Merge branch 'develop' into public/drinfeld_module

.github/workflows/ci-linux.yml

@@ -89,7 +89,7 @@ jobs:
       targets: build doc-html
       targets_optional: ptest
       tox_packages_factors: >-
-          ["minimal]
+          ["minimal"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
 
   maximal-pre:

.github/workflows/docker.yml

@@ -18,22 +18,22 @@ on:
         default: >-
           ["ubuntu-trusty-toolchain-gcc_9",
            "ubuntu-xenial-toolchain-gcc_9",
-           "ubuntu-bionic-gcc_8",
+           "ubuntu-bionic-gcc_8-python3.8",
            "ubuntu-focal",
            "ubuntu-jammy",
            "ubuntu-kinetic",
            "debian-buster",
            "debian-bullseye",
            "debian-bookworm",
            "debian-sid",
-           "linuxmint-19-gcc_8",
-           "linuxmint-19.3-gcc_8",
+           "linuxmint-19-gcc_8-python3.8",
+           "linuxmint-19.3-gcc_8-python3.8",
            "linuxmint-20.1",
            "linuxmint-20.2",
            "linuxmint-20.3",
            "linuxmint-21",
-           "fedora-29",
-           "fedora-30",
+           "fedora-29-python3.8",
+           "fedora-30-python3.8",
            "fedora-31",
            "fedora-32",
            "fedora-33",
@@ -42,17 +42,16 @@ on:
            "fedora-36",
            "fedora-37",
            "centos-7-devtoolset-gcc_11",
-           "centos-stream-8",
-           "centos-stream-9",
+           "centos-stream-8-python3.9",
+           "centos-stream-9-python3.9",
            "gentoo-python3.9",
            "gentoo-python3.10",
            "archlinux-latest",
-           "opensuse-15.3-gcc_11",
-           "opensuse-15.4-gcc_11",
-           "opensuse-tumbleweed",
+           "opensuse-15.3-gcc_11-python3.9",
+           "opensuse-15.4-gcc_11-python3.10",
+           "opensuse-tumbleweed-python3.10",
            "conda-forge",
-           "ubuntu-bionic-i386",
-           "manylinux-2_24-i686",
+           "ubuntu-bionic-gcc_8-i386",
            "debian-buster-i386",
            ]
       tox_packages_factors:
@@ -128,6 +127,7 @@ jobs:
       FROM_DOCKER_REPOSITORY: ${{ inputs.from_docker_repository }}
       FROM_DOCKER_TARGET: ${{ inputs.from_docker_target }}
       FROM_DOCKER_TAG:    ${{ inputs.from_docker_tag }}
+      EXTRA_CONFIGURE_ARGS: --enable-fat-binary
 
     steps:
       - name: Check out SageMath

.gitignore

@@ -131,9 +131,15 @@ __pycache__/
 # Generated Cython files
 *.so
 **/*.so
+/src/cython_debug
+# Most C and C++ files are generated by Cython and should not
+# be included in the sdist.
 /src/sage/**/*.c
 /src/sage/**/*.cpp
+# 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
 !/src/sage/cpython/debugimpl.c
 !/src/sage/graphs/base/boost_interface.cpp
 !/src/sage/graphs/cliquer/cl.c
@@ -156,7 +162,6 @@ __pycache__/
 !/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.*/

.gitpod-setup-trac-remote.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+
+# Exit on error
+set -e
+
+# Setup trac as remote
+## In order to push to trac, generate a new key with `ssh-keygen -f tempkey` and save the private key to gitpod `gp env PRIVATE_SSH_KEY="$(<tempkey)"` (or by following https://www.gitpod.io/docs/environment-variables#using-the-account-settings)
+## then follow https://doc.sagemath.org/html/en/developer/trac.html#linking-your-public-key-to-your-trac-account to register the public key with trac.
+## Afterwards, create a new gitpod workspace.
+git remote remove trac 2> /dev/null || true # might still exists from a previous run/prebuild
+if [[ -n "${PRIVATE_SSH_KEY}" ]]; then
+  # Setup ssh key for authentication with trac
+  mkdir -p ~/.ssh
+  echo $PRIVATE_SSH_KEY | sed 's/\(-----\(BEGIN\|END\) OPENSSH PRIVATE KEY-----\)/\n\1\n/g' > ~/.ssh/id_rsa
+  sed -i '/^$/d' ~/.ssh/id_rsa
+  chmod 600 ~/.ssh/id_rsa
+  echo "PubkeyAcceptedKeyTypes +ssh-rsa" > ~/.ssh/config
+  ssh-keyscan -H trac.sagemath.org >> ~/.ssh/known_hosts
+
+  # Setup trac repo
+  git remote add trac git@trac.sagemath.org:sage.git -t master -t develop -t $(git branch --show-current)
+  git remote set-url --push trac git@trac.sagemath.org:sage.git
+  git fetch trac
+  git branch -u trac/$(git branch --show-current)
+else
+  # Fallback to sagemath mirror
+  git remote add trac https://github.com/sagemath/sagetrac-mirror.git -t master -t develop
+  git remote set-url --push trac pushing-needs-ssh-key
+fi

.gitpod.yml

@@ -5,53 +5,24 @@ image:
 # Start up tasks. https://www.gitpod.io/docs/config-start-tasks/
 tasks:
   - name: Setup
-    init: |
-      # Create conda environment
+    # Create conda environment, then configure and build sage
+    init: >-
       ./bootstrap-conda
-      mamba env create --file src/environment-dev.yml --prefix venv
-      conda config --append envs_dirs $(pwd)
-      conda activate $(pwd)/venv
-      
-      # Build sage
-      ./bootstrap
-      ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX 
-      pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup 
-      pip install --no-build-isolation -v -v -e ./src
-
-    command: |
-      # Activate conda environment
-      conda config --append envs_dirs $(pwd)
-      conda activate $(pwd)/venv
-
-      # RestructuredText extension recommends python extension, although we have already installed it
-      ## So disable the recommendation dialog
+      && mamba env create --file src/environment-dev.yml --prefix venv
+      && conda config --append envs_dirs $(pwd)
+      && conda activate $(pwd)/venv
+      && ./bootstrap
+      && ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX
+      && pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
+      && pip install --no-build-isolation -v -v -e ./src
+    # Activate conda environment, set up Trac remote
+    # RestructuredText extension recommends python extension, although we have already installed it
+    # So disable the recommendation dialog
+    command: >-
       echo "{\"restructuredtext.pythonRecommendation.disabled\": true}" > /workspace/.vscode-remote/data/Machine/settings.json
-
-      # Setup trac as remote
-      ## In order to push to trac, generate a new key with `ssh-keygen -f tempkey` and save the private key to gitpod `gp env PRIVATE_SSH_KEY="$(<tempkey)"` (or by following https://www.gitpod.io/docs/environment-variables#using-the-account-settings)
-      ## then follow https://doc.sagemath.org/html/en/developer/trac.html#linking-your-public-key-to-your-trac-account to register the public key with trac.
-      ## Afterwards, create a new gitpod workspace.
-      git remote remove trac 2> /dev/null # might still exists from a previous run/prebuild
-      if [[ -n "${PRIVATE_SSH_KEY}" ]]; then
-        # Setup ssh key for authentication with trac
-        mkdir -p ~/.ssh
-        echo $PRIVATE_SSH_KEY | sed 's/\(-----\(BEGIN\|END\) OPENSSH PRIVATE KEY-----\)/\n\1\n/g' > ~/.ssh/id_rsa
-        sed -i '/^$/d' ~/.ssh/id_rsa
-        chmod 600 ~/.ssh/id_rsa
-        echo "PubkeyAcceptedKeyTypes +ssh-rsa" > ~/.ssh/config
-        ssh-keyscan -H trac.sagemath.org >> ~/.ssh/known_hosts
-
-        # Setup trac repo
-        git remote add trac git@trac.sagemath.org:sage.git -t master -t develop -t $(git branch --show-current)
-        git remote set-url --push trac git@trac.sagemath.org:sage.git
-        git fetch trac
-        git branch -u trac/$(git branch --show-current)
-      else
-        # Fallback to sagemath mirror
-        git remote add trac https://github.com/sagemath/sagetrac-mirror.git -t master -t develop
-        git remote set-url --push trac pushing-needs-ssh-key
-      fi
-
+      && conda config --append envs_dirs $(pwd)
+      && conda activate $(pwd)/venv
+      && ./.gitpod-setup-trac-remote.sh
     env:
       SAGE_NUM_THREADS: 8
 

.vscode/settings.json

@@ -27,7 +27,7 @@
     "python.linting.enabled": true,
     // The following pycodestyle arguments are the same as the pycodestyle-minimal
     // tox environnment, see the file SAGE_ROOT/src/tox.ini
-    "python.linting.pycodestyleArgs": ["--select=E111,E306,E401,E701,E702,E703,W605,E711,E712,E713,E721,E722"],
+    "python.linting.pycodestyleArgs": ["--select=E111,E306,E401,E701,E702,E703,W391,W605,E711,E712,E713,E721,E722"],
     "cSpell.words": [
         "furo",
         "Conda",

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.8.beta1", 
-    "version": "9.8.beta1", 
+    "title": "sagemath/sage: 9.8.beta3", 
+    "version": "9.8.beta3", 
     "upload_type": "software", 
-    "publication_date": "2022-09-29", 
+    "publication_date": "2022-10-30", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.8.beta1", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.8.beta3", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -101,7 +101,7 @@ pypi-wheels:
 	    rm -f venv/var/lib/sage/installed/$$a-*; \
 	done
 	for a in $(PYPI_WHEEL_PACKAGES); do \
-	    $(MAKE) SAGE_EDITABLE=no $$a; \
+	    $(MAKE) SAGE_EDITABLE=no SAGE_WHEELS=yes $$a; \
 	done
 	@echo "Built wheels are in venv/var/lib/sage/wheels/"
 
@@ -112,7 +112,7 @@ wheels:
 	    rm -f venv/var/lib/sage/installed/$$a-*; \
 	done
 	for a in $(WHEEL_PACKAGES); do \
-	    $(MAKE) SAGE_EDITABLE=no $$a; \
+	    $(MAKE) SAGE_EDITABLE=no SAGE_WHEELS=yes $$a; \
 	done
 	@echo "Built wheels are in venv/var/lib/sage/wheels/"
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.8.beta1, Release Date: 2022-09-29
+SageMath version 9.8.beta3, Release Date: 2022-10-30

build/bin/sage-build-env

@@ -31,6 +31,10 @@ if [ "x$SAGE_BUILD_ENV_SOURCED" = "x" ]; then
     if [ "x$SAGE_EDITABLE" = "x" ]; then
         export SAGE_EDITABLE="$CONFIGURED_SAGE_EDITABLE"
     fi
+    # Likewise for SAGE_WHEELS
+    if [ "x$SAGE_WHEELS" = "x" ]; then
+        export SAGE_WHEELS="$CONFIGURED_SAGE_WHEELS"
+    fi
 
     # This is usually blank if the system GMP is used, or $SAGE_LOCAL otherwise
     if [ -n "$SAGE_GMP_PREFIX" ]; then

build/bin/sage-build-env-config.in

@@ -58,3 +58,4 @@ export SAGE_SUITESPARSE_PREFIX="@SAGE_SUITESPARSE_PREFIX@"
 export SAGE_CONFIGURE_FFLAS_FFPACK="@SAGE_CONFIGURE_FFLAS_FFPACK@"
 
 export CONFIGURED_SAGE_EDITABLE="@SAGE_EDITABLE@"
+export CONFIGURED_SAGE_WHEELS="@SAGE_WHEELS@"

build/bin/sage-pip-install

@@ -28,7 +28,7 @@ PIP=pip3
 # We should avoid running pip while installing a package because that
 # is prone to race conditions. Therefore, we use a lockfile while
 # running pip. This is implemented in the Python script sage-flock
-LOCK="$SAGE_LOCAL/var/lock/$PIP.lock"
+LOCK="$SAGE_VENV/var/lock/$PIP.lock"
 
 # Trac #33155: Pythons installed using the python.org macOS installers
 # for Python < 3.10 identify macOS Big Sur and newer as "10.16", causing

build/bin/sage-pip-uninstall

@@ -14,7 +14,7 @@ PIP=pip3
 # We should avoid running pip while uninstalling a package because that
 # is prone to race conditions. Therefore, we use a lockfile while
 # running pip. This is implemented in the Python script sage-flock
-LOCK="$SAGE_LOCAL/var/lock/$PIP.lock"
+LOCK="$SAGE_VENV/var/lock/$PIP.lock"
 
     # --disable-pip-version-check: Don't periodically check PyPI to determine whether a new version of pip is available
     # --no-input: Disable prompting for input.

build/bin/sage-site

@@ -98,7 +98,7 @@ fi
 
 if [ "$1" = '-package' -o "$1" = "--package" ]; then
     shift
-    exec sage-package $@
+    exec sage-package "$@"
 fi
 
 if [ "$1" = '-optional' -o "$1" = "--optional" ]; then

build/make/Makefile.in

@@ -677,7 +677,7 @@ $(1)-$(4)-no-deps:
 		SAGE_SPKG_WHEELS=$$($(4))/var/lib/sage/wheels \
 		SAGE_INST_LOCAL=$$($(4)) \
 		sage-logger -p 'SAGE_CHECK=$$(SAGE_CHECK_$(1)) $$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1)-$(2).log' && \
-	    rm -f "$$($(4))/$(SPKG_INST_RELDIR)/$(1)-*" && \
+	    rm -f "$$($(4))/$(SPKG_INST_RELDIR)/$(1)"-* && \
 	    touch "$$($(4))/$(SPKG_INST_RELDIR)/$(1)-$(2)"; \
 	else ( \
 	    echo; \
@@ -704,7 +704,7 @@ $(1)-$(4)-uninstall:
 		. '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		. '$$(SAGE_ROOT)/build/bin/sage-build-env' && \
 		'$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-uninstall'
-	-rm -f "$$($(4))/$(SPKG_INST_RELDIR)/$(1)-$(2)"
+	-rm -f "$$($(4))/$(SPKG_INST_RELDIR)/$(1)"-*
 
 $(1)-uninstall: $(1)-$(4)-uninstall
 

build/pkgs/_develop/dependencies

@@ -1 +1 @@
-_bootstrap git pytest pytest_xdist
+_bootstrap git pytest pytest_xdist github_cli

build/pkgs/_python3.10/distros/arch.txt

@@ -0,0 +1 @@
+python310

build/pkgs/_python3.10/distros/cygwin.txt

@@ -0,0 +1 @@
+python310

build/pkgs/_python3.10/distros/debian.txt

@@ -0,0 +1,3 @@
+python3.10
+python3.10-dev
+python3.10-venv

build/pkgs/_python3.10/distros/fedora.txt

@@ -0,0 +1,2 @@
+python310
+python310-devel

build/pkgs/_python3.10/distros/freebsd.txt

@@ -0,0 +1 @@
+python310

build/pkgs/_python3.10/distros/homebrew.txt

@@ -0,0 +1 @@
+python@3.10

build/pkgs/_python3.10/distros/macports.txt

@@ -0,0 +1 @@
+python310

build/pkgs/_python3.10/distros/opensuse.txt

@@ -0,0 +1,2 @@
+python310
+python310-devel

build/pkgs/_python3.11/distros/arch.txt

@@ -0,0 +1 @@
+python311

build/pkgs/_python3.11/distros/cygwin.txt

@@ -0,0 +1 @@
+python311

build/pkgs/_python3.11/distros/debian.txt

@@ -0,0 +1,3 @@
+python3.11
+python3.11-dev
+python3.11-venv

build/pkgs/_python3.11/distros/fedora.txt

@@ -0,0 +1,2 @@
+python311
+python311-devel

build/pkgs/_python3.11/distros/freebsd.txt

@@ -0,0 +1 @@
+python311

build/pkgs/_python3.11/distros/homebrew.txt

@@ -0,0 +1 @@
+python@3.11

build/pkgs/_python3.11/distros/macports.txt

@@ -0,0 +1 @@
+python311

build/pkgs/_python3.11/distros/opensuse.txt

@@ -0,0 +1,2 @@
+python311
+python311-devel

build/pkgs/_python3.8/distros/arch.txt

@@ -0,0 +1 @@
+python38

build/pkgs/_python3.8/distros/cygwin.txt

@@ -0,0 +1 @@
+python38

build/pkgs/_python3.8/distros/debian.txt

@@ -0,0 +1,3 @@
+python3.8
+python3.8-dev
+python3.8-venv

build/pkgs/_python3.8/distros/fedora.txt

@@ -0,0 +1,2 @@
+python38
+python38-devel

build/pkgs/_python3.8/distros/freebsd.txt

@@ -0,0 +1 @@
+python38

build/pkgs/_python3.8/distros/homebrew.txt

@@ -0,0 +1 @@
+python@3.8

build/pkgs/_python3.8/distros/macports.txt

@@ -0,0 +1 @@
+python38

build/pkgs/_python3.8/distros/opensuse.txt

@@ -0,0 +1,2 @@
+python38
+python38-devel

build/pkgs/_python3.9/distros/arch.txt

@@ -0,0 +1 @@
+python39

build/pkgs/_python3.9/distros/cygwin.txt

@@ -0,0 +1 @@
+python39

build/pkgs/_python3.9/distros/debian.txt

@@ -0,0 +1,3 @@
+python3.9
+python3.9-dev
+python3.9-venv

build/pkgs/_python3.9/distros/fedora.txt

@@ -0,0 +1,2 @@
+python39
+python39-devel

build/pkgs/_python3.9/distros/freebsd.txt

@@ -0,0 +1 @@
+python39

build/pkgs/_python3.9/distros/homebrew.txt

@@ -0,0 +1 @@
+python@3.9

build/pkgs/_python3.9/distros/macports.txt

@@ -0,0 +1 @@
+python39

build/pkgs/_python3.9/distros/opensuse.txt

@@ -0,0 +1,2 @@
+python39
+python39-devel