Trac sagemath#34081: Upgrade scipy to 1.9.x, add meson toolchain

- https://scipy.github.io/devdocs/release.1.9.0.html (released)
  - scipy.optimize.milp (HiGHS MIP solver)
  - https://scipy.github.io/devdocs/release.1.9.0.html#scipy-switched-
to-meson-as-its-build-system

This ticket is also the target ticket for https://github.com/FFY00
/meson-python/blob/main/.github/workflows/ci-sage.yml

Previous update:
- sagemath#32423 Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x

See also:
- sagemath#34110 numpy 1.23.x

URL: https://trac.sagemath.org/34081
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Dima Pasechnik

.github/workflows/ci-linux.yml

@@ -51,6 +51,7 @@ jobs:
     with:
       # Build incrementally from previous stage (pre)
       incremental: true
+      free_disk_space: true
       from_docker_repository: ghcr.io/${{ github.repository }}/
       from_docker_target: "with-targets-pre"
       docker_targets: "with-targets with-targets-optional"
@@ -82,6 +83,7 @@ jobs:
     with:
       # Build incrementally from previous stage (pre)
       incremental: true
+      free_disk_space: true
       from_docker_repository: ghcr.io/${{ github.repository }}/
       from_docker_target: "with-targets-pre"
       docker_targets: "with-targets with-targets-optional"
@@ -97,6 +99,7 @@ jobs:
     needs: [minimal]
     uses: ./.github/workflows/docker.yml
     with:
+      free_disk_space: true
       # Build from scratch
       docker_targets: "with-system-packages configured with-targets-pre"
       # FIXME: duplicated from env.TARGETS
@@ -111,6 +114,7 @@ jobs:
     uses: ./.github/workflows/docker.yml
     with:
       incremental: true
+      free_disk_space: true
       from_docker_repository: ghcr.io/${{ github.repository }}/
       from_docker_target: "with-targets-pre"
       tox_packages_factors: >-
@@ -125,6 +129,7 @@ jobs:
     uses: ./.github/workflows/docker.yml
     with:
       incremental: true
+      free_disk_space: true
       from_docker_repository: ghcr.io/${{ github.repository }}/
       from_docker_target: "with-targets-pre"
       tox_packages_factors: >-
@@ -138,6 +143,7 @@ jobs:
     uses: ./.github/workflows/docker.yml
     with:
       incremental: true
+      free_disk_space: true
       from_docker_repository: ghcr.io/${{ github.repository }}/
       from_docker_target: "with-targets-pre"
       tox_packages_factors: >-
@@ -151,6 +157,7 @@ jobs:
     uses: ./.github/workflows/docker.yml
     with:
       incremental: true
+      free_disk_space: true
       from_docker_repository: ghcr.io/${{ github.repository }}/
       from_docker_target: "with-targets-pre"
       tox_packages_factors: >-

.github/workflows/docker.yml

@@ -61,9 +61,16 @@ on:
           ["minimal",
            "standard",
            ]
+      extra_sage_packages:
+        description: 'Extra Sage packages to install as system packages'
+        type: string
+        default: ""
       max_parallel:
         type: number
         default: 24
+      free_disk_space:
+        default: false
+        type: boolean
       #
       # Publishing to GitHub Packages
       #
@@ -128,14 +135,14 @@ jobs:
       FROM_DOCKER_TARGET: ${{ inputs.from_docker_target }}
       FROM_DOCKER_TAG:    ${{ inputs.from_docker_tag }}
       EXTRA_CONFIGURE_ARGS: --enable-fat-binary
-
+      EXTRA_SAGE_PACKAGES:  ${{ inputs.extra_sage_packages }}
     steps:
       - name: Check out SageMath
         uses: actions/checkout@v2
         with:
           repository: ${{ inputs.sage_repo }}
           ref: ${{ inputs.sage_ref }}
-          fetch-depth: 2000
+          fetch-depth: 10000
       - name: fetch tags
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
@@ -149,6 +156,7 @@ jobs:
           dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
           sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
+        if: inputs.free_disk_space
       - name: Check out git-trac-command
         uses: actions/checkout@v2
         with:
@@ -190,7 +198,7 @@ jobs:
               TOKEN="${{ secrets.GITHUB_TOKEN }}"
             fi
             if echo "$TOKEN" | docker login ghcr.io -u ${{ github.actor }} --password-stdin; then
-              echo "DOCKER_PUSH_REPOSITORY=${{ inputs.docker_push_repository }}" >> $GITHUB_ENV
+              echo "DOCKER_PUSH_REPOSITORY=$(echo ${{ inputs.docker_push_repository }} | tr "[:upper:]" "[:lower:]")" >> $GITHUB_ENV
               echo "DOCKER_CONFIG_FILE=$HOME/.docker/config.json" >> $GITHUB_ENV
             fi
             # From the docker documentation via .ci/update-env.sh:

build/make/Makefile.in

@@ -443,8 +443,9 @@ $(foreach pkgname, $(NORMAL_PACKAGES) $(SCRIPT_PACKAGES),\
 #
 # Since Python's self-tests seem to fail on all platforms, we disable
 # its test suite by default.
+# meson_python 0.10.0 fails on some platforms, so we reduce it to warnings.
 # However, if SAGE_CHECK=warn, we do not do that.
-SAGE_CHECK_PACKAGES_DEFAULT_yes := !python3
+SAGE_CHECK_PACKAGES_DEFAULT_yes := !python3,?meson_python
 SAGE_CHECK_PACKAGES_DEFAULT_warn :=
 SAGE_CHECK_PACKAGES_DEFAULT_no :=
 comma := ,

build/pkgs/git/distros/arch.txt

@@ -0,0 +1 @@
+git

build/pkgs/gitpython/SPKG.rst

@@ -0,0 +1,18 @@
+gitpython: GitPython is a python library used to interact with Git repositories
+===============================================================================
+
+Description
+-----------
+
+GitPython is a python library used to interact with Git repositories
+
+License
+-------
+
+BSD
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/GitPython/
+

build/pkgs/gitpython/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.

build/pkgs/gitpython/requirements.txt

@@ -0,0 +1 @@
+GitPython

build/pkgs/gitpython/type

@@ -0,0 +1 @@
+optional

build/pkgs/meson/SPKG.rst

@@ -0,0 +1,18 @@
+meson: A high performance build system
+======================================
+
+Description
+-----------
+
+A high performance build system
+
+License
+-------
+
+Apache License, Version 2.0
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/meson/
+

build/pkgs/meson/checksums.ini

@@ -0,0 +1,5 @@
+tarball=meson-VERSION.tar.gz
+sha1=3bce963302f547547c82fda35f84838ebc608e8a
+md5=b2f2757b5dd84cc754b9df53ce37a175
+cksum=2257545181
+upstream_url=https://pypi.io/packages/source/m/meson/meson-VERSION.tar.gz

build/pkgs/meson/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.

build/pkgs/meson/install-requires.txt

@@ -0,0 +1 @@
+meson

build/pkgs/meson/package-version.txt

@@ -0,0 +1 @@
+0.63.3

build/pkgs/meson/spkg-install.in

@@ -0,0 +1,2 @@
+cd src
+sdh_pip_install .

build/pkgs/meson/type

@@ -0,0 +1 @@
+standard

build/pkgs/meson_python/SPKG.rst

@@ -0,0 +1,16 @@
+meson_python: Meson Python build backend (PEP 517)
+==================================================
+
+Description
+-----------
+
+Meson Python build backend (PEP 517)
+
+License
+-------
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/meson-python/
+

build/pkgs/meson_python/checksums.ini

@@ -0,0 +1,5 @@
+tarball=meson_python-VERSION.tar.gz
+sha1=6ff574d17feb98165a2678c78a429d3ff32aaa7b
+md5=afd824bf61e79cd5eeab2a6dc7863eaf
+cksum=3939516041
+upstream_url=https://pypi.io/packages/source/m/meson_python/meson_python-VERSION.tar.gz

build/pkgs/meson_python/dependencies

@@ -0,0 +1,10 @@
+$(PYTHON) meson pyproject_metadata tomli ninja_build patchelf | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+
+meson_python actually declares a dependency on ninja, the Python distribution package.
+But it only needs the ninja executable.
+
+buildelf is needed by projects that use meson_python as their build system
+for wheel building.

build/pkgs/meson_python/dependencies_check

@@ -0,0 +1 @@
+pytest pytest_mock gitpython cython auditwheel_or_delocate

build/pkgs/meson_python/install-requires.txt

@@ -0,0 +1 @@
+meson-python

build/pkgs/meson_python/package-version.txt

@@ -0,0 +1 @@
+0.10.0

build/pkgs/meson_python/spkg-check.in

@@ -0,0 +1,2 @@
+cd src
+pytest

build/pkgs/meson_python/spkg-install.in

@@ -0,0 +1,2 @@
+cd src
+sdh_pip_install --no-build-isolation --no-deps .

build/pkgs/meson_python/type

@@ -0,0 +1 @@
+standard

build/pkgs/patchelf/SPKG.rst

@@ -0,0 +1,17 @@
+patchelf: A small utility to modify the dynamic linker and RPATH of ELF executables
+===================================================================================
+
+Description
+-----------
+
+A small utility to modify the dynamic linker and RPATH of ELF executables.
+
+License
+-------
+
+GPL-3.0-or-later
+
+Upstream Contact
+----------------
+
+https://github.com/NixOS/patchelf

build/pkgs/patchelf/checksums.ini

@@ -0,0 +1,5 @@
+tarball=patchelf-VERSION.tar.bz2
+sha1=5d9c1690c0fbe70c312f43d597e04b6c1eeffc60
+md5=04d243d3626a33201b0d6eef0e2c4317
+cksum=92812155
+upstream_url=https://github.com/NixOS/patchelf/releases/download/VERSION/patchelf-VERSION.tar.bz2

build/pkgs/patchelf/dependencies

@@ -0,0 +1,4 @@
+| bzip2
+
+----------
+All lines of this file are ignored except the first.

build/pkgs/patchelf/package-version.txt

@@ -0,0 +1 @@
+0.13.1

build/pkgs/patchelf/spkg-install.in

@@ -0,0 +1,6 @@
+cd src
+if [ "$UNAME" = "Linux" ]; then
+   sdh_configure
+   sdh_make
+   sdh_make_install
+fi

build/pkgs/patchelf/type

@@ -0,0 +1 @@
+standard

build/pkgs/pyproject_metadata/checksums.ini

@@ -1,5 +1,5 @@
 tarball=pyproject-metadata-VERSION.tar.gz
-sha1=5421824aa29786bde43f510365c4d035a0614ba5
-md5=85fcbd5d777809ca2217a996e06fe2e0
-cksum=1327227039
+sha1=c2b7679b1e56a341aa00c186c0d1a6bbd7bd5c2c
+md5=e13b11cb723da96f8397addddca963cc
+cksum=2246727402
 upstream_url=https://pypi.io/packages/source/p/pyproject_metadata/pyproject-metadata-VERSION.tar.gz

build/pkgs/pyproject_metadata/package-version.txt

@@ -1 +1 @@
-0.5.0
+0.6.1

build/pkgs/pytest_mock/SPKG.rst

@@ -0,0 +1,18 @@
+pytest_mock: Thin-wrapper around the mock package for easier use with pytest
+============================================================================
+
+Description
+-----------
+
+Thin-wrapper around the mock package for easier use with pytest
+
+License
+-------
+
+MIT
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/pytest-mock/
+

build/pkgs/pytest_mock/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) pytest packaging attrs pluggy tomli py pyparsing | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.

build/pkgs/pytest_mock/requirements.txt

@@ -0,0 +1 @@
+pytest-mock

build/pkgs/pytest_mock/type

@@ -0,0 +1 @@
+optional

build/pkgs/scipy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=scipy-VERSION.tar.gz
-sha1=6dfee9fe5f021409b4d294b0a7d9da05b810d207
-md5=df5ce79288fc457238aeef18e8f70dfc
-cksum=3909760197
+sha1=f93163946802657fcd1c10821a1330497045ef6b
+md5=ee6db269d03b2d47d04e876d38515d0d
+cksum=3886027417
 upstream_url=https://pypi.io/packages/source/s/scipy/scipy-VERSION.tar.gz

build/pkgs/scipy/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) $(BLAS) gfortran numpy pybind11 pythran | $(PYTHON_TOOLCHAIN)
+$(PYTHON) $(BLAS) gfortran numpy pybind11 cython pythran | $(PYTHON_TOOLCHAIN) meson_python
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/scipy/dependencies_check

@@ -0,0 +1 @@
+pytest

build/pkgs/scipy/package-version.txt

@@ -1 +1 @@
-1.8.1
+1.9.2

build/pkgs/scipy/spkg-check.in

@@ -0,0 +1 @@
+python3 -c 'import scipy; scipy.test()'