Merge branch develop

.github/workflows/build.yml

@@ -24,7 +24,8 @@ jobs:
           node-version: '12'
 
       - name: Install pyright
-        run: npm install -g pyright
+        # Fix to v232 due to bug https://github.com/microsoft/pyright/issues/3239
+        run: npm install -g pyright@1.1.232
 
       - name: Prepare
         run: |

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

@@ -353,7 +353,7 @@ jobs:
     env:
       STAGE: ii-d
       PREVIOUS_STAGES: i-*
-      TARGETS: ipython ipywidgets notebook thebe
+      TARGETS: ipython ipywidgets notebook
       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

@@ -353,7 +353,7 @@ jobs:
     env:
       STAGE: ii-d
       PREVIOUS_STAGES: i-*
-      TARGETS: ipython ipywidgets notebook thebe
+      TARGETS: ipython ipywidgets notebook
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
 

.github/workflows/tox-experimental.yml

@@ -41,7 +41,7 @@ jobs:
         # 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
         # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
-        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-hirsute, ubuntu-impish, ubuntu-jammy, debian-stretch, debian-buster, debian-bullseye, debian-bookworm, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2. linuxmint-20.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, fedora-36,  centos-7-gcc_spkg, centos-stream-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15.2.1, 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_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-hirsute, ubuntu-impish, ubuntu-jammy, debian-stretch, debian-buster, debian-bullseye, debian-bookworm, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2. linuxmint-20.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, fedora-36,  centos-7-gcc_spkg, centos-stream-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, 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:
@@ -50,7 +50,7 @@ jobs:
       DOCKER_TARGETS: configured with-targets with-targets-optional
       # 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 '^[${{ matrix.targets_pattern }}]' ) )"
+      TARGETS_OPTIONAL: "$( echo $(export PATH=build/bin:$PATH && (for a in spkg-install.in spkg-install requirements.txt; do sage-package list :experimental: --has-file $a --no-file huge --no-file has_nonfree_dependencies; done) | grep -v ^_ | grep -v sagemath_doc | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
         with:

.github/workflows/tox-optional.yml

@@ -41,7 +41,7 @@ jobs:
         # 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
         # Trac #32281 removes gcc 4.x-based distributions whose binutils are unusable
-        tox_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-hirsute, ubuntu-impish, ubuntu-jammy, debian-stretch, debian-buster, debian-bullseye, debian-bookworm, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2. linuxmint-20.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, fedora-36,  centos-7-gcc_spkg, centos-stream-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15.2.1, 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_system_factor: [ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-hirsute, ubuntu-impish, ubuntu-jammy, debian-stretch, debian-buster, debian-bullseye, debian-bookworm, debian-sid, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2. linuxmint-20.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, fedora-36,  centos-7-gcc_spkg, centos-stream-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, 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:
@@ -50,7 +50,7 @@ jobs:
       DOCKER_TARGETS: configured with-targets with-targets-optional
       # Test all non-dummy optional 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 :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 '^[${{ matrix.targets_pattern }}]' ) )"
+      TARGETS_OPTIONAL: "$( echo $(export PATH=build/bin:$PATH && (for a in spkg-install.in spkg-install requirements.txt; do sage-package list :optional: --has-file $a --no-file huge --no-file has_nonfree_dependencies; done) | grep -v ^_ | grep -v sagemath_doc | grep '^[${{ matrix.targets_pattern }}]' ) )"
     steps:
       - uses: actions/checkout@v2
         with:

.github/workflows/tox.yml

@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       max-parallel: 20
       matrix:
-        tox_system_factor: [gitpod, ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-hirsute, ubuntu-impish, ubuntu-jammy,  debian-stretch, debian-buster, debian-bullseye, debian-bookworm, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2, linuxmint-20.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, fedora-36, centos-7, centos-stream-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, opensuse-15.2.1, 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: [gitpod, ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-hirsute, ubuntu-impish, ubuntu-jammy,  debian-stretch, debian-buster, debian-bullseye, debian-bookworm, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2, linuxmint-20.3, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, fedora-36, centos-7, centos-stream-8, gentoo-python3.9, gentoo-python3.10, archlinux-latest, 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 }}
@@ -169,12 +169,12 @@ jobs:
             2-optional*)     export TARGETS_PRE="build/make/Makefile" TARGETS="build/make/Makefile"
                              targets_pattern="${{ matrix.stage }}"
                              targets_pattern="${targets_pattern#2-optional-}"
-                             export 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 "^[$targets_pattern]" ) )
+                             export TARGETS_OPTIONAL=$( echo $(export PATH=build/bin:$PATH && (for a in spkg-install.in spkg-install requirements.txt; do sage-package list :optional: --has-file $a --no-file huge --no-file has_nonfree_dependencies; done) | grep -v ^_ | grep -v sagemath_doc | grep '^[${{ matrix.targets_pattern }}]' ) )
                              ;;
             2-experimental*) export TARGETS_PRE="build/make/Makefile" TARGETS="build/make/Makefile"
                              targets_pattern="${{ matrix.stage }}"
                              targets_pattern="${targets_pattern#2-experimental-}"
-                             export 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 "^[$targets_pattern]" ) )
+                             export TARGETS_OPTIONAL=$( echo $(export PATH=build/bin:$PATH && (for a in spkg-install.in spkg-install requirements.txt; do sage-package list :experimental: --has-file $a --no-file huge --no-file has_nonfree_dependencies; done) | grep -v ^_ | grep -v sagemath_doc | grep '^[${{ matrix.targets_pattern }}]' ) )
                              ;;
           esac
           MAKE="make -j12" tox -e $TOX_ENV -- SAGE_NUM_THREADS=4 $TARGETS

.gitpod.yml

@@ -36,18 +36,34 @@ image:
 tasks:
   - name: Setup
     before: |
-      # Setup ssh key for authentication with trac
-      ## In order to use this, generate a new key with `ssh-keygen -f tempkey` and save the private key to gitpod `gp env PRIVATE_SSH_KEY="$(<tempkey)"` (or by following https://www.gitpod.io/docs/environment-variables#using-the-account-settings)
+      # Setup trac as remote
+      ## In order to push to trac, generate a new key with `ssh-keygen -f tempkey` and save the private key to gitpod `gp env PRIVATE_SSH_KEY="$(<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.
-      mkdir -p ~/.ssh
-      echo $PRIVATE_SSH_KEY | sed 's/\(-----\(BEGIN\|END\) OPENSSH PRIVATE KEY-----\)/\n\1\n/g' > ~/.ssh/id_rsa
-      sed -i '/^$/d' ~/.ssh/id_rsa
-      chmod 600 ~/.ssh/id_rsa
-      unset PRIVATE_SSH_KEY
-      ssh-keyscan -H trac.sagemath.org >> ~/.ssh/known_hosts
+      ## Afterwards, create a new gitpod workspace.
+      git remote remove trac 2> /dev/null # might still exists from a previous run/prebuild
+      if [[ -n "${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
+        unset PRIVATE_SSH_KEY
+        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
+      
       ## No need for pyenv
-      pyenv shell --unset
-      pyenv global system
+      pyenv shell --unset 2> /dev/null
+      pyenv global system 2> /dev/null
       if [ -d local ]; then
         mkdir -p logs && echo '### .gitpod.yml Setup.before: Prebuild init script has been run. Running "make" again in case the build had timed out.' >> logs/install.log
         # The init script has already populated the SAGE_LOCAL,
@@ -75,10 +91,6 @@ tasks:
       rm -Rf $HOME/sage
       ln -s $(pwd) $HOME/sage
     init: |
-      # Setup trac repo
-      git remote add trac git@trac.sagemath.org:sage.git -t master
-      git remote set-url --push trac git@trac.sagemath.org:sage.git
-
       # Start build
       mkdir -p logs && echo '### .gitpod.yml Setup.init: Starting build' >> logs/install.log
       ./bootstrap

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.6.beta7", 
-    "version": "9.6.beta7", 
+    "title": "sagemath/sage: 9.6.rc0", 
+    "version": "9.6.rc0", 
     "upload_type": "software", 
-    "publication_date": "2022-04-02", 
+    "publication_date": "2022-04-10", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.6.beta7", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.6.rc0", 
             "relation": "isSupplementTo"
         }, 
         {

AUTHORS.md

@@ -0,0 +1,9 @@
+# Authors of SageMath #
+
+[Over 800 people](https://www.sagemath.org/development-map.html) have
+contributed code to the Sage library (see [src/](src/)) or have
+contributed to the maintenance of the SageMath distribution (see
+[build/](build/)).
+
+See https://www.sagemath.org/development-map.html for information
+about the developers and their contributions.

CODE_OF_CONDUCT.md

@@ -0,0 +1,42 @@
+# Code of Conduct #
+
+Approved by the Sage community by a vote which ended on November 24, 2014
+
+The Sage community is comprised of an international mixture of mathematicians,
+computer scientists, engineers, researchers, teachers, amateurs, and others
+with varied backgrounds. This diversity is one of our strengths, but it can
+also lead to communication problems and unhappiness. People who love working on
+Sage can more effectively collaborate with others if they follow this code.
+
+1. Be friendly and patient.
+
+2. Be welcoming. We strive to be a community that welcomes and supports people
+   of all backgrounds and identities.
+
+3. Be considerate. Your work will be used by other people and you in turn will
+   depend on the work of others. Any decision you take will affect users and
+   developers, so you should take those consequences into account when making
+   decisions. Conversely, Sage is constantly evolving, and earlier decisions
+   that were made in good faith may sometimes need to be reconsidered.
+   Nonetheless, we should still appreciate the hard work done in the past.
+
+4. Be respectful and polite. Not all of us will agree all the time, but
+   disagreement is no excuse for poor behavior and poor manners. We might all
+   experience some frustration now and then, but we cannot allow that
+   frustration to morph into personal attacks. It is important to remember that
+   a community where people feel uncomfortable or threatened is not a
+   productive one. Members of the Sage community should be respectful when
+   dealing with other developers and users.
+
+   When we disagree, we should try to understand why. Disagreements, both
+   social and technical, happen all the time. It is important that we resolve
+   disagreements and differing views constructively. Being unable to understand
+   why someone holds a viewpoint does not mean that they are wrong. Do not
+   forget that it is human to err. Blame alone gets us nowhere, it is better to
+   help resolve issues so we can all learn from our mistakes.
+
+If you believe someone is violating the code of conduct, we ask that you report
+it to https://groups.google.com/g/sage-abuse. The group administrators will
+consider the issue and explore resolutions. It is also possible to move heated
+discussions to https://groups.google.com/g/sage-flame.
+

README.md

@@ -5,7 +5,7 @@
 >   "Creating a Viable Open Source Alternative to
 >   Magma, Maple, Mathematica, and MATLAB"
 
->   Copyright (C) 2005-2021 The Sage Development Team
+>   Copyright (C) 2005-2022 The Sage Development Team
 
 https://www.sagemath.org
 
@@ -148,8 +148,9 @@ read the following step-by-step instructions for building Sage.
 
 The instructions cover all of Linux, macOS, and Cygwin.
 
-More detailed instructions are contained in the [Installation
-Guide](https://doc.sagemath.org/html/en/installation).
+More details, providing a background for these instructions, can be found
+in the [section "Install from Source Code"](https://doc.sagemath.org/html/en/installation/source.html).
+in the Installation Guide.
 
 1.  Decide on the source/build directory (`SAGE_ROOT`):
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.6.beta7, Release Date: 2022-04-02
+SageMath version 9.6.rc0, Release Date: 2022-04-10

build/bin/sage-site

@@ -236,6 +236,13 @@ if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
         export OMP_NUM_THREADS=1
     fi
 
+    # Trac #33650: Make sure that user configuration of Jupyter does not
+    # shadow our sagemath kernel when jupyter-sphinx is invoked
+    export JUPYTER_CONFIG_DIR=/doesnotexist
+    export JUPYTER_CONFIG_PATH=/doesnotexist
+    export JUPYTER_DATA_DIR=/doesnotexist
+    export JUPYTER_PATH=/doesnotexist
+
     exec sage-python -m sage_docbuild "$@" </dev/null
 fi
 

build/pkgs/beautifulsoup4/SPKG.rst

@@ -1,5 +1,5 @@
-beautifulsoup4: A screen-scraping library
-=========================================
+beautifulsoup4: Screen-scraping library
+=======================================
 
 Description
 -----------
@@ -16,4 +16,3 @@ Upstream Contact
 
 https://pypi.org/project/beautifulsoup4/
 
-https://www.crummy.com/software/BeautifulSoup/

build/pkgs/beautifulsoup4/checksums.ini

@@ -0,0 +1,5 @@
+tarball=beautifulsoup4-VERSION.tar.gz
+sha1=4fcafb012dd6dfad556dc144cffa64ee72ebe316
+md5=e754242642253dd31d249d00358d552e
+cksum=679040307
+upstream_url=https://pypi.io/packages/source/b/beautifulsoup4/beautifulsoup4-VERSION.tar.gz

build/pkgs/beautifulsoup4/dependencies

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

build/pkgs/beautifulsoup4/package-version.txt

@@ -0,0 +1 @@
+4.10.0

build/pkgs/beautifulsoup4/spkg-install.in

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

build/pkgs/beautifulsoup4/type

@@ -1 +1 @@
-optional
+standard

build/pkgs/cbc/SPKG.rst

@@ -11,8 +11,7 @@ open-source software for the operations research community.
 The COIN Branch and Cut solver (CBC) is an open-source mixed-integer
 program (MIP) solver written in C++. CBC is intended to be used
 primarily as a callable library to create customized branch-and-cut
-solvers. A basic, stand-alone executable version is also available. CBC
-is an active open-source project led by John Forrest at www.coin-or.org.
+solvers. A basic, stand-alone executable version is also available.
 
 License
 -------
@@ -24,11 +23,4 @@ Eclipse Public License, Version 1.0 (EPL-1.0)
 Upstream Contact
 ----------------
 
--  John Forrest <jjforre@us.ibm.com>
--  Robin Lougee-Heimer
-
-
-Project Home Page
------------------
-
--  https://projects.coin-or.org/Cbc
+-  https://github.com/coin-or/Cbc

build/pkgs/cbc/checksums.ini

@@ -2,3 +2,4 @@ tarball=cbc-VERSION.tar.gz
 sha1=d937d6af1ee8838d44659ebd4cf7bbb1b20372ce
 md5=2134576233cc95cdfedc63991a4944ec
 cksum=1215468781
+upstream_url=https://github.com/coin-or/Cbc/archive/refs/tags/releases/VERSION.tar.gz

build/pkgs/cbc/distros/gentoo.txt

@@ -0,0 +1 @@
+sci-libs/coinor-cbc

build/pkgs/cbc/distros/nix.txt

@@ -0,0 +1 @@
+cbc

build/pkgs/cbc/distros/repology.txt

@@ -1 +1,2 @@
 coin-or-cbc
+cbc

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=4f7f6e9e49e702f7a00ea446aa6145c81f430de8
-md5=b90d3aac0d34dcade19ea0879a94d8d1
-cksum=1127886742
+sha1=ffb658a0ff2c9baafe48b0986c8f4a752b8165e2
+md5=ca16d1e5c783c44d765afc0673dad562
+cksum=2868305934

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-199ee74bddecaf754d0e0bd9c26d128ebe2bf78e
+547ddc2096a611d3273bd5a1c93445dc7348014a