemath-flint/requirements*.txt
+/pkgs/sagemath-gap/requirements*.txt
+/pkgs/sagemath-giac/requirements*.txt
+/pkgs/sagemath-glpk/requirements*.txt
+/pkgs/sagemath-homfly/requirements*.txt
+/pkgs/sagemath-linbox/requirements*.txt
+/pkgs/sagemath-mpmath/requirements*.txt
+/pkgs/sagemath-ntl/requirements*.txt
+/pkgs/sagemath-pari/requirements*.txt
+/pkgs/sagemath-singular/requirements*.txt
+/pkgs/sagemath-brial/requirements*.txt
+/pkgs/sagemath-eclib/requirements*.txt
+/pkgs/sagemath-lcalc/requirements*.txt
+/pkgs/sagemath-libbraiding/requirements*.txt
+/pkgs/sagemath-libecm/requirements*.txt
+
 /pkgs/sagemath-categories/MANIFEST.in
+/pkgs/sagemath-polyhedra/MANIFEST.in
+/pkgs/sagemath-combinat/MANIFEST.in
+/pkgs/sagemath-graphs/MANIFEST.in
+/pkgs/sagemath-groups/MANIFEST.in
+/pkgs/sagemath-modules/MANIFEST.in
+/pkgs/sagemath-plot/MANIFEST.in
+/pkgs/sagemath-schemes/MANIFEST.in
+/pkgs/sagemath-symbolics/MANIFEST.in
+/pkgs/sagemath-standard-no-symbolics/MANIFEST.in
+
+/pkgs/sagemath-mpmath/vendor.txt
 
 # same for old locations - before Issue #31577
 /build/pkgs/*/src/build
@@ -274,6 +333,9 @@ src/*.egg-info/
 /src/bin/sage-env-config
 /src/bin/sage-src-env-config
 
+# Generated by sage-generate-meson
+/src/**/meson.build
+
 # Virtual environments
 /venv
 src/.env
@@ -299,3 +361,8 @@ src/.coverage/
 # git worktree
 worktree*
 **/worktree*
+
+# Pyodide
+**/.pyodide-xbuildenv
+/emsdk/
+/venv-pyodide*/

Makefile

@@ -178,17 +178,6 @@ bootstrap-clean:
 	rm -f src/Pipfile
 	rm -f src/requirements.txt
 	rm -f src/setup.cfg
-	rm -f build/pkgs/cypari/version_requirements.txt
-	rm -f build/pkgs/cysignals/version_requirements.txt
-	rm -f build/pkgs/cython/version_requirements.txt
-	rm -f build/pkgs/gmpy2/version_requirements.txt
-	rm -f build/pkgs/jupyter_core/version_requirements.txt
-	rm -f build/pkgs/memory_allocator/version_requirements.txt
-	rm -f build/pkgs/numpy/version_requirements.txt
-	rm -f build/pkgs/pkgconfig/version_requirements.txt
-	rm -f build/pkgs/pplpy/version_requirements.txt
-	rm -f build/pkgs/setuptools/version_requirements.txt
-	rm -f build/pkgs/wheel/version_requirements.txt
 
 # Remove absolutely everything which isn't part of the git repo
 maintainer-clean: distclean bootstrap-clean

bootstrap

@@ -33,15 +33,6 @@ MAKE="${MAKE:-make}"
 
 
 bootstrap () {
-    for pkgname in cypari cysignals cython gmpy2 jupyter_core memory_allocator numpy pkgconfig pplpy setuptools wheel; do
-        # Write the version_requirements.txt files for dependencies declared in pyproject.toml
-        target=build/pkgs/${pkgname}/version_requirements.txt
-        if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
-            echo "bootstrap:$LINENO: installing '"$target"'"
-        fi
-        echo "# Generated by SAGE_ROOT/bootstrap based on src/pyproject.toml; do not edit directly" > $target
-        sage-get-system-packages install-requires ${pkgname} >> $target
-    done
     for a in m4/sage_spkg_configures.m4 m4/sage_spkg_versions.m4 m4/sage_spkg_versions_toml.m4; do
         if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
             echo "bootstrap:$LINENO: installing '"$a"'"
@@ -232,19 +223,7 @@ save () {
 	src/environment-optional-3.[89].yml src/environment-optional-3.1[0-9].yml \
 	src/Pipfile \
 	src/pyproject.toml \
-	src/requirements.txt \
-	src/setup.cfg \
-	build/pkgs/cypari/version_requirements.txt \
-	build/pkgs/cysignals/version_requirements.txt \
-	build/pkgs/cython/version_requirements.txt \
-	build/pkgs/gmpy2/version_requirements.txt \
-	build/pkgs/jupyter_core/version_requirements.txt \
-	build/pkgs/memory_allocator/version_requirements.txt \
-	build/pkgs/numpy/version_requirements.txt \
-	build/pkgs/pkgconfig/version_requirements.txt \
-	build/pkgs/pplpy/version_requirements.txt \
-	build/pkgs/setuptools/version_requirements.txt \
-	build/pkgs/wheel/version_requirements.txt
+	src/requirements.txt
 
     # Update version; this re-computes the checksum
     sage-package update configure "$NEWCONFVERSION"

bootstrap-conda

@@ -10,7 +10,8 @@ STRIP_COMMENTS="sed s/#.*//;"
 
 shopt -s extglob
 
-DEVELOP_SPKG_PATTERN="@(_develop$(for a in $(head -n 1 build/pkgs/_develop/dependencies); do echo -n "|"$a; done))"
+eval $(sage-package dependencies --format=shell :all:)
+DEVELOP_SPKG_PATTERN="@(_develop|${runtime_deps__develop// /|})"
 BOOTSTRAP_PACKAGES=_bootstrap
 PACKAGES=
 OPTIONAL_PACKAGES=
@@ -139,18 +140,22 @@ echo >&2 $0:$LINENO: generate conda environment files
             if [ ! -f $SYSTEM_PACKAGES_FILE ]; then
                 SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/version_requirements.txt
             fi
-            if grep -q SAGERUNTIME $PKG_SCRIPTS/dependencies $PKG_SCRIPTS/dependencies_order_only 2>/dev/null; then
-                : # cannot install packages that depend on the Sage library
-            else
-                case "$PKG_BASE:$PKG_TYPE" in
-                    $DEVELOP_SPKG_PATTERN:*) FD=4;;
-                    *:standard)              FD="4 5";;
-                    *)                       FD=5;;
-                esac
-                ${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE | while read -r line; do
-                    [ -n "$line" ] && for fd in $FD; do echo >&$fd "    - $line"; done
-                done
-            fi
+            eval DEPS=\"\$runtime_deps_$PKG_BASE\ \$build_deps_$PKG_BASE\ \$order_only_deps_$PKG_BASE\"
+            case "$DEPS" in
+                *SAGERUNTIME*)
+                    # cannot install packages that depend on the Sage library
+                    ;;
+                *)
+                    case "$PKG_BASE:$PKG_TYPE" in
+                        $DEVELOP_SPKG_PATTERN:*) FD=4;;
+                        *:standard)              FD="4 5";;
+                        *)                       FD=5;;
+                    esac
+                    ${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE | while read -r line; do
+                        [ -n "$line" ] && for fd in $FD; do echo >&$fd "    - $line"; done
+                    done
+                    ;;
+            esac
         done
     ) 4>> /dev/null 5>> src/environment-optional-template.yml
 

build/bin/sage-get-system-packages

@@ -101,9 +101,14 @@ for PKG_BASE in $SPKGS; do
             *pyproject.toml)
                 SYSTEM_PACKAGES_FILE="$SAGE_ROOT"/$NAME
                 if [ -f "$SYSTEM_PACKAGES_FILE" ]; then
-                    # Extract from the "requires" block in src/pyproject.toml
+                    # Extract from src/pyproject.toml:
+                    #  - from the "[build-system] requires" value
+                    #  - from "[project] dependencies",
+                    #  - from "[project.optional-dependencies]"
                     # Packages are in the format "'sage-conf ~= 10.3b3',"
-                    PACKAGE_INFO=$(sed -n '/requires *= *\[/,/^\]/s/^ *'\''\('$PKG_BASE'.*\)'\'',/\1/p' "$SAGE_ROOT/src/pyproject.toml")
+                    # Accept dashes and underscores in package names as equivalent:
+                    PKG_REGEX=$(echo $PKG_BASE | sed 's/[-_]/[-_]/g')
+                    PACKAGE_INFO=$(sed -En '/(requires|dependencies|R) *= *\[/,/^\]/s/^ *'\''('$PKG_REGEX'.*)'\'',/\1/p' "$SAGE_ROOT/src/pyproject.toml" | sort -u)
                     if [ -n "$PACKAGE_INFO" ]; then
                         echo "$PACKAGE_INFO" | ${STRIP_COMMENTS}
                         [ $SYSTEM = versions ] || break

build/bin/sage-site

@@ -92,6 +92,19 @@ if [ "$1" = "-advanced" -o "$1" = "--advanced" ]; then
     exit 0
 fi
 
+# Delegation
+
+if [ "$1" = '-distribution' -o "$1" = '--distribution' ]; then
+    distribution=$(echo "$2" | cut -f1 -d'[' | tr _ -)
+    case "$2" in
+        *\[*\]) extras_suffix=-$(echo "$2" | cut -f2 -d'[' | sed 's/,/--/;s/]//;');;
+        *)    extras_suffix=
+    esac
+    shift 2
+
+    exec "$SAGE_ROOT"/pkgs/$distribution/.tox/sagepython-sagewheels-nopypi-norequirements$extras_suffix/bin/sage "$@"
+fi
+
 #####################################################################
 # Package handling
 #####################################################################

build/bin/sage-spkg

@@ -97,6 +97,7 @@ Other options:
        use at your own risk
    -n: automatically reply "n" for all prompts regarding
        experimental and old-style packages
+   -d: only download the package
    -o: allow fetching the package from its upstream URL
        when it is not available from the Sage mirrors (yet)
    -c: after installing, run the test suite for the package;