Merge tag '9.4.beta0' into t/31593/configure__paths_within__sage_local___prefix__for_sage_conf

SageMath version 9.4.beta0, Release Date: 2021-05-25

Author: Matthias Koeppe

.github/workflows/tox-experimental.yml

@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       max-parallel: 6
       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, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-focal-i386, debian-buster-i386, centos-7-i386]
+        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, 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: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:
@@ -54,15 +54,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |
@@ -106,54 +112,35 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        tox_system_factor: [homebrew-macos, conda-forge-macos]
-        tox_packages_factor: [minimal, standard]
+        tox_system_factor: [homebrew-macos, conda-forge-macos, homebrew-macos-python3_xcode]
+        tox_packages_factor: [maximal]
         # As of 2021-03, default xcode is 12.4
         # https://github.com/actions/virtual-environments/blob/main/images/macos/macos-10.15-Readme.md#xcode
         xcode_version_factor: [default]
+        targets_pattern: [0-g, h-o, p, q-z]
         os: [ macos-10.15, macos-11.0 ]
         include:
           # Test xcode 11.7 only on macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: minimal
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: 0-g
             os: macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: standard
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: h-o
             os: macos-10.15
-          # python3_xcode is only accepted if enough packages are available from the system
-          # --> to test "minimal", we will need https://trac.sagemath.org/ticket/30949
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: p
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
+            xcode_version_factor: 11.7
+            targets_pattern: q-z
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: homebrew-macos-python3_xcode-nokegonly
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # likewise for python3_pythonorg
-          - tox_system_factor: homebrew-macos-python3_pythonorg
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # conda-forge-macos-environment
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment-optional
-            xcode_version_factor: default
-            os: macos-11.0
     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 }}

.github/workflows/tox-gcc_spkg.yml

@@ -52,15 +52,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.github/workflows/tox-optional.yml

@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       max-parallel: 6
       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, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-focal-i386, debian-buster-i386, centos-7-i386]
+        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, 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: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:
@@ -56,15 +56,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |
@@ -108,54 +114,35 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        tox_system_factor: [homebrew-macos, conda-forge-macos]
-        tox_packages_factor: [minimal, standard]
+        tox_system_factor: [homebrew-macos, conda-forge-macos, homebrew-macos-python3_xcode]
+        tox_packages_factor: [maximal]
         # As of 2021-03, default xcode is 12.4
         # https://github.com/actions/virtual-environments/blob/main/images/macos/macos-10.15-Readme.md#xcode
         xcode_version_factor: [default]
+        targets_pattern: [0-g, h-o, p, q-z]
         os: [ macos-10.15, macos-11.0 ]
         include:
           # Test xcode 11.7 only on macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: minimal
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: 0-g
             os: macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: standard
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: h-o
             os: macos-10.15
-          # python3_xcode is only accepted if enough packages are available from the system
-          # --> to test "minimal", we will need https://trac.sagemath.org/ticket/30949
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: p
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
+            xcode_version_factor: 11.7
+            targets_pattern: q-z
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: homebrew-macos-python3_xcode-nokegonly
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # likewise for python3_pythonorg
-          - tox_system_factor: homebrew-macos-python3_pythonorg
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # conda-forge-macos-environment
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment-optional
-            xcode_version_factor: default
-            os: macos-11.0
     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 }}

.github/workflows/tox.yml

@@ -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, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-focal-i386, debian-buster-i386, centos-7-i386]
+        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_packages_factor: [minimal, standard]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
@@ -52,15 +52,21 @@ jobs:
         run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
       - name: free disk space
         run: |
+          df -h
           sudo swapoff -a
           sudo rm -f /swapfile
-          sudo apt clean
+          sudo apt-get clean
           docker rmi $(docker image ls -aq)
+          echo "Largest packages:"
+          dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
+          sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
           df -h
       - name: Install test prerequisites
         run: |
           sudo DEBIAN_FRONTEND=noninteractive apt-get update
           sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
+          sudo apt-get clean
+          df -h
       - name: Try to login to docker.pkg.github.com
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
         run: |

.gitignore

@@ -23,6 +23,14 @@
 /src/environment.yml
 /src/environment-optional.yml
 
+/src/setup.cfg
+/src/requirements.txt
+/src/pyproject.toml
+/src/Pipfile
+/src/Pipfile.lock
+/Pipfile
+/Pipfile.lock
+
 # Various editors
 *~
 
@@ -93,6 +101,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# Generated by sage_setup.autogen
+/src/sage/ext/interpreters
+
 # Generated Cython files
 *.so
 src/sage/**/*.c
@@ -130,6 +141,14 @@ build/bin/sage-build-env-config
 /build/pkgs/*/src/*.egg-info
 /build/pkgs/*/src/.tox
 
+# Generated by docbuild
+/src/doc/en/reference/*/sage
+/src/doc/en/reference/sage
+/src/doc/en/reference/spkg/*.rst
+/src/doc/output
+/src/doc/en/installation/*.txt
+/src/doc/en/reference/repl/*.txt
+
 # Distribution / packaging
 src/*.egg-info/
 /src/.cython_version
@@ -152,5 +171,8 @@ src/venv.bak/
 
 # tox generated files
 /.tox
+/build/.tox
 /prefix
+
+# git worktree
 worktree*

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3.rc1", 
-    "version": "9.3.rc1", 
+    "title": "sagemath/sage: 9.4.beta0", 
+    "version": "9.4.beta0", 
     "upload_type": "software", 
-    "publication_date": "2021-03-29", 
+    "publication_date": "2021-05-25", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3.rc1", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta0", 
             "relation": "isSupplementTo"
         }, 
         {

Pipfile.m4

@@ -0,0 +1,41 @@
+## Pipfile with all packages in the Sage distribution and version information locked
+## FIXME: Many packages still missing.
+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+pkgconfig = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../pkgconfig/package-version.txt)')"
+cython = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cython/package-version.txt)')"
+pycodestyle = "*"
+ipykernel = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../ipykernel/package-version.txt)')"
+tox = "*"
+jinja2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../jinja2/package-version.txt)')"
+pytest = "*"
+ipywidgets = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../ipywidgets/package-version.txt)')"
+sphinx = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../sphinx/package-version.txt)')"
+rope = "*"
+six = "*"
+jupyter-core = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../jupyter_core/package-version.txt)')"
+
+[packages]
+numpy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../numpy/package-version.txt)')"
+cysignals = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cysignals/package-version.txt)')"
+cypari2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cypari/package-version.txt)')"
+gmpy2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../gmpy2/package-version.txt)')"
+psutil = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../psutil/package-version.txt)')"
+pexpect = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../pexpect/package-version.txt)')"
+ipython = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../ipython/package-version.txt)')"
+sympy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../sympy/package-version.txt)')"
+scipy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../scipy/package-version.txt)')"
+pplpy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../pplpy/package-version.txt)')"
+matplotlib = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../matplotlib/package-version.txt)')"
+cvxopt = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cvxopt/package-version.txt)')"
+rpy2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../rpy2/package-version.txt)')"
+networkx = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../networkx/package-version.txt)')"
+
+sagemath-standard = { path = "src" }
+
+[requires]
+python_version = "3.9"

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.3.rc1, Release Date: 2021-03-29
+SageMath version 9.4.beta0, Release Date: 2021-05-25