Merge branch 'conda_remove_broken_packages' into 10.2.beta5+updates

.devcontainer/onCreate-conda.sh

@@ -4,7 +4,7 @@ set -e
 # Create conda environment
 ./bootstrap-conda
 conda install mamba -n base -c conda-forge -y
-mamba env create --file src/environment-dev.yml || mamba env update --file src/environment-dev.yml
+mamba env create --file src/environment-dev-3.11.yml || mamba env update --file src/environment-dev-3.11.yml
 conda init bash
 
 # Build sage

.github/workflows/ci-conda.yml

@@ -77,17 +77,17 @@ jobs:
         with:
           path: ~/conda_pkgs_dir
           key:
-            ${{ runner.os }}-conda-${{ hashFiles('src/environment.yml') }}
+            ${{ runner.os }}-conda-${{ hashFiles('src/environment-3.11.yml') }}
 
       - name: Setup Conda
         uses: conda-incubator/setup-miniconda@v2
         with:
           python-version: ${{ matrix.python }}
           mamba-version: "*"
           channels: conda-forge,defaults
-          channel-priority: true
+          channel-priority: strict
           activate-environment: sage-build
-          environment-file: src/${{ matrix.conda-env }}.yml
+          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}.yml
 
       - name: Print Conda environment
         shell: bash -l {0}
@@ -101,7 +101,7 @@ jobs:
         run: |
           ./bootstrap
           echo "::add-matcher::.github/workflows/configure-systempackage-problem-matcher.json"
-          ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX $(for pkg in $(./sage -package list :standard: --has-file spkg-configure.m4 --has-file distros/conda.txt --exclude rpy2); do echo --with-system-$pkg=force; done)
+          ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX --enable-system-site-packages $(for pkg in $(./sage -package list :standard: --has-file spkg-configure.m4 --has-file distros/conda.txt --exclude rpy2); do echo --with-system-$pkg=force; done)
           echo "::remove-matcher owner=configure-system-package-warning::"
           echo "::remove-matcher owner=configure-system-package-error::"
 
@@ -110,7 +110,7 @@ jobs:
         run: |
           # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda.
           pip install --no-build-isolation --no-deps -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
-          pip install --no-build-isolation --no-deps -v -v -e ./src
+          pip install --no-build-isolation --no-deps --config-settings editable_mode=compat -v -v -e ./src
         env:
           SAGE_NUM_THREADS: 2
 

.gitignore

@@ -27,11 +27,29 @@
 # no longer generated, but may still be in user worktrees
 /src/lib/pkgconfig
 
+# Environment files generated by bootstrap-conda.
+# The files without Python version are no longer generated
+# but may still be in users' directories.
 /environment.yml
+/environment-3.9.yml
+/environment-3.10.yml
+/environment-3.11.yml
 /environment-optional.yml
+/environment-optional-3.9.yml
+/environment-optional-3.10.yml
+/environment-optional-3.11.yml
 /src/environment.yml
+/src/environment-3.9.yml
+/src/environment-3.10.yml
+/src/environment-3.11.yml
 /src/environment-dev.yml
+/src/environment-dev-3.9.yml
+/src/environment-dev-3.10.yml
+/src/environment-dev-3.11.yml
 /src/environment-optional.yml
+/src/environment-optional-3.9.yml
+/src/environment-optional-3.10.yml
+/src/environment-optional-3.11.yml
 
 /src/setup.cfg
 /src/requirements.txt

.gitpod.yml

@@ -8,7 +8,7 @@ tasks:
     # Create conda environment, then configure and build sage
     init: >-
       ./bootstrap-conda
-      && mamba env create --file src/environment-dev.yml --prefix venv
+      && mamba env create --file src/environment-dev-3.11.yml --prefix venv
       && conda config --append envs_dirs $(pwd)
       && conda activate $(pwd)/venv
       && ./bootstrap

Makefile

@@ -158,11 +158,7 @@ bootstrap-clean:
 	rm -rf config/install-sh config/compile config/config.guess config/config.sub config/missing configure build/make/Makefile-auto.in
 	rm -f src/doc/en/installation/*.txt
 	rm -rf src/doc/en/reference/spkg/*.rst
-	rm -f environment.yml
-	rm -f src/environment.yml
-	rm -f src/environment-dev.yml
-	rm -f environment-optional.yml
-	rm -f src/environment-optional.yml
+	for a in environment environment-optional src/environment src/environment-dev src/environment-optional; do rm -f $$a.yml $$a-3.[89].yml $$a-3.1[0-9].yml; done
 	rm -f src/Pipfile
 	rm -f src/pyproject.toml
 	rm -f src/requirements.txt

bootstrap

@@ -216,10 +216,10 @@ save () {
 	build/make/Makefile-auto.in \
 	src/doc/en/installation/*.txt \
 	src/doc/en/reference/spkg/*.rst \
-	environment.yml \
-	src/environment.yml \
-	environment-optional.yml \
-	src/environment-optional.yml \
+	environment-3.[89].yml environment-3.1[0-9].yml \
+	src/environment-3.[89].yml src/environment-3.1[0-9].yml \
+	environment-optional-3.[89].yml environment-optional-3.1[0-9].yml \
+	src/environment-optional-3.[89].yml src/environment-optional-3.1[0-9].yml \
 	src/Pipfile \
 	src/pyproject.toml \
 	src/requirements.txt \

bootstrap-conda

@@ -51,72 +51,75 @@ for PKG_BASE in $(sage-package list --has-file distros/conda.txt --exclude _sage
     fi
 done
 echo >&2 $0:$LINENO: generate conda environment files
-(
-    echo "name: sage-build"
-    echo "channels:"
-    echo "  - conda-forge"
-    echo "  - nodefaults"
-    echo "dependencies:"
-    for pkg in $SYSTEM_PACKAGES; do
-        echo "  - $pkg"
-    done
-    echo "  # Packages needed for ./bootstrap"
-    for pkg in $BOOTSTRAP_PACKAGES; do
-        echo "  - $pkg"
-    done
-) > environment.yml
+for python_version in 3.9 3.10 3.11; do
+    (
+        echo "name: sage-build"
+        echo "channels:"
+        echo "  - conda-forge"
+        echo "  - nodefaults"
+        echo "dependencies:"
+        echo "  - python=$python_version"
+        for pkg in $SYSTEM_PACKAGES; do
+            echo "  - $pkg"
+        done
+        echo "  # Packages needed for ./bootstrap"
+        for pkg in $BOOTSTRAP_PACKAGES; do
+            echo "  - $pkg"
+        done
+    ) > environment-$python_version.yml
+    (
+        sed 's/name: sage-build/name: sage/' environment-$python_version.yml
+        echo "  # Additional packages providing all dependencies for the Sage library"
+        for pkg in $SAGELIB_SYSTEM_PACKAGES; do
+            echo "  - $pkg"
+        done
+    ) > src/environment-$python_version.yml
 
-(
-    sed 's/name: sage-build/name: sage/' environment.yml
-    echo "  # Additional packages providing all dependencies for the Sage library"
-    for pkg in $SAGELIB_SYSTEM_PACKAGES; do
-        echo "  - $pkg"
-    done
-) > src/environment.yml
+    (
+        cat environment-$python_version.yml
+        echo "  # optional packages"
+        for pkg in $OPTIONAL_SYSTEM_PACKAGES; do
+            echo "  - $pkg"
+        done
+    ) > environment-optional-$python_version.yml
 
-(
-    sed 's/name: sage/name: sage-dev/' src/environment.yml
-    echo "  # Additional dev tools"
-    for pkg in $DEVELOP_SYSTEM_PACKAGES; do
-        echo "  - $pkg"
-    done
-) > src/environment-dev.yml
-
-(
-    cat environment.yml
-    echo "  # optional packages"
-    for pkg in $OPTIONAL_SYSTEM_PACKAGES; do
-        echo "  - $pkg"
-    done
-) > environment-optional.yml
-
-(
-    cat src/environment.yml
-    echo "  # optional packages"
-    for pkg in $OPTIONAL_SYSTEM_PACKAGES $SAGELIB_OPTIONAL_SYSTEM_PACKAGES; do
-        echo "  - $pkg"
-    done
-) > src/environment-optional.yml
-(
-    echo >&4 "  - pip:"
-    echo >&5 "  - pip:"
-    for PKG_BASE in $((sage-package list :standard: :optional: --has-file requirements.txt --no-file distros/conda.txt --no-file src; sage-package list :standard: :optional: --has-file install-requires.txt --no-file requirements.txt --no-file distros/conda.txt --no-file src) | sort); do
-        PKG_SCRIPTS=build/pkgs/$PKG_BASE
-        SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
-        if [ ! -f $SYSTEM_PACKAGES_FILE ]; then
-            SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/install-requires.txt
-        fi
-        PKG_TYPE=$(cat $PKG_SCRIPTS/type)
-        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;;
-                *)                       FD=5;;
-            esac
-            ${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE | while read -r line; do
-                [ -n "$line" ] && echo >&$FD "    - $line"
+    (
+        (
+            sed 's/name: sage/name: sage-dev/' src/environment-$python_version.yml
+            echo "  # Additional dev tools"
+            for pkg in $DEVELOP_SYSTEM_PACKAGES; do
+                echo "  - $pkg"
             done
-        fi
-    done
-) 4>> src/environment-dev.yml 5>> src/environment-optional.yml
+        ) >&4
+        (
+            cat src/environment-$python_version.yml
+            echo "  # optional packages"
+            for pkg in $OPTIONAL_SYSTEM_PACKAGES $SAGELIB_OPTIONAL_SYSTEM_PACKAGES; do
+                echo "  - $pkg"
+            done
+        ) >&5
+        echo >&4 "  - pip:"
+        echo >&5 "  - pip:"
+        echo >&6 "  - pip:"
+        for PKG_BASE in $((sage-package list :standard: :optional: --has-file requirements.txt --no-file distros/conda.txt --no-file src; sage-package list :standard: :optional: --has-file install-requires.txt --no-file requirements.txt --no-file distros/conda.txt --no-file src) | sort); do
+            PKG_SCRIPTS=build/pkgs/$PKG_BASE
+            SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
+            if [ ! -f $SYSTEM_PACKAGES_FILE ]; then
+                SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/install-requires.txt
+            fi
+            PKG_TYPE=$(cat $PKG_SCRIPTS/type)
+            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 6";;
+                    *)                       FD=5;;
+                esac
+                ${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE | while read -r line; do
+                    [ -n "$line" ] && for fd in $FD; do echo >&$fd "    - $line"; done
+                done
+            fi
+        done
+    ) 4>> src/environment-dev-$python_version.yml 5>> src/environment-optional-$python_version.yml 6>> src/environment-$python_version.yml
+done

build/pkgs/argon2_cffi_bindings/distros/conda.txt

@@ -0,0 +1 @@
+argon2-cffi-bindings

build/pkgs/cachetools/distros/conda.txt

@@ -0,0 +1 @@
+cachetools

build/pkgs/calver/distros/conda.txt

@@ -0,0 +1 @@
+calver

build/pkgs/chardet/distros/conda.txt

@@ -0,0 +1 @@
+chardet

build/pkgs/colorama/distros/conda.txt

@@ -0,0 +1 @@
+colorama

build/pkgs/contourpy/distros/conda.txt

@@ -0,0 +1 @@
+contourpy

build/pkgs/cryptominisat/distros/conda.txt

@@ -1 +1,2 @@
-cryptominisat
+# This is not yet compatible with Python 3.11: https://github.com/conda-forge/cryptominisat-feedstock/pull/45
+#cryptominisat

build/pkgs/hatch_fancy_pypi_readme/distros/conda.txt

@@ -0,0 +1 @@
+hatch-fancy-pypi-readme

build/pkgs/hatch_nodejs_version/distros/conda.txt

@@ -0,0 +1 @@
+hatch-nodejs-version

build/pkgs/hatch_vcs/distros/conda.txt

@@ -0,0 +1 @@
+hatch-vcs

build/pkgs/ipywidgets/distros/conda.txt

@@ -1 +1 @@
-ipywidgets<8.0.0
+ipywidgets>=7.5.1

build/pkgs/jupymake/distros/conda.txt

@@ -0,0 +1 @@
+# The presence of this file ensures that we do not try to pip-install JuPyMake (there is no polymake conda package).

build/pkgs/jupyterlab_widgets/distros/conda.txt

@@ -0,0 +1 @@
+jupyterlab_widgets

build/pkgs/matplotlib/distros/conda.txt

@@ -1,2 +1,2 @@
 # Trac #33642: For unknown reasons, without the version constraint, conda installs only 3.3.2
-"matplotlib>=3.5.1"
+matplotlib>=3.5.1

build/pkgs/meson/distros/conda.txt

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

build/pkgs/meson_python/distros/conda.txt

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

build/pkgs/networkx/distros/conda.txt

@@ -1 +1 @@
-networkx<3.0,>=2.4
+networkx<3.2,>=2.4

build/pkgs/numpy/patches/cython3-legacy.patch

@@ -0,0 +1,12 @@
+diff --git a/tools/cythonize.py b/tools/cythonize.py
+index 002b2fa..c04422e 100755
+--- a/tools/cythonize.py
++++ b/tools/cythonize.py
+@@ -47,6 +47,7 @@ def process_pyx(fromfile, tofile):
+     flags = ['-3', '--fast-fail']
+     if tofile.endswith('.cxx'):
+         flags.append('--cplus')
++    flags += ['--directive', 'legacy_implicit_noexcept=true']
+
+     subprocess.check_call(
+         [sys.executable, '-m', 'cython'] + flags + ["-o", tofile, fromfile])

build/pkgs/pycygwin/distros/conda.txt

@@ -0,0 +1 @@
+# The presence of this file ensures that we do not try to pip-install pycygwin -- which would fail with a compilation error

build/pkgs/pyproject_api/distros/conda.txt

@@ -0,0 +1 @@
+pyproject-api

build/pkgs/pyproject_metadata/distros/conda.txt

@@ -0,0 +1 @@
+pyproject-metadata

build/pkgs/sagenb_export/install-requires.txt

@@ -1 +1 @@
-sagenb_export >=3.3
+git+https://github.com/vbraun/ExportSageNB.git#egg=sagenb_export

build/pkgs/scipy/distros/conda.txt

@@ -1 +1 @@
-scipy<1.11,>=1.5
+scipy<1.12,>=1.5

build/pkgs/setuptools/distros/conda.txt

@@ -1,4 +1 @@
-# Set this bound until https://github.com/sagemath/sage/issues/34209 adds support for PEP660 editable builds
-# By setting this version bound, we avoid having to include the following in our installation instructions.
-#   export SETUPTOOLS_ENABLE_FEATURES=legacy-editable
-"setuptools<64"
+setuptools

build/pkgs/setuptools_wheel/distros

@@ -0,0 +1 @@
+../setuptools/distros

build/pkgs/sphinx/distros/conda.txt

@@ -1 +1 @@
-sphinx<8,>=5.2
+sphinx>=5.2,<8

build/pkgs/trove_classifiers/distros/conda.txt

@@ -0,0 +1 @@
+trove-classifiers