Merge #29865

.github/workflows/ci-cygwin-minimal.yml

@@ -13,7 +13,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   CYGWIN: winsymlinks:native
-  CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url --enable-fat-binary
+  EXTRA_CONFIGURE_ARGS: --enable-fat-binary
   SAGE_LOCAL: /opt/sage-${{ github.sha }}
 
 jobs:
@@ -84,7 +84,7 @@ jobs:
   cygwin-stage-i-b:
     env:
       STAGE: i-b
-      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing nose certifi pkgconfig pplpy
+      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing certifi pkgconfig pplpy
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
 

.github/workflows/ci-cygwin-standard.yml

@@ -13,7 +13,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   CYGWIN: winsymlinks:native
-  CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url --enable-fat-binary
+  EXTRA_CONFIGURE_ARGS: --enable-fat-binary
   SAGE_LOCAL: /opt/sage-${{ github.sha }}
 
 jobs:
@@ -84,7 +84,7 @@ jobs:
   cygwin-stage-i-b:
     env:
       STAGE: i-b
-      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing nose certifi pkgconfig pplpy
+      TARGETS: cython setuptools_scm kiwisolver dateutil cycler pyparsing certifi pkgconfig pplpy
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
 

.github/workflows/lint.yml

@@ -31,17 +31,3 @@ jobs:
       run: pip install tox relint
     - name: Lint using relint
       run: tox -e relint src/sage/
-  lint-pyright:
-    name: Static type check with pyright
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v2
-    - name: Set up node to install pyright
-      uses: actions/setup-node@v1
-      with:
-        node-version: '12'
-    - name: Install pyright
-      run: npm install -g pyright
-    - name: Lint using pyright
-      run: pyright

.github/workflows/sdist.yml

@@ -0,0 +1,45 @@
+name: Prepare source distributions
+
+on:
+  push:
+    tags:
+      # Match all release tags including beta, rc
+      - '[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.beta[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+.beta[0-9]+'
+      - '[0-9]+.[0-9]+.rc[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+.rc[0-9]+'
+
+  workflow_dispatch:
+    # Allow to run manually
+
+jobs:
+
+  release_dist:
+
+    # This job, in contrast to "dist" in tox.yml,
+    # does not use "configure --enable-download-from-upstream-url".
+    #
+    # In this way, we check that all necessary package tarballs
+    # have already been uploaded to the Sage server at the time
+    # of pushing a release tag.
+    #
+    # It also uses "bootstrap -D", thus checking that the "configure"
+    # tarball has been uploaded to the Sage server at the time
+    # of pushing a release tag.
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install bootstrap prerequisites
+        run: |
+          sudo DEBIAN_FRONTEND=noninteractive apt-get update
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install $(build/bin/sage-get-system-packages debian _bootstrap)
+      - name: make dist
+        run: |
+          ./bootstrap -D && ./configure && make dist
+      - uses: actions/upload-artifact@v2
+        with:
+          path: "dist/*.tar.gz"
+          name: release_dist

.github/workflows/tox-experimental.yml

@@ -40,14 +40,17 @@ jobs:
       matrix:
         # This list is different from the one in tox.yml:
         # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
-        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-gcc_spkg]
+        # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
+        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       DOCKER_TARGETS: configured with-targets with-targets-optional
-      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :experimental: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep '^[${{ matrix.targets_pattern }}]' ) )"
+      # Test all non-dummy experimental packages, but do not test huge packages
+      # and do not test packages that require external software
+      TARGETS_OPTIONAL: "$( echo $(export PATH=build/bin:$PATH && sage-package list :experimental: --has-file spkg-install.in && sage-package list :experimental: --has-file spkg-install && sage-package list :experimental: --has-file requirements.txt | grep -v ^_ | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
         with:
@@ -146,7 +149,9 @@ jobs:
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
-      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :experimental: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep '^[${{ matrix.targets_pattern }}]' ) )"
+      # Test all non-dummy experimental packages, but do not test huge packages
+      # and do not test packages that require external software
+      TARGETS_OPTIONAL: "$( echo $(export PATH=build/bin:$PATH && sage-package list :experimental: --has-file spkg-install.in && sage-package list :experimental: --has-file spkg-install && sage-package list :experimental: --has-file requirements.txt | grep -v ^_ | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
       - name: Select Xcode version

.github/workflows/tox-gcc_spkg.yml

@@ -27,7 +27,7 @@ on:
     # Allow to run manually
 
 env:
-  TARGETS_PRE: sagelib-build-deps
+  TARGETS_PRE: all-sage-local
   TARGETS: build doc-html
   TARGETS_OPTIONAL: ptest
 

.github/workflows/tox-optional.yml

@@ -40,16 +40,17 @@ jobs:
       matrix:
         # This list is different from the one in tox.yml:
         # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
-        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-gcc_spkg]
+        # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
+        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       DOCKER_TARGETS: configured with-targets with-targets-optional
-      # Test all optional packages, but do not test huge packages,
+      # Test all non-dummy optional packages, but do not test huge packages
       # and do not test packages that require external software
-      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :optional: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
+      TARGETS_OPTIONAL: "$( echo $(export PATH=build/bin:$PATH && (sage-package list :optional: --has-file spkg-install.in && sage-package list :optional: --has-file spkg-install && sage-package list :optional: --has-file requirements.txt) | grep -v ^_ | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
         with:
@@ -148,9 +149,9 @@ jobs:
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}
-      # Test all optional packages, but do not test huge packages
+      # Test all non-dummy optional packages, but do not test huge packages
       # and do not test packages that require external software
-      TARGETS_OPTIONAL: "$( echo $(PATH=build/bin:$PATH build/bin/sage-package list :optional: | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
+      TARGETS_OPTIONAL: "$( echo $(export PATH=build/bin:$PATH && (sage-package list :optional: --has-file spkg-install.in && sage-package list :optional: --has-file spkg-install && sage-package list :optional: --has-file requirements.txt) | grep -v ^_ | grep -v  database_stein_watkins\\$ | grep -v polytopes_db_4d | grep -v cplex | grep -v gurobi | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
       - name: Select Xcode version

.github/workflows/tox.yml

@@ -27,7 +27,7 @@ on:
     # Allow to run manually
 
 env:
-  TARGETS_PRE: sagelib-build-deps
+  TARGETS_PRE: all-sage-local
   TARGETS: build doc-html
   TARGETS_OPTIONAL: ptest
 
@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       max-parallel: 20
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, gentoo-python3.7, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
+        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, ubuntu-impish, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, centos-7, centos-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
         tox_packages_factor: [minimal, standard]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
@@ -257,7 +257,7 @@ jobs:
           SAGE_ROOT=. SAGE_SRC=./src src/bin/sage-update-version $(git describe) || echo "(ignoring error)"
       - name: make dist
         run: |
-          ./configure && make dist
+          ./configure --enable-download-from-upstream-url && make dist
       - uses: actions/upload-artifact@v2
         with:
           path: "dist/*.tar.gz"

.gitignore

@@ -1,4 +1,6 @@
-*.pyc
+## We use this file both as .gitignore and .dockerignore,
+## which have different semantics.
+
 /dist
 /local
 /logs
@@ -33,15 +35,21 @@
 
 # Various editors
 *~
+**/*~
 
 # Emacs
 \#*\#
+**/\#*\#
 .\#*
+**/.\#*
 
 # Vim
 *.swp
+**/*.swp
 *.swo
+**/*.swo
 *.swn
+**/*.swn
 *.un~
 .netrwhist
 
@@ -51,6 +59,7 @@
 
 # VSCode
 .vscode/*
+**/.vscode/*
 
 # XCode
 xcuserdata/
@@ -61,6 +70,7 @@ xcuserdata/
 .metadata
 *.tmp
 *.bak
+**/*.bak
 *.swp
 *~.nib
 .classpath
@@ -72,6 +82,7 @@ xcuserdata/
 
 # OSX specific temporary files
 .DS_Store
+**/.DS_Store
 ._*
 .AppleDouble
 .LSOverride
@@ -98,44 +109,64 @@ gitlab-build-docker.log
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
+**/__pycache__
 *.py[cod]
+**/*.py[cod]
 *$py.class
 
 # Generated by sage_setup.autogen
 /src/sage/ext/interpreters
 
 # Generated Cython files
 *.so
-src/sage/**/*.c
-src/sage/**/*.cpp
-src/sage/modular/arithgroup/farey_symbol.h
-!src/sage/cpython/debugimpl.c
-!src/sage/graphs/base/boost_interface.cpp
-!src/sage/graphs/cliquer/cl.c
-!src/sage/graphs/graph_decompositions/sage_tdlib.cpp
-!src/sage/libs/eclib/wrap.cpp
-!src/sage/libs/linkages/padics/relaxed/flint_helper.c
-!src/sage/misc/inherit_comparison_impl.c
-!src/sage/modular/arithgroup/farey.cpp
-!src/sage/modular/arithgroup/sl2z.cpp
-!src/sage/rings/bernmm/bern_modp.cpp
-!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/polynomial/weil/power_sums.c
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
-!src/sage/stats/distributions/dgs_bern.c
-!src/sage/stats/distributions/dgs_gauss_dp.c
-!src/sage/stats/distributions/dgs_gauss_mp.c
+**/*.so
+/src/sage/**/*.c
+/src/sage/**/*.cpp
+/src/sage/modular/arithgroup/farey_symbol.h
+!/src/sage/cpython/debugimpl.c
+!/src/sage/graphs/base/boost_interface.cpp
+!/src/sage/graphs/cliquer/cl.c
+!/src/sage/graphs/graph_decompositions/sage_tdlib.cpp
+!/src/sage/libs/eclib/wrap.cpp
+!/src/sage/libs/linkages/padics/relaxed/flint_helper.c
+!/src/sage/misc/inherit_comparison_impl.c
+!/src/sage/modular/arithgroup/farey.cpp
+!/src/sage/modular/arithgroup/sl2z.cpp
+!/src/sage/rings/bernmm/bern_modp.cpp
+!/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/polynomial/weil/power_sums.c
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
+!/src/sage/stats/distributions/dgs_bern.c
+!/src/sage/stats/distributions/dgs_gauss_dp.c
+!/src/sage/stats/distributions/dgs_gauss_mp.c
+!/src/sage/symbolic/ginac/*.cpp
 /src/cython_debug
 
 # Temporary build files
 build/temp.*/
 build/bin/sage-build-env-config
 
+# Generated files in the top-level source trees
+/pkgs/*/build
+/pkgs/*/dist
+/pkgs/*/MANIFEST
+/pkgs/*/*.egg-info
+/pkgs/*/.tox
+
+/pkgs/sagemath-objects/setup.cfg
+/pkgs/sagemath-categories/setup.cfg
+/pkgs/sagemath-objects/pyproject.toml
+/pkgs/sagemath-categories/pyproject.toml
+/pkgs/sagemath-objects/requirements.txt
+/pkgs/sagemath-categories/requirements.txt
+/pkgs/sagemath-categories/MANIFEST.in
+
+# same for old locations - before Trac #31577
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist
 /build/pkgs/*/src/MANIFEST
@@ -159,6 +190,7 @@ src/*.egg-info/
 /src/bin/sage-src-env-config
 
 # Virtual environments
+/venv
 src/.env
 src/.venv
 src/env/
@@ -173,7 +205,9 @@ src/venv.bak/
 # tox generated files
 /.tox
 /build/.tox
+**/.tox
 /prefix
 
 # git worktree
 worktree*
+**/worktree*

.homebrew-build-env

@@ -2,7 +2,7 @@
 # that activate keg-only homebrew package installations
 
 HOMEBREW=`brew --prefix` || return 1
-for l in gettext bzip2 texinfo; do
+for l in gettext bzip2 texinfo polymake; do
     if [ -d "$HOMEBREW/opt/$l/bin" ]; then
         PATH="$HOMEBREW/opt/$l/bin:$PATH"
     fi
@@ -23,15 +23,15 @@ export PKG_CONFIG_PATH
 LIBRARY_PATH="$HOMEBREW/lib$LIBRARY_PATH"
 [ -z "$CPATH" ] || CPATH=":${CPATH}"
 CPATH="$HOMEBREW/include$CPATH"
-for l in readline bzip2 ntl; do
+for l in readline bzip2 ntl polymake; do
     if [ -d "$HOMEBREW/opt/$l/lib" ]; then
         LIBRARY_PATH="$HOMEBREW/opt/$l/lib:$LIBRARY_PATH"
     fi
     if [ -d "$HOMEBREW/opt/$l/include" ]; then
         CPATH="$HOMEBREW/opt/$l/include:$CPATH"
     fi
 done
-for l in "gcc/lib/gcc/10 gcc/lib/gcc/9"; do
+for l in "gcc/lib/gcc/11 gcc/lib/gcc/10 gcc/lib/gcc/9"; do
     if [ -d "$HOMEBREW/opt/$l" ]; then
         LIBRARY_PATH="$HOMEBREW/opt/$l:$LIBRARY_PATH"
         break