Merge #31959

.github/workflows/tox-experimental.yml

@@ -38,7 +38,9 @@ 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, 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]
+        # 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
+        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, 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-gcc_spkg, 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-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

.github/workflows/tox-optional.yml

@@ -38,7 +38,9 @@ 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, 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]
+        # 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
+        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, 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-gcc_spkg, 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-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:

.gitignore

@@ -114,6 +114,7 @@ src/sage/modular/arithgroup/farey_symbol.h
 !src/sage/graphs/cliquer/cl.c
 !src/sage/graphs/graph_decompositions/sage_tdlib.cpp
 !src/sage/libs/eclib/wrap.cpp
+!src/sage/libs/linkages/padics/relaxed/flint_helper.c
 !src/sage/misc/inherit_comparison_impl.c
 !src/sage/modular/arithgroup/farey.cpp
 !src/sage/modular/arithgroup/sl2z.cpp

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.4.beta0", 
-    "version": "9.4.beta0", 
+    "title": "sagemath/sage: 9.4.beta1", 
+    "version": "9.4.beta1", 
     "upload_type": "software", 
-    "publication_date": "2021-05-25", 
+    "publication_date": "2021-06-06", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta0", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta1", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.4.beta0, Release Date: 2021-05-25
+SageMath version 9.4.beta1, Release Date: 2021-06-06

build/bin/sage-bootstrap-python

@@ -30,6 +30,15 @@ fi
 # is accessible by this python; this is to guard on Cygwin against Pythons
 # installed somewhere else in Windows.
 
+# Trac #30008: Make it work even if the environment tries to sabotage UTF-8
+# operation in Python 3.0.x-3.6.x by setting LC_ALL=C or similar.
+
+if [ "$LC_ALL" = "C" -o "$LANG" = "C" -o "$LC_CTYPE" = "C" ]; then
+    LC_ALL=$(locale -a | grep -E -i '^(c|en_us)[-.]utf-?8$' | head -n 1)
+    LANG=$LC_ALL
+    export LC_ALL
+    export LANG
+fi
 
 PYTHONS="python python3 python3.8 python3.7 python2.7 python3.6 python2"
 for PY in $PYTHONS; do

build/bin/sage-dist-helpers

@@ -39,10 +39,10 @@
 #
 # - sdh_configure [...]
 #
-#    Runs `./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib"`,
-#    (for autoconf'd projects with extra
-#        --disable-maintainer-mode --disable-dependency-tracking)
-#    Additional arguments to `./configure` may be given as arguments.
+#    Runs `./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib"`
+#    --disable-static, (for autoconf'd projects with extra
+#    --disable-maintainer-mode --disable-dependency-tracking) Additional
+#    arguments to `./configure` may be given as arguments.
 #
 # - sdh_make [...]
 #
@@ -160,9 +160,16 @@ sdh_configure() {
     if [ -z "$CONFIG_SHELL" ]; then
         export CONFIG_SHELL=`command -v bash`
     fi
-    ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" --disable-maintainer-mode --disable-dependency-tracking "$@"
+    if [ "$UNAME" = "CYGWIN" ]; then
+        # TODO: To use --disable-static for all packages on Cygwin, need
+        # #30814: Cygwin: Fix remaining packages to build shared libraries, using AM_LDFLAGS=-no-undefined
+        DISABLE_STATIC=
+    else
+        DISABLE_STATIC=--disable-static
+    fi
+    ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" $DISABLE_STATIC --disable-maintainer-mode --disable-dependency-tracking "$@"
     if [ $? -ne 0 ]; then # perhaps it is a non-autoconf'd project
-      ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" "$@"
+      ./configure --prefix="$SAGE_INST_LOCAL" --libdir="$SAGE_INST_LOCAL/lib" $DISABLE_STATIC "$@"
       if [ $? -ne 0 ]; then
         if [ -f "$(pwd)/config.log" ]; then
             sdh_die <<_EOF_

build/pkgs/cliquer/spkg-install.in

@@ -1,5 +1,5 @@
 cd src
 
-sdh_configure --disable-static
+sdh_configure
 sdh_make
 sdh_make_install

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=fc049bba332acf1d0e40275f20cdbcb734ad5bb3
-md5=971a6e2f0f92060a85aefa4130ddc287
-cksum=2143691469
+sha1=4b1b427c4e1cc5e3b7226a5c84d2312ada851086
+md5=ad2e1c54a9421a63d975f95dc771d11b
+cksum=3168609300

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-9e7b0bd3124630ebf368909dbcea7c2480ea1f27
+7690208434ed1d4aab0ea40b760669494d502c42

build/pkgs/database_knotinfo/SPKG.rst

@@ -0,0 +1,18 @@
+database_knotinfo: Content of the KnotInfo and LinkInfo databases as lists of dictionaries
+==========================================================================================
+
+Description
+-----------
+
+Content of the KnotInfo and LinkInfo databases as lists of dictionaries
+
+License
+-------
+
+GPL
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/database-knotinfo/
+

build/pkgs/database_knotinfo/checksums.ini

@@ -0,0 +1,5 @@
+tarball=database_knotinfo-VERSION.tar.gz
+sha1=2d758c5f8bf346162d13bec1d5bccfec9d27baa1
+md5=ec20d43af0c4ecf59dfd281c6ccc4ef0
+cksum=2792610748
+upstream_url=https://pypi.io/packages/source/d/database_knotinfo/database_knotinfo-VERSION.tar.gz

build/pkgs/database_knotinfo/dependencies

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

build/pkgs/database_knotinfo/install-requires.txt

@@ -0,0 +1 @@
+database-knotinfo

build/pkgs/database_knotinfo/package-version.txt

@@ -0,0 +1 @@
+0.7

build/pkgs/database_knotinfo/spkg-check.in

@@ -0,0 +1,10 @@
+cd $SAGE_ROOT/src/sage/
+
+echo "Testing databases/knotinfo_db.py"
+sage -t --long --optional="sage,database_knotinfo" databases/knotinfo_db.py  || sdh_die "Error testing KnotInfo databases"
+
+echo "Testing knots/knotinfo.py"
+sage -t --optional="sage,database_knotinfo" knots/knotinfo.py  || sdh_die "Error testing KnotInfo funcionality"
+
+echo "Testing knots/link.py"
+sage -t --optional="sage,database_knotinfo" knots/link.py  || sdh_die "Error testing KnotInfo funcionality"

build/pkgs/database_knotinfo/spkg-install.in

@@ -0,0 +1,9 @@
+cd src
+sdh_pip_install .
+
+FILECACHE="${SAGE_SHARE}/knotinfo"
+if [ -d $FILECACHE ]
+then
+    echo "Clearing former filecache of knotinfo"
+    rm -rf $FILECACHE
+fi

build/pkgs/database_knotinfo/type

@@ -0,0 +1 @@
+optional

build/pkgs/giac/spkg-configure.m4

@@ -2,7 +2,7 @@ SAGE_SPKG_CONFIGURE([giac], [
     SAGE_SPKG_DEPCHECK([pari], [
        dnl giac does not seem to reveal its patchlevel
        m4_pushdef([GIAC_MIN_VERSION], [1.5.0])
-       m4_pushdef([GIAC_MAX_VERSION], [1.6.999])
+       m4_pushdef([GIAC_MAX_VERSION], [1.7.999])
        AC_CACHE_CHECK([for giac >= ]GIAC_MIN_VERSION[, <= ]GIAC_MAX_VERSION, [ac_cv_path_GIAC], [
          AC_PATH_PROGS_FEATURE_CHECK([GIAC], [giac], [
             giac_version=$($ac_path_GIAC --version 2> /dev/null | tail -1)

build/pkgs/libatomic_ops/spkg-install.in

@@ -9,6 +9,6 @@ if [ "$UNAME" = "CYGWIN" ]; then
     LIBATOMIC_OPS_CONFIGURE="$LIBATOMIC_OPS_CONFIGURE --enable-shared --disable-static"
 fi
 
-sdh_configure $LIBATOMIC_OPS_CONFIGURE
+sdh_configure --enable-static $LIBATOMIC_OPS_CONFIGURE
 sdh_make
 sdh_make_install

build/pkgs/pari/spkg-install.in

@@ -135,4 +135,4 @@ sdh_make $PARI_MAKEFLAGS gp
 
 
 # install non-parallel (-j1) because of race conditions
-sdh_make_install -j1 install-lib-sta
+sdh_make_install -j1

build/pkgs/sagelib/package-version.txt

@@ -1 +1 @@
-9.4.beta0
+9.4.beta1

build/pkgs/sympy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=sympy-VERSION.tar.gz
-sha1=e9a321af141998638cc822505f07107736776c39
-md5=f5973bcbe33fdc86203ca397cc901994
-cksum=1357232010
+sha1=c52dd135f675cee79e46984b8454d9bb6b127edd
+md5=37af34367e3f05692e6ddede95eccddb
+cksum=4053721036
 upstream_url=https://github.com/sympy/sympy/releases/download/sympy-VERSION/sympy-VERSION.tar.gz

build/pkgs/sympy/package-version.txt

@@ -1 +1 @@
-1.7.1
+1.8

build/pkgs/zlib/spkg-install.in

@@ -12,7 +12,10 @@ if [ "$UNAME" = CYGWIN ]; then
     # We want to install shared objects
     sed -i 's/SHARED_MODE=0/SHARED_MODE=1/' Makefile
 else
-    sdh_configure --shared
+    # Trac #28890: zlib does not use a standard autoconf-generated configure
+    # script, so don't use the sdh_configure helper as it may have minor
+    # incompatibilities
+    ./configure --shared --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" || sdh_die "Error configuring $PKG_NAME"
 fi
 
 sdh_make

src/VERSION.txt

@@ -1 +1 @@
-9.4.beta0
+9.4.beta1

src/bin/sage-version.sh

@@ -1,5 +1,5 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='9.4.beta0'
-SAGE_RELEASE_DATE='2021-05-25'
-SAGE_VERSION_BANNER='SageMath version 9.4.beta0, Release Date: 2021-05-25'
+SAGE_VERSION='9.4.beta1'
+SAGE_RELEASE_DATE='2021-06-06'
+SAGE_VERSION_BANNER='SageMath version 9.4.beta1, Release Date: 2021-06-06'

src/doc/en/developer/packaging.rst

@@ -385,9 +385,9 @@ begin with ``sdh_``, which stands for "Sage-distribution helper".
 
 - ``sdh_configure [...]``: Runs ``./configure`` with arguments
   ``--prefix="$SAGE_LOCAL"``, ``--libdir="$SAGE_LOCAL/lib"``,
-  ``--disable-maintainer-mode``, and
-  ``--disable-dependency-tracking``. Additional arguments to
-  ``./configure`` may be given as arguments.
+  ``--disable-static``, ``--disable-maintainer-mode``, and
+  ``--disable-dependency-tracking``. Additional arguments to ``./configure``
+  may be given as arguments.
 
 - ``sdh_make [...]``: Runs ``$MAKE`` with the default target.
    Additional arguments to ``$MAKE`` may be given as arguments.

src/doc/en/reference/combinat/module_list.rst

@@ -145,6 +145,7 @@ Comprehensive Module list
     sage/combinat/integer_vector_weighted
     sage/combinat/integer_vectors_mod_permgroup
     sage/combinat/interval_posets
+    sage/combinat/k_regular_sequence
     sage/combinat/k_tableau
     sage/combinat/kazhdan_lusztig
     sage/combinat/knutson_tao_puzzles

src/doc/en/reference/databases/index.rst

@@ -62,5 +62,6 @@ database engine.
    sage/databases/cunningham_tables
    sage/databases/db_class_polynomials
    sage/databases/db_modular_polynomials
+   sage/databases/knotinfo_db
 
 .. include:: ../footer.txt

src/doc/en/reference/discrete_geometry/index.rst

@@ -105,6 +105,7 @@ Miscellaneous
 .. toctree::
    :maxdepth: 1
 
+   sage/geometry/convex_set
    sage/geometry/linear_expression
    sage/geometry/newton_polygon
    sage/geometry/relative_interior

src/doc/en/reference/knots/index.rst

@@ -6,5 +6,6 @@ Knot Theory
 
    sage/knots/knot
    sage/knots/link
+   sage/knots/knotinfo
 
 .. include:: ../footer.txt

src/doc/en/reference/manifolds/diff_manifold.rst

@@ -24,6 +24,8 @@ Differentiable Manifolds
 
    mixed_form
 
+   sage/manifolds/differentiable/de_rham_cohomology
+
    multivector
 
    sage/manifolds/differentiable/affine_connection

src/doc/en/reference/references/index.rst

@@ -304,6 +304,10 @@ REFERENCES:
             of crystals for the quantum queer superalgebra*.
             Preprint (2018). :arxiv:`1803.06317`
 
+.. [AS2003] Jean-Paul Allouche, Jeffrey Shallit,
+            *Automatic Sequences: Theory, Applications, Generalizations*,
+            Cambridge University Press, 2003.
+
 .. [As2008b] Sami Assaf. *Dual equivalence graphs and a
              combinatorial proof of LLT and Macdonald positivity*.
              (2008). :arxiv:`1005.3759v5`.
@@ -4766,6 +4770,9 @@ REFERENCES:
 .. [Rea2009] Nathan Reading, *Noncrossing partitions and the shard
              intersection order*, DMTCS Proceedings of FPSAC 2009, 745--756
 
+.. [ReSt2020] Nathan Reading and Salvatore Stella, *An affine almost positive
+              roots model*, J. Comb. Algebra Volume 4, Issue 1, 2020, pp. 1--59
+
 .. [Red2001] Maria Julia Redondo. *Hochschild cohomology: some methods
              for computations*. Resenhas IME-USP 5 (2), 113-137
              (2001). http://inmabb.criba.edu.ar/gente/mredondo/crasp.pdfc

src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/nf_galois_groups.rst

@@ -40,7 +40,7 @@ Some more advanced number-theoretical tools are available via G:
 
     sage: P = K.primes_above(2)[0]
     sage: G.inertia_group(P)
-    Subgroup [(), (1,4,6)(2,5,3), (1,6,4)(2,3,5)] of Galois group 6T2 ([3]2) with order 6 of x^6 + 40*x^3 + 1372
+    Subgroup generated by [(1,4,6)(2,5,3)] of (Galois group 6T2 ([3]2) with order 6 of x^6 + 40*x^3 + 1372)
     sage: sorted([G.artin_symbol(Q) for Q in K.primes_above(5)])  # random order, see Trac #18308
     [(1,3)(2,6)(4,5), (1,2)(3,4)(5,6), (1,5)(2,4)(3,6)]
 

src/doc/en/thematic_tutorials/vector_calculus/vector_calc_plane.rst

@@ -647,8 +647,7 @@ A vector field evaluated at a point $p$ is a vector in the tangent space
     sage: isinstance(Tp, FiniteRankFreeModule)
     True
     sage: sorted(Tp.bases(), key=str)
-    [Basis (d/dr,d/dph) on the Tangent space at Point p on the Euclidean plane E^2,
-     Basis (e_r,e_ph) on the Tangent space at Point p on the Euclidean plane E^2,
+    [Basis (e_r,e_ph) on the Tangent space at Point p on the Euclidean plane E^2,
      Basis (e_x,e_y) on the Tangent space at Point p on the Euclidean plane E^2]