Merge tag '9.6.beta1' into t/32966/tox___gh_actions__add_ubuntu_varia…

…nts_using_ppa_ubuntu_toolchain_r

SageMath version 9.6.beta1, Release Date: 2022-02-13

.github/workflows/doc-build.yml

@@ -0,0 +1,72 @@
+name: Build documentation
+
+on:
+  push:
+  workflow_dispatch:
+    # Allow to run manually
+
+concurrency:
+  # Cancel previous runs of this workflow for the same branch
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    container: ghcr.io/sagemath/sage/sage-docker-ubuntu-focal-standard-with-targets:9.5
+    if: github.repository == 'sagemath/sagetrac-mirror'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Prepare
+        run: |
+          # Reuse built SAGE_LOCAL contained in the Docker image 
+          ./bootstrap
+          ./configure --enable-build-as-root --prefix=/sage/local --with-sage-venv
+
+      - name: Build
+        run: make doc-html
+        env:
+          MAKE: make -j2
+          SAGE_NUM_THREADS: 2
+
+      - name: Copy docs
+        run: |
+          # For some reason the deploy step below cannot find /sage/...
+          # So copy everything from there to local folder
+          # We also need to replace the symlinks because netlify is not following them
+          mkdir -p ./docs
+          cp -r -L /sage/local/share/doc/sage/html/en/* ./docs
+
+      - name: Deploy to Netlify preview
+        id: preview-netlify
+        if: github.ref != 'refs/heads/develop'
+        uses: netlify/actions/cli@master
+        with:
+          args: deploy --dir=docs --alias="${NETLIFY_ALIAS}"
+        env:
+          # Set deployment url to commit hash to easily link from the trac.
+          # We could also set NETLIFY_ALIAS to the branch name.
+          # However, netlify currently doesn't support updates to a deployment with the same alias
+          # https://github.com/netlify/cli/issues/948
+          # https://github.com/netlify/cli/issues/1984
+          # Note that even if this feature is implemented, one would also need to first process the branch name
+          # to workaround the bug https://github.com/netlify/cli/issues/969.
+          NETLIFY_ALIAS: ${{ github.sha }}
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+
+      - name: Deploy to Netlify production
+        id: deploy-netlify
+        if: github.ref == 'refs/heads/develop'
+        uses: netlify/actions/cli@master
+        with:
+          args: deploy --dir=docs --prod
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+
+      - name: Report deployment url
+        run: |
+          echo "::notice::The documentation has being automatically deployed to Netlify. %0A ✅ Preview: ${{ steps.preview-netlify.outputs.NETLIFY_URL || steps.deploy-netlify.outputs.NETLIFY_URL }}"

.github/workflows/tox.yml

@@ -124,7 +124,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        stage: ["1", "2", "2-optional-0-g", "2-optional-h-o", "2-optional-p", "2-optional-q-z", "2-experimental-0-g", "2-experimental-h-o", "2-experimental-p", "2-experimental-q-z"]
+        stage: ["1", "2", "2-optional-0-o", "2-optional-p-z", "2-experimental-0-o", "2-experimental-p-z"]
         # python3_xcode is only accepted if enough packages are available from the system
         # --> to test "minimal", we would need https://trac.sagemath.org/ticket/30949
         tox_env: [homebrew-macos-usrlocal-minimal, homebrew-macos-usrlocal-standard, homebrew-macos-usrlocal-maximal, homebrew-macos-usrlocal-python3_xcode-standard, conda-forge-macos-minimal, conda-forge-macos-standard, conda-forge-macos-maximal]
@@ -174,7 +174,7 @@ jobs:
             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 && (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]" ) )
                              ;;
           esac
           MAKE="make -j12" tox -e $TOX_ENV -- SAGE_NUM_THREADS=4 $TARGETS

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.6.beta0", 
-    "version": "9.6.beta0", 
+    "title": "sagemath/sage: 9.6.beta1", 
+    "version": "9.6.beta1", 
     "upload_type": "software", 
-    "publication_date": "2022-02-06", 
+    "publication_date": "2022-02-13", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.6.beta0", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.6.beta1", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.6.beta0, Release Date: 2022-02-06
+SageMath version 9.6.beta1, Release Date: 2022-02-13

build/pkgs/_prereq/distros/void.txt

@@ -1,10 +1,11 @@
+bc
 binutils
-make
+gcc
+libgomp-devel
 m4
+make
 perl
 pkg-config
 python3
 tar
-bc
-gcc
 which

build/pkgs/_recommended/dependencies

@@ -0,0 +1 @@
+pandoc ffmpeg imagemagick texlive git

build/pkgs/_recommended/distros/debian.txt

@@ -1,17 +1,7 @@
 # From https://wiki.sagemath.org/prerequisitesUbuntu
+# - see also separate script packages texlive, pandoc, ffmpeg
 
-# to generate pdf documentation
-texlive-latex-extra
-# to convert Jupyter notebooks to pdf
-texlive-xetex
-# to generate pdf documentation
-latexmk
-# to convert Jupyter notebooks to pdf
-# pandoc -- this is a separate script package
-# to render text with LaTeX in Matplotlib
-dvipng
 # to run the Jmol 3D viewer from the console and generate images for 3D plots in the documentation
 default-jdk
 # to produce animations
-# ffmpeg -- this is a separate script package
 libavdevice-dev

build/pkgs/alabaster/distros/void.txt

@@ -0,0 +1 @@
+python3-alabaster

build/pkgs/appdirs/distros/void.txt

@@ -0,0 +1 @@
+python3-appdirs

build/pkgs/arb/checksums.ini

@@ -1,5 +1,5 @@
 tarball=arb-VERSION.tar.gz
-sha1=33c069505b30d1668f5d873499e290e517d92c74
-md5=0a60ab546a8ad3d8d46ad9f040aeca98
-cksum=1430425209
+sha1=b49978d7a54febbc408297683085f3252b5a3281
+md5=6521245e826eb337eddedd6159eabcb8
+cksum=3488846289
 upstream_url=https://github.com/fredrik-johansson/arb/archive/VERSION.tar.gz

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.19.0.p0
+2.22.1

build/pkgs/argcomplete/distros/void.txt

@@ -0,0 +1 @@
+python3-argcomplete

build/pkgs/argon2_cffi/distros/void.txt

@@ -0,0 +1 @@
+python3-argon2

build/pkgs/attrs/distros/void.txt

@@ -0,0 +1 @@
+python3-attrs

build/pkgs/babel/distros/void.txt

@@ -0,0 +1 @@
+python3-Babel

build/pkgs/backcall/distros/void.txt

@@ -0,0 +1 @@
+python3-backcall

build/pkgs/beautifulsoup4/distros/void.txt

@@ -0,0 +1 @@
+python3-BeautifulSoup4

build/pkgs/beniget/distros/void.txt

@@ -0,0 +1 @@
+python3-beniget

build/pkgs/bleach/distros/void.txt

@@ -0,0 +1 @@
+python3-bleach

build/pkgs/brial/distros/void.txt

@@ -0,0 +1 @@
+brial-devel

build/pkgs/cddlib/distros/void.txt

@@ -0,0 +1 @@
+cddlib-devel

build/pkgs/certifi/distros/void.txt

@@ -0,0 +1 @@
+python3-certifi

build/pkgs/cffi/distros/void.txt

@@ -0,0 +1 @@
+python3-cffi

build/pkgs/charset_normalizer/distros/void.txt

@@ -0,0 +1 @@
+python3-charset-normalizer

build/pkgs/cliquer/distros/void.txt

@@ -0,0 +1 @@
+cliquer-devel

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=345924fc41ea858557c397fb38060606c868b0bd
-md5=2e5d32301a1c1debf4ec508ebc157ec2
-cksum=1618326589
+sha1=8e164215068f39fcaa971350baa69da13b9b5cff
+md5=7b3d1f477ac6491f55ebee7b575963e0
+cksum=506943323

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-f0df3d8b40169709426fd20a9f71cdcb30851c90
+33dd1c9955f5509472380e5ac6ca07ea8618fb2f

build/pkgs/cycler/distros/void.txt

@@ -0,0 +1 @@
+python3-cycler

build/pkgs/cython/distros/void.txt

@@ -0,0 +1 @@
+python3-Cython

build/pkgs/dateutil/distros/void.txt

@@ -0,0 +1 @@
+python3-dateutil

build/pkgs/debugpy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=debugpy-VERSION.zip
-sha1=c0162bd8d68a43702eea2591c67624fd5b4aa87b
-md5=0c1103c7234b1f547eb705aff150ab31
-cksum=676752698
+sha1=169efd648ce0903c30cd300f8040136ec0ee16cc
+md5=7c8ef4f136c9bcf501e80a12b8e21ac1
+cksum=422456395
 upstream_url=https://pypi.io/packages/source/d/debugpy/debugpy-VERSION.zip

build/pkgs/debugpy/package-version.txt

@@ -1 +1 @@
-1.4.1
+1.5.1

build/pkgs/decorator/checksums.ini

@@ -1,4 +1,5 @@
 tarball=decorator-VERSION.tar.gz
-sha1=24d4560ff3e89a6cec068d323383577343c086fb
-md5=d83c624cce93e6bdfab144821b526e1d
-cksum=1324765948
+sha1=4035760ce781a93181eeb3f8a36435eb799ceb76
+md5=a90526e45e7a30cf2710d6467f403e03
+cksum=1796541525
+upstream_url=https://pypi.io/packages/source/d/decorator/decorator-VERSION.tar.gz

build/pkgs/decorator/dependencies

@@ -2,4 +2,3 @@ $(PYTHON) | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.
-It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/decorator/distros/void.txt

@@ -0,0 +1 @@
+python3-decorator

build/pkgs/decorator/package-version.txt

@@ -1 +1 @@
-4.4.2
+5.0.9

build/pkgs/defusedxml/checksums.ini

@@ -1,4 +1,5 @@
 tarball=defusedxml-VERSION.tar.gz
-sha1=0bba33cc1e6d59f8fc71ceb8d12ad951072ad122
-md5=a59741f675c4cba649de40a99f732897
-cksum=2504737728
+sha1=37667af1dc1357eb96b005c4f408ad5292d77b9f
+md5=a50e7f21aa60a741efe6b1b658dfb3f8
+cksum=3442371004
+upstream_url=https://pypi.io/packages/source/d/defusedxml/defusedxml-VERSION.tar.gz

build/pkgs/defusedxml/dependencies

@@ -2,4 +2,3 @@ $(PYTHON) | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.
-It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/defusedxml/distros/void.txt

@@ -0,0 +1 @@
+python3-defusedxml

build/pkgs/defusedxml/package-version.txt

@@ -1 +1 @@
-0.6.0
+0.7.1

build/pkgs/distlib/checksums.ini

@@ -1,5 +1,5 @@
 tarball=distlib-VERSION.zip
-sha1=47db238631902dbd0fbf730ca303438eaecbb0c8
-md5=442dc114d7e59deec1c727b8a27d7e7c
-cksum=4135782264
+sha1=e7927ebc964676c17d466ed6a345222c34167a85
+md5=c886b7d99b4085c5d960e7435dcbd397
+cksum=10374426
 upstream_url=https://pypi.io/packages/source/d/distlib/distlib-VERSION.zip

build/pkgs/distlib/distros/void.txt

@@ -0,0 +1 @@
+python3-distlib

build/pkgs/distlib/package-version.txt

@@ -1 +1 @@
-0.3.3
+0.3.4

build/pkgs/docutils/distros/void.txt

@@ -0,0 +1 @@
+python3-docutils

build/pkgs/ecl/spkg-install.in

@@ -45,7 +45,7 @@ else
     fi
 fi
 
-sdh_configure $SAGE_CONFIGURE_GMP --disable-threads \
+sdh_configure $SAGE_CONFIGURE_GMP \
               --enable-unicode=yes --with-defsystem $ECL_CONFIGURE
 
 # Before running make we touch build/TAGS so its building process is never triggered

build/pkgs/entrypoints/distros/void.txt

@@ -0,0 +1 @@
+python3-entrypoints

build/pkgs/fflas_ffpack/distros/void.txt

@@ -0,0 +1 @@
+fflas-ffpack

build/pkgs/ffmpeg/distros/fedora.txt

@@ -1 +1,3 @@
-ffmpeg
+# ffmpeg is not in the standard Fedora repository
+# Need "RPM Fusion Free"
+#ffmpeg

build/pkgs/filelock/distros/void.txt

@@ -0,0 +1 @@
+python3-filelock

build/pkgs/flint/checksums.ini

@@ -1,5 +1,5 @@
 tarball=flint-VERSION.tar.gz
-sha1=0e095e667ed4424e2280c49a9e6a513d12622823
-md5=05a5f77732a05b590972d2349e6f6bb0
-cksum=2043627147
+sha1=d17a245bddec753c6eb5841b28d0322ba0c9e2b6
+md5=484e62dd7326a4af6e2072f4edbc769f
+cksum=1002348409
 upstream_url=http://flintlib.org/flint-VERSION.tar.gz

build/pkgs/flint/package-version.txt

@@ -1 +1 @@
-2.7.1.p0
+2.8.4

build/pkgs/flintqs/distros/void.txt

@@ -0,0 +1 @@
+FlintQS

build/pkgs/flit_core/distros/void.txt

@@ -0,0 +1 @@
+python3-flit_core

build/pkgs/fplll/distros/void.txt

@@ -0,0 +1 @@
+fplll-devel

build/pkgs/gast/distros/void.txt

@@ -0,0 +1 @@
+python3-gast

build/pkgs/gdb/distros/void.txt

@@ -0,0 +1 @@
+gdb

build/pkgs/gfan/distros/void.txt

@@ -0,0 +1 @@
+gfan

build/pkgs/givaro/distros/void.txt

@@ -0,0 +1 @@
+givaro-devel

build/pkgs/gmp/distros/void.txt

@@ -1 +1,2 @@
+gmp-devel
 gmpxx-devel

build/pkgs/gmpy2/checksums.ini

@@ -1,5 +1,5 @@
 tarball=gmpy2-VERSION.tar.gz
-sha1=6564cfd78f552a8db82136c10b19aa7465856865
-md5=a1555e0d7ca28b3a49c9a81aa06e2bb6
-cksum=2826987588
+sha1=fcb929ab9a44d96bfb47b7ed411cc2f048b484b2
+md5=877d324e676b162053772affda5c0de7
+cksum=2408333571
 upstream_url=https://pypi.io/packages/source/g/gmpy2/gmpy2-VERSION.tar.gz

build/pkgs/gmpy2/distros/void.txt

@@ -0,0 +1 @@
+python3-gmpy2

build/pkgs/gmpy2/install-requires.txt

@@ -1,3 +1 @@
-# We would like to write gmpy2 >=2.1.0b5, but pipenv does not accept prereleases in version ranges
-# https://github.com/pypa/pipenv/issues/1760
-gmpy2 ==2.1.0rc1
+gmpy2 >=2.1.0

build/pkgs/gmpy2/package-version.txt

@@ -1 +1 @@
-2.1.0rc1
+2.1.1

build/pkgs/graphviz/distros/void.txt

@@ -1 +1,2 @@
 graphviz
+graphviz-devel

build/pkgs/html5lib/distros/void.txt

@@ -0,0 +1 @@
+python3-html5lib