Merge branch 'develop' into graded_lattices

Author: fchapoton

.devcontainer/onCreate-meson.sh

@@ -23,7 +23,7 @@ uv pip install \
     "cypari2 >=2.2.1" \
     "cysignals >=1.11.2, != 1.12.0" \
     "cython >=3.0, != 3.0.3, < 3.1.0" \
-    "gmpy2 ~=2.1.b999" \
+    "gmpy2 >=2.1.5" \
     memory_allocator \
     "numpy >=1.25" \
     jinja2 \

.devcontainer/portability-debian-forky/devcontainer.json

@@ -0,0 +1,24 @@
+// See https://aka.ms/devcontainer.json for format details.
+{
+    "name": "debian-forky",
+    "image": "debian:forky",
+    "onCreateCommand": ".devcontainer/onCreate-meson.sh || true",
+    "features": {
+        "ghcr.io/devcontainers/features/git": {},
+        "ghcr.io/devcontainers/features/python:1": {},
+        "../uv": {
+			"version": "latest"
+		}
+    },
+    "containerEnv": {
+        "devcontainerId": "${devcontainerId}",
+        "UV_PROJECT_ENVIRONMENT": ".venv-${devcontainerId}" 
+    },
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python"
+            ]
+        }
+    }
+}

.github/workflows/ci-distro.yml

@@ -19,13 +19,8 @@ on:
     paths:
       - '.github/workflows/ci-distro.yml'
       - 'build/pkgs/**'
+      - 'build/make/**'
       - 'configure.ac'
-      - '!build/pkgs/sage_conf/**'
-      - '!build/pkgs/sage_docbuild/**'
-      - '!build/pkgs/sage_setup/**'
-      - '!build/pkgs/sage_sws2rst/**'
-      - '!build/pkgs/sagelib/**'
-      - '!build/pkgs/sagemath_*/**'
   push:
     tags:
       - '*'
@@ -35,7 +30,7 @@ on:
 env:
   TARGETS_PRE: all-sage-local
   TARGETS: build
-  TARGETS_OPTIONAL: ptest
+  TARGETS_OPTIONAL: ptestlong
 
 permissions:
   packages: write
@@ -56,7 +51,7 @@ jobs:
       # FIXME: duplicated from env.TARGETS
       targets_pre: all-sage-local
       targets: build
-      targets_optional: ptest
+      targets_optional: ptestlong
       tox_system_factors: >-
           ["ubuntu-jammy"]
       tox_packages_factors: >-
@@ -71,7 +66,7 @@ jobs:
       docker_targets: "with-system-packages configured with-targets-pre with-targets with-targets-optional"
       targets_pre: all-sage-local
       targets: build
-      targets_optional: ptest
+      targets_optional: ptestlong
       tox_packages_factors: >-
           ["standard"]
       docker_push_repository: ghcr.io/${{ github.repository }}/

.github/workflows/ci-macos.yml

@@ -35,7 +35,6 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '13'
           - '14'
           - '15'
 

.github/workflows/ci-meson.yml

@@ -28,22 +28,24 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu', 'macos', 'windows']
-        python: ['3.11', '3.12']
+        python: ['3.12', '3.13']
         tests: ['all']
         editable:
           ${{ fromJson(github.event_name == 'pull_request' && '[false]' || '[false, true]') }}
         include:
+          # One run for oldest supported Python
+          - os: 'ubuntu'
+            python: '3.11'
+            tests: 'all'
+          # Test only changed files
           - os: 'ubuntu'
             python: '3.12'
             tests: 'new'
-          # one additional editable run in pull_request, this has no effect if not pull_request
+          # One additional editable run in pull_request, this has no effect if not pull_request
           - os: 'ubuntu'
             python: '3.12'
             editable: true
             tests: 'all'
-          - os: windows
-            python: '3.13'
-            tests: 'all'
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/ci.yml

@@ -23,6 +23,7 @@ jobs:
         container:
           - fedora:41
           - fedora:42
+          - debian:forky
           - ghcr.io/void-linux/void-glibc-full
           - archlinux
           #- ubuntu:22.04 - fails due to issue with cypari2
@@ -91,7 +92,7 @@ jobs:
             "cypari2 >=2.2.1" \
             "cysignals >=1.11.2, != 1.12.0" \
             "cython >=3.0, != 3.0.3, < 3.1.0" \
-            "gmpy2 ~=2.1.b999" \
+            "gmpy2 >=2.1.5" \
             memory_allocator \
             "numpy >=1.25" \
             jinja2 \

.github/workflows/dist.yml

@@ -185,7 +185,7 @@ 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 tdlib
       CIBW_BUILD: "*${{ matrix.build }}*"
       # Disable building PyPy wheels on all platforms
       CIBW_SKIP: "pp*"
@@ -241,7 +241,7 @@ jobs:
         run: |
           "${{ steps.python.outputs.python-path }}" -m pip install cibuildwheel==3.0.1
           export PATH=build/bin:$PATH
-          echo CIBW_BEFORE_ALL="( $(sage-print-system-package-command debian --yes --no-install-recommends install $(sage-get-system-packages debian $SPKGS)) || $(sage-print-system-package-command fedora --yes --no-install-recommends install $(sage-get-system-packages fedora $SPKGS | sed s/pkg-config/pkgconfig/)) || ( $(sage-print-system-package-command homebrew --yes --no-install-recommends install $(sage-get-system-packages homebrew $SPKGS)) || $(sage-print-system-package-command alpine --yes --no-install-recommends install $(sage-get-system-packages alpine $SPKGS)) || echo error ignored) ) && if cp /host/sage-\$AUDITWHEEL_PLAT/config.status . 2>/dev/null; then chmod +x config.status; fi && if [ -x ./config.status ]; then ./config.status; else ./configure --enable-build-as-root ${{ startsWith(matrix.os, 'ubuntu') && '--prefix=/host/sage-\$AUDITWHEEL_PLAT' || '' }} && cp config.status prefix/; fi && MAKE=\"make -j6\" make V=0 $TARGETS_PRE && (echo \"sage_conf @ file://\$(pwd)/pkgs/sage-conf\" && echo \"sage_setup @ file://\$(pwd)/pkgs/sage-setup\") > constraints.txt" >> "$GITHUB_ENV"
+          echo CIBW_BEFORE_ALL="( $(sage-print-system-package-command debian --yes --no-install-recommends install $(sage-get-system-packages debian $SPKGS)) || $(sage-print-system-package-command fedora --yes --no-install-recommends install $(sage-get-system-packages fedora $SPKGS | sed s/pkg-config/pkgconfig/)) || ( $(sage-print-system-package-command homebrew --yes --no-install-recommends install $(sage-get-system-packages homebrew $SPKGS)) || $(sage-print-system-package-command alpine --yes --no-install-recommends install $(sage-get-system-packages alpine $SPKGS)) || echo error ignored) ) && if cp /host/sage-\$AUDITWHEEL_PLAT/config.status . 2>/dev/null; then chmod +x config.status; fi && if [ -x ./config.status ]; then ./config.status; else ./configure --enable-build-as-root ${{ startsWith(matrix.os, 'ubuntu') && '--prefix=/host/sage-\$AUDITWHEEL_PLAT' || '' }} && cp config.status prefix/; fi && MAKE=\"make -j6\" make V=0 $TARGETS_PRE && echo \"sage_setup @ file://\$(pwd)/pkgs/sage-setup\") > constraints.txt" >> "$GITHUB_ENV"
           mkdir -p unpacked
           for sdist in dist/$pkg*.tar.gz; do
               (cd unpacked && tar xfz - ) < $sdist

.gitignore

@@ -157,7 +157,7 @@ __pycache__/
 # C header generated by Cython
 /src/sage/modular/arithgroup/farey_symbol.h
 # List of C and C++ files that are actual source files,
-# NOT generated by Cython. The same list appears in src/MANIFEST.in
+# NOT generated by Cython
 !/src/sage/graphs/base/boost_interface.cpp
 !/src/sage/graphs/cliquer/cl.c
 !/src/sage/graphs/graph_decompositions/sage_tdlib.cpp
@@ -170,7 +170,7 @@ __pycache__/
 !/src/sage/rings/bernmm/bern_modp_util.cpp
 !/src/sage/rings/bernmm/bern_rat.cpp
 !/src/sage/rings/bernmm/bernmm-test.cpp
-!/src/sage/rings/padics/transcendantal.c
+!/src/sage/rings/padics/transcendental.c
 !/src/sage/rings/polynomial/weil/power_sums.c
 !/src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
 !/src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
@@ -205,16 +205,6 @@ build/pkgs/wheel/version_requirements.txt
 /pkgs/*/venv*
 /pkgs/*/.venv*
 
-/pkgs/sage-conf_pypi/sage_root/config.log
-/pkgs/sage-conf_pypi/sage_root/config.status
-/pkgs/sage-conf_pypi/sage_root/local/
-/pkgs/sage-conf_pypi/sage_root/logs/
-/pkgs/sage-conf_pypi/sage_root/prefix
-/pkgs/sage-conf_pypi/sage_root/src/bin/sage-env-config
-/pkgs/sage-conf_pypi/sage_root/src/bin/sage-src-env-config
-/pkgs/sage-conf_pypi/sage_root/upstream/
-/pkgs/sage-conf_pypi/sage_root/venv
-
 /pkgs/sagemath-objects/setup.cfg
 /pkgs/sagemath-bliss/setup.cfg
 /pkgs/sagemath-coxeter3/setup.cfg
@@ -462,6 +452,7 @@ src/sage/graphs/graph_decompositions/__init__.py
 src/sage/graphs/generators/__init__.py
 src/sage/graphs/__init__.py
 src/sage/graphs/base/__init__.py
+src/sage/graphs/tests/__init__.py
 src/sage/databases/__init__.py
 src/sage/stats/hmm/__init__.py
 src/sage/stats/__init__.py

.homebrew-build-env

@@ -8,7 +8,11 @@ for l in bzip2 texinfo polymake; do
     fi
 done
 export PATH
-PKG_CONFIG_PATH="$HOMEBREW/lib/pkgconfig:$PKG_CONFIG_PATH"
+if [ -z "$PKG_CONFIG_PATH" ]; then
+    PKG_CONFIG_PATH="$HOMEBREW/lib/pkgconfig"
+else
+    PKG_CONFIG_PATH="$HOMEBREW/lib/pkgconfig:$PKG_CONFIG_PATH"
+fi
 # libpng.pc depends on zlib.pc
 for l in openblas openssl readline sqlite zlib; do
     if [ -d "$HOMEBREW/opt/$l/lib/pkgconfig" ]; then

.vscode/settings.json

@@ -8,7 +8,6 @@
         // Exclude symbolic links into SAGE_ROOT/pkgs/
         "build/pkgs/*/src": true,
         // Exclude symbolic links into SAGE_ROOT/src/
-        "pkgs/sage-conf_pypi/sage_root": true,
         "pkgs/sage-docbuild/sage_docbuild": true,
         "pkgs/sage-setup/sage_setup": true,
         "pkgs/sagemath-*/sage": true,
@@ -43,6 +42,7 @@
         "Cython",
         "d'Alembertian",
         "dalembertian",
+        "devcontainers",
         "disp",
         "doctest",
         "doctests",