Merge tag '10.1.beta5' into decouple_tuple

SageMath version 10.1.beta5, Release Date: 2023-07-01

.github/workflows/doc-build.yml

@@ -50,7 +50,7 @@ jobs:
           if [ ! -f worktree-image/.gitignore ]; then cp .gitignore worktree-image/; fi
           (cd worktree-image && git add -A && git commit --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset old)
           # Keep track of changes to built HTML
-          (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage dev /'; git init && (echo ".buildinfo"; echo ".inv") > .gitignore; git add -A && git commit --quiet -m "old")
+          new_version=$(cat src/VERSION.txt); (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage '$new_version' /'; git init && (echo "*.svg binary"; echo "*.pdf binary") >> .gitattributes && (echo ".buildinfo"; echo '*.inv'; echo '.git*'; echo '*.svg'; echo '*.pdf'; echo '*.png'; echo 'searchindex.js') > .gitignore; git add -A && git commit --quiet -m "old")
 
       - name: Incremental build
         id: incremental
@@ -80,7 +80,10 @@ jobs:
         # incremental docbuild may introduce broken links (inter-file references) though build succeeds
         run: |
           set -ex
-          make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage && ./config.status && make doc-html
+          mv /sage/local/share/doc/sage/html/en/.git /sage/.git-doc
+          make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage
+          mkdir -p /sage/local/share/doc/sage/html/en/ && mv /sage/.git-doc /sage/local/share/doc/sage/html/en/.git
+          ./config.status && make doc-html
         working-directory: ./worktree-image
         env:
           MAKE: make -j2
@@ -94,7 +97,7 @@ jobs:
           mkdir -p ./docs
           # Create changelog
           echo '## Preview of CHANGES.html'
-          (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage dev /'; git diff --name-only) | tee ./docs/CHANGES.txt
+          (cd /sage/local/share/doc/sage/html/en && git diff --name-only) | tee ./docs/CHANGES.txt
           (cd /sage/local/share/doc/sage/html/en && git diff; rm -rf .git) > ./docs/html.diff
           echo '## Preview of html.diff'; head -n 400 ./docs/html.diff
           (echo '<p><a href="html.diff">HTML diff</a>'; sed -E 's,(.*),<p><a href="\1">\1</a>,' ./docs/CHANGES.txt) > ./docs/CHANGES.html

.github/workflows/docker.yml

@@ -50,6 +50,8 @@ on:
            "centos-7-devtoolset-gcc_11",
            "centos-stream-8-python3.9",
            "centos-stream-9-python3.9",
+           "almalinux-8-python3.9",
+           "almalinux-9-python3.11",
            "gentoo-python3.10",
            "gentoo-python3.11",
            "archlinux-latest",

.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,E211,E271,E303,E306,E401,E502,E701,E702,E703,E714,W291,W293,W391,W605,E711,E712,E713,E721,E722"],
+    "python.linting.pycodestyleArgs": ["--select= E111,E21,E222,E227,E251,E271,E303,E306,E401,E502,E701,E702,E703,E71,E72,W291,W293,W391,W605"],
     "cSpell.words": [
         "furo",
         "Conda",

CITATION.cff

@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.1.beta4
+version: 10.1.beta5
 doi: 10.5281/zenodo.593563
-date-released: 2023-06-21
+date-released: 2023-07-01
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.1.beta4, Release Date: 2023-06-21
+SageMath version 10.1.beta5, Release Date: 2023-07-01

build/pkgs/bliss/SPKG.rst

@@ -10,17 +10,21 @@ canonical forms of graphs.
 License
 -------
 
-LGPL
+LGPL3
 
 
 Upstream Contact
 ----------------
 
-Bliss is currently being maintained by Tommi Junttila and Petteri Kaski.
+Bliss is currently being maintained by Tommi Junttila at
+
+https://users.aalto.fi/~tjunttil/bliss/index.html
+
+Bliss used to be maintained by Tommi Junttila and Petteri Kaski up to version 0.73 at
 
 http://www.tcs.tkk.fi/Software/bliss/index.html
 
-We apply patches generated from https://github.com/mkoeppe/bliss (branch
-apply_debian_patches) as our upstream. This tracks the patches from the
-Debian package, adding an autotools build system and adjusting the
-include file locations.
+Dependencies
+------------
+
+None

build/pkgs/bliss/checksums.ini

@@ -1,4 +1,5 @@
-tarball=bliss-VERSION.tar.gz
-sha1=1da8f098046824fbfff4c64c337e28b2a082f74f
-md5=452aea8737d3c4ad0d8ff39180be8004
-cksum=2193930007
+tarball=bliss-VERSION.zip
+sha1=c91c9dcbc11d66ffbcf6415e09ebe793df37be2a
+md5=5707cbfd9fd00980571c64ab3584c505
+cksum=1626493724
+upstream_url=https://users.aalto.fi/~tjunttil/bliss/downloads/bliss-VERSION.zip

build/pkgs/bliss/dependencies

@@ -1,4 +1,4 @@
-# no dependencies
+| cmake
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/bliss/package-version.txt

@@ -1 +1 @@
-0.73+debian-1+sage-2016-08-02.p0
+0.77

build/pkgs/bliss/patches/bliss-0.77-install.patch

@@ -0,0 +1,32 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 01ed093..cfdb0a6 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -62,3 +62,27 @@ if(USE_GMP)
+   target_link_libraries(bliss-executable ${GMP_LIBRARIES})
+ endif(USE_GMP)
+ set_target_properties(bliss-executable PROPERTIES OUTPUT_NAME bliss)
++
++include(GNUInstallDirs)
++
++set(
++  BLISS_HEADERS
++  src/bliss_C.h
++  src/uintseqhash.hh
++  src/abstractgraph.hh
++  src/stats.hh
++  src/digraph.hh
++  src/defs.hh
++  src/heap.hh
++  src/graph.hh
++  src/partition.hh
++  src/kqueue.hh
++  src/utils.hh
++  src/orbit.hh
++  src/timer.hh
++  src/bignum.hh
++)
++
++install(TARGETS bliss-executable RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
++install(TARGETS bliss LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
++install(FILES ${BLISS_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bliss)

build/pkgs/bliss/spkg-install.in

@@ -1,4 +1,4 @@
 cd src
-sdh_configure --disable-gmp
+sdh_cmake -DUSE_GMP=OFF -DCMAKE_VERBOSE_MAKEFILE=ON
 sdh_make
 sdh_make_install

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=b3604052037bc57fb64fcbe347b289dcd959366c
-md5=603842fccbd68e1125d32fed8d81ca86
-cksum=2053680048
+sha1=1b0149d4cc9bc0ca1bff27d84e8495143866225f
+md5=3aacea16772e577bcab91ab773ff1aa6
+cksum=6323298

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-4fa9c1c33b69fc6c3b948e9df3f7688b61b70589
+9161c6c27bfd10f49de79e02c21347b1084a0c77

build/pkgs/onetbb/distros/opensuse.txt

@@ -0,0 +1 @@
+tbb

build/pkgs/sage_conf/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-conf ~= 10.1b4
+sage-conf ~= 10.1b5

build/pkgs/sage_docbuild/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-docbuild ~= 10.1b4
+sage-docbuild ~= 10.1b5

build/pkgs/sage_setup/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-setup ~= 10.1b4
+sage-setup ~= 10.1b5

build/pkgs/sage_sws2rst/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-sws2rst ~= 10.1b4
+sage-sws2rst ~= 10.1b5

build/pkgs/sagelib/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagelib ~= 10.1b4
+sagelib ~= 10.1b5

build/pkgs/sagemath_categories/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-categories ~= 10.1b4
+sagemath-categories ~= 10.1b5

build/pkgs/sagemath_environment/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-environment ~= 10.1b4
+sagemath-environment ~= 10.1b5

build/pkgs/sagemath_objects/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-objects ~= 10.1b4
+sagemath-objects ~= 10.1b5

build/pkgs/sagemath_repl/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-repl ~= 10.1b4
+sagemath-repl ~= 10.1b5

pkgs/sage-conf/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sage-conf_pypi/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sage-docbuild/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sage-setup/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sage-sws2rst/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sagemath-categories/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sagemath-environment/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sagemath-objects/MANIFEST.in

@@ -82,7 +82,8 @@ graft sage/libs/gmp
 
 
 ## FIXME: Needed for doctesting
-include sage/misc/misc.*              # walltime, cputime used in sage.doctest
+include sage/misc/misc.*                # some_tuples used in sage.misc.sage_unittest
+include sage/misc/timing.p*             # walltime, cputime used in sage.doctest
 
 
 global-exclude *.c

pkgs/sagemath-objects/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

pkgs/sagemath-repl/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

src/.relint.yml

@@ -49,7 +49,7 @@
     namespace package. Type import_statements("SOME_IDENTIFIER") to find a more specific import,
     or use 'sage --fiximports' to fix automatically in the source file.
   # Keep in sync with SAGE_ROOT/src/sage/misc/replace_dot_all.py
-  pattern: 'from\s+sage(|[.](arith|categories|combinat|crypto|databases|data_structures|dynamics|ext|game_theory|games|graphs|groups|interfaces|manifolds|matrix|matroids|misc|modules|monoids|numerical|probability|quadratic_forms|quivers|rings|sat|schemes|sets|stats|symbolic|tensor)[a-z0-9_.]*|[.]libs)[.]all\s+import'
+  pattern: 'from\s+sage(|[.](arith|categories|combinat|crypto|databases|data_structures|dynamics|ext|game_theory|games|geometry|graphs|groups|interfaces|manifolds|matrix|matroids|misc|modules|monoids|numerical|probability|quadratic_forms|quivers|rings|sat|schemes|sets|stats|symbolic|tensor)[a-z0-9_.]*|[.]libs)[.]all\s+import'
   # imports from .all are allowed in all.py; also allow in some modules that need sage.all
   filePattern: '(.*/|)(?!(all|benchmark|dev_tools|parsing|sage_eval))[^/.]*[.](py|pyx|pxi)$'
 

src/VERSION.txt

@@ -1 +1 @@
-10.1.beta4
+10.1.beta5

src/bin/sage-runtests

@@ -52,6 +52,10 @@ if __name__ == "__main__":
              'if set to "all", then all tests will be run; '
              'use "!FEATURE" to disable tests marked "# optional - FEATURE". '
              'Note that "!" needs to be quoted or escaped in the shell.')
+    parser.add_argument("--hide", metavar="FEATURES", default="",
+        help='run tests pretending that the software listed in FEATURES (separated by commas) is not installed; '
+             'if "all" is listed, will also hide features corresponding to all optional or experimental packages; '
+             'if "optional" is listed, will also hide features corresponding to optional packages.')
     parser.add_argument("--randorder", type=int, metavar="SEED", help="randomize order of tests")
     parser.add_argument("--random-seed", dest="random_seed", type=int, metavar="SEED", help="random seed (integer) for fuzzing doctests",
                         default=os.environ.get("SAGE_DOCTEST_RANDOM_SEED"))

src/bin/sage-version.sh

@@ -4,6 +4,6 @@
 # which stops "setup.py develop" from rewriting it as a Python file.
 :
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='10.1.beta4'
-SAGE_RELEASE_DATE='2023-06-21'
-SAGE_VERSION_BANNER='SageMath version 10.1.beta4, Release Date: 2023-06-21'
+SAGE_VERSION='10.1.beta5'
+SAGE_RELEASE_DATE='2023-07-01'
+SAGE_VERSION_BANNER='SageMath version 10.1.beta5, Release Date: 2023-07-01'

src/doc/de/tutorial/interfaces.rst

@@ -272,8 +272,8 @@ deren :math:`i,j` Eintrag gerade :math:`i/j` ist, für :math:`i,j=1,\ldots,4`.
     matrix([1,1/2,1/3,1/4],[0,0,0,0],[0,0,0,0],[0,0,0,0])
     sage: A.eigenvalues()
     [[0,4],[3,1]]
-    sage: A.eigenvectors()
-    [[[0,4],[3,1]],[[[1,0,0,-4],[0,1,0,-2],[0,0,1,-4/3]],[[1,2,3,4]]]]
+    sage: A.eigenvectors().sage()
+    [[[0, 4], [3, 1]], [[[1, 0, 0, -4], [0, 1, 0, -2], [0, 0, 1, -4/3]], [[1, 2, 3, 4]]]]
 
 Hier ein anderes Beispiel:
 
@@ -332,12 +332,9 @@ Und der letzte ist die berühmte Kleinsche Flasche:
 
 ::
 
-    sage: maxima("expr_1: 5*cos(x)*(cos(x/2)*cos(y) + sin(x/2)*sin(2*y)+ 3.0) - 10.0")
-    5*cos(x)*(sin(x/2)*sin(2*y)+cos(x/2)*cos(y)+3.0)-10.0
-    sage: maxima("expr_2: -5*sin(x)*(cos(x/2)*cos(y) + sin(x/2)*sin(2*y)+ 3.0)")
-    -5*sin(x)*(sin(x/2)*sin(2*y)+cos(x/2)*cos(y)+3.0)
-    sage: maxima("expr_3: 5*(-sin(x/2)*cos(y) + cos(x/2)*sin(2*y))")
-    5*(cos(x/2)*sin(2*y)-sin(x/2)*cos(y))
+    sage: _ = maxima("expr_1: 5*cos(x)*(cos(x/2)*cos(y) + sin(x/2)*sin(2*y)+ 3.0) - 10.0")
+    sage: _ = maxima("expr_2: -5*sin(x)*(cos(x/2)*cos(y) + sin(x/2)*sin(2*y)+ 3.0)")
+    sage: _ = maxima("expr_3: 5*(-sin(x/2)*cos(y) + cos(x/2)*sin(2*y))")
     sage: maxima.plot3d ("[expr_1, expr_2, expr_3]", "[x, -%pi, %pi]", # not tested
     ....:     "[y, -%pi, %pi]", "['grid, 40, 40]",
     ....:     '[plot_format, openmath]')

src/doc/de/tutorial/tour_algebra.rst

@@ -209,9 +209,12 @@ Lösung: Berechnen Sie die Laplace-Transformierte der ersten Gleichung
 
 ::
 
-    sage: de1 = maxima("2*diff(x(t),t, 2) + 6*x(t) - 2*y(t)")
-    sage: lde1 = de1.laplace("t","s"); lde1
-    2*((-%at('diff(x(t),t,1),t = 0))+s^2*'laplace(x(t),t,s)-x(0)*s) -2*'laplace(y(t),t,s)+6*'laplace(x(t),t,s)
+    sage: t,s = SR.var('t,s')
+    sage: x = function('x')
+    sage: y = function('y')
+    sage: f = 2*x(t).diff(t,2) + 6*x(t) - 2*y(t)
+    sage: f.laplace(t,s)
+    2*s^2*laplace(x(t), t, s) - 2*s*x(0) + 6*laplace(x(t), t, s) - 2*laplace(y(t), t, s) - 2*D[0](x)(0)
 
 Das ist schwierig zu lesen, es besagt jedoch, dass
 
@@ -226,8 +229,8 @@ Laplace-Transformierte der zweiten Gleichung:
 ::
 
     sage: de2 = maxima("diff(y(t),t, 2) + 2*y(t) - 2*x(t)")
-    sage: lde2 = de2.laplace("t","s"); lde2
-    (-%at('diff(y(t),t,1),t = 0))+s^2*'laplace(y(t),t,s) +2*'laplace(y(t),t,s)-2*'laplace(x(t),t,s) -y(0)*s
+    sage: lde2 = de2.laplace("t","s"); lde2.sage()
+    s^2*laplace(y(t), t, s) - s*y(0) - 2*laplace(x(t), t, s) + 2*laplace(y(t), t, s) - D[0](y)(0)
 
 Dies besagt
 

src/doc/en/constructions/linear_algebra.rst

@@ -277,8 +277,8 @@ Another approach is to use the interface with Maxima:
 
     sage: A = maxima("matrix ([1, -4], [1, -1])")
     sage: eig = A.eigenvectors()
-    sage: eig
-    [[[-sqrt(3)*%i,sqrt(3)*%i],[1,1]], [[[1,(sqrt(3)*%i+1)/4]],[[1,-(sqrt(3)*%i-1)/4]]]]
+    sage: eig.sage()
+    [[[-I*sqrt(3), I*sqrt(3)], [1, 1]], [[[1, 1/4*I*sqrt(3) + 1/4]], [[1, -1/4*I*sqrt(3) + 1/4]]]]
 
 This tells us that :math:`\vec{v}_1 = [1,(\sqrt{3}i + 1)/4]` is
 an eigenvector of :math:`\lambda_1 = - \sqrt{3}i` (which occurs

src/doc/en/faq/faq-usage.rst

@@ -322,7 +322,7 @@ ints. For example::
     sage: RealNumber = float; Integer = int
     sage: from scipy import stats
     sage: stats.ttest_ind([1,2,3,4,5], [2,3,4,5,.6])
-    Ttest_indResult(statistic=0.0767529..., pvalue=0.940704...)
+    Ttest...Result(statistic=0.0767529..., pvalue=0.940704...)
     sage: stats.uniform(0,15).ppf([0.5,0.7])
     array([  7.5,  10.5])
 

src/doc/en/installation/conda.rst

@@ -178,3 +178,8 @@ After editing any Cython files, rebuild the Sage library using::
 In order to update the conda environment later, you can run::
 
   $ mamba env update --file src/environment-dev.yml --name sage-dev
+
+To build the documentation, use::
+
+  $ pip install --no-build-isolation -v -v --editable ./pkgs/sage-docbuild
+  $ sage --docbuild all html