[arch-commits] Commit in sagemath/trunk (7 files)
Antonio Rojas
arojas at gemini.archlinux.org
Mon May 16 06:50:36 UTC 2022
Date: Monday, May 16, 2022 @ 06:50:35
Author: arojas
Revision: 1207511
Update to 9.6
Modified:
sagemath/trunk/PKGBUILD
sagemath/trunk/latte-count.patch
sagemath/trunk/sagemath-bliss-0.77.patch
sagemath/trunk/sagemath-optional-packages.patch
sagemath/trunk/test-optional.patch
Deleted:
sagemath/trunk/sagemath-doc-sphinx4.3.patch
sagemath/trunk/sagemath-lrcalc2.patch
----------------------------------+
PKGBUILD | 29 -
latte-count.patch | 71 ---
sagemath-bliss-0.77.patch | 96 ++++-
sagemath-doc-sphinx4.3.patch | 12
sagemath-lrcalc2.patch | 685 -------------------------------------
sagemath-optional-packages.patch | 2
test-optional.patch | 5
7 files changed, 93 insertions(+), 807 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2022-05-16 06:50:08 UTC (rev 1207510)
+++ PKGBUILD 2022-05-16 06:50:35 UTC (rev 1207511)
@@ -6,8 +6,8 @@
# Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
pkgname=sagemath
-pkgver=9.5
-pkgrel=4
+pkgver=9.6
+pkgrel=1
pkgdesc='Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab'
arch=(x86_64)
url='http://www.sagemath.org'
@@ -45,8 +45,9 @@
'python-pycosat: picosat SAT solver'
'python-pip: to install optional packages with sage -pip'
'sage-notebook-exporter: convert flask notebooks to Jupyter'
- 'python-database-knotinfo: interface to the KnotInfo and LinkInfo databases')
-makedepends=(cython boost ratpoints python-jinja sirocco mcqd coxeter bliss tdlib python-pkgconfig shared_meataxe)
+ 'python-database-knotinfo: interface to the KnotInfo and LinkInfo databases'
+ 'python-phitigra: graph editor')
+makedepends=(cython boost python-jinja sirocco mcqd coxeter bliss tdlib python-pkgconfig shared_meataxe)
conflicts=(sagemath-jupyter)
replaces=(sagemath-jupyter)
source=(https://github.com/sagemath/sage/archive/$pkgver/$pkgname-$pkgver.tar.gz
@@ -53,31 +54,23 @@
sagemath-optional-packages.patch
latte-count.patch
test-optional.patch
- sagemath-lrcalc2.patch
sagemath-linbox-1.7.patch
- sagemath-bliss-0.77.patch
- sagemath-doc-sphinx4.3.patch)
-sha256sums=('8d70a3b26080802c5b2e33dda4c23795d494d8216a0c2ecfcd608ebab0e64ff6'
- 'eee5fa15d8c7be7e009166dbde3ea24bb10d7793dc12880516f278f86b1a6694'
- '2bf9e2b44c20c5bec9d90782f59a87374a3c726241179191e9589179e1550a03'
- '9d042070df3dfd53a1248659677798da888f733548eda91a6d5169c7aa1907e1'
- 'c8a1fb98f454dfd52101373e478e396d83a7d55c2c658b1d246a86603cbb15e8'
+ sagemath-bliss-0.77.patch)
+sha256sums=('c6225d48f70ac955fceed5c1fddfdd7294001d460b43a686329d5d44d836f6a3'
+ 'e24c075a9f8e562fe9d85e6fd5b01eac4691683c01d4d22c83cde145b63f4dba'
+ 'bd188af45ce31579b82407adee8e9bf6033a996f7ea6e328fabca526f31c08ba'
+ '89c1f82dbba376087f08b39b11f43bf781cec199d7d894713167d09dc32e3e18'
'eacea27b214d32cb886a75695153dfc36b5bad2fd2517e8e4eee18e74220e9e3'
- '49ede468b8e1e7b8d7a390aab9ff1a6e899a0c5e487632cbf76902d80c637505'
- '4e311733bc4c1d7ab4e898356838f101eff26738e7d24fb50c1879fa13a75c6e')
+ 'b467a41e1e0a0850f7722d875a743233751966a206c2f61401c7582aa722f84e')
prepare(){
cd sage-$pkgver
# Upstream patches
-# Replace lrcalc.pyx with a wrapper over lrcalc's python bindings https://trac.sagemath.org/ticket/31355
- patch -p1 -i ../sagemath-lrcalc2.patch
# Fix build with linbox 1.7 https://trac.sagemath.org/ticket/32959
patch -p1 -i ../sagemath-linbox-1.7.patch
# Fix build with bliss 0.77 https://trac.sagemath.org/ticket/33010
patch -p1 -i ../sagemath-bliss-0.77.patch
-# Fix sagemath-doc build with Sphinx 4.3 https://trac.sagemath.org/ticket/32968
- patch -p1 -i ../sagemath-doc-sphinx4.3.patch
# Arch-specific patches
# assume all optional packages are installed
Modified: latte-count.patch
===================================================================
--- latte-count.patch 2022-05-16 06:50:08 UTC (rev 1207510)
+++ latte-count.patch 2022-05-16 06:50:35 UTC (rev 1207511)
@@ -1,74 +1,3 @@
-diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py
-index 268af9db0d..70d41dfa30 100644
---- a/src/sage/geometry/polyhedron/base_ZZ.py
-+++ b/src/sage/geometry/polyhedron/base_ZZ.py
-@@ -194,7 +194,7 @@ class Polyhedron_ZZ(Polyhedron_base):
- sage: p = P._ehrhart_polynomial_latte(maxdet=5, verbose=True) # optional - latte_int
- This is LattE integrale ...
- ...
-- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
-+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
- ...
- sage: p # optional - latte_int
- 1/2*t^2 + 3/2*t + 1
-@@ -202,7 +202,7 @@ class Polyhedron_ZZ(Polyhedron_base):
- sage: p = P._ehrhart_polynomial_latte(dual=True, verbose=True) # optional - latte_int
- This is LattE integrale ...
- ...
-- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
-+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
- ...
- sage: p # optional - latte_int
- 1/2*t^2 + 3/2*t + 1
-@@ -210,7 +210,7 @@ class Polyhedron_ZZ(Polyhedron_base):
- sage: p = P._ehrhart_polynomial_latte(irrational_primal=True, verbose=True) # optional - latte_int
- This is LattE integrale ...
- ...
-- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
-+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
- ...
- sage: p # optional - latte_int
- 1/2*t^2 + 3/2*t + 1
-@@ -218,7 +218,7 @@ class Polyhedron_ZZ(Polyhedron_base):
- sage: p = P._ehrhart_polynomial_latte(irrational_all_primal=True, verbose=True) # optional - latte_int
- This is LattE integrale ...
- ...
-- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
-+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
- ...
- sage: p # optional - latte_int
- 1/2*t^2 + 3/2*t + 1
-@@ -230,7 +230,7 @@ class Polyhedron_ZZ(Polyhedron_base):
- ...
- RuntimeError: LattE integrale program failed (exit code 1):
- ...
-- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
-+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
- Unknown command/option --bim-bam-boum=19
- """
- # note: the options below are explicitly written in the function
-diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py
-index 066cedd401..302b39910d 100644
---- a/src/sage/interfaces/latte.py
-+++ b/src/sage/interfaces/latte.py
-@@ -95,7 +95,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
- sage: n = count(cddin, cdd=True, verbose=True, raw_output=True) # optional - latte_int
- This is LattE integrale ...
- ...
-- Invocation: count '--redundancy-check=none' --cdd /dev/stdin
-+ Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin
- ...
- Total Unimodular Cones: ...
- Maximum number of simplicial cones in memory at once: ...
-@@ -127,7 +127,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
-
- arg = str_to_bytes(arg)
-
-- args = ['count']
-+ args = ['latte-count']
- if ehrhart_polynomial and multivariate_generating_function:
- raise ValueError
- if ehrhart_polynomial:
diff --git a/src/sage/features/latte.py b/src/sage/features/latte.py
index 63d227fd35..040a5cf1f9 100644
--- a/src/sage/features/latte.py
Modified: sagemath-bliss-0.77.patch
===================================================================
--- sagemath-bliss-0.77.patch 2022-05-16 06:50:08 UTC (rev 1207510)
+++ sagemath-bliss-0.77.patch 2022-05-16 06:50:35 UTC (rev 1207511)
@@ -1,3 +1,34 @@
+diff --git a/build/pkgs/bliss/SPKG.rst b/build/pkgs/bliss/SPKG.rst
+index 236b87a199..77407f16ac 100644
+--- a/build/pkgs/bliss/SPKG.rst
++++ b/build/pkgs/bliss/SPKG.rst
+@@ -10,20 +10,19 @@ 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
+
+-http://www.tcs.tkk.fi/Software/bliss/index.html
++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
+
+-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.
++http://www.tcs.tkk.fi/Software/bliss/index.html
+
+ Dependencies
+ ------------
diff --git a/build/pkgs/bliss/checksums.ini b/build/pkgs/bliss/checksums.ini
index e97d89587b..0c1ebf647b 100644
--- a/build/pkgs/bliss/checksums.ini
@@ -29,19 +60,54 @@
@@ -1 +1 @@
-0.73+debian-1+sage-2016-08-02.p0
+0.77
+diff --git a/build/pkgs/bliss/patches/bliss-0.77-install.patch b/build/pkgs/bliss/patches/bliss-0.77-install.patch
+new file mode 100644
+index 0000000000..caab14aa40
+--- /dev/null
++++ b/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)
diff --git a/build/pkgs/bliss/spkg-install.in b/build/pkgs/bliss/spkg-install.in
-index aaf4c3037b..ad1fe8176c 100644
+index aaf4c3037b..4124a2338e 100644
--- a/build/pkgs/bliss/spkg-install.in
+++ b/build/pkgs/bliss/spkg-install.in
-@@ -1,4 +1,6 @@
+@@ -1,4 +1,4 @@
cd src
-sdh_configure --disable-gmp
+sdh_cmake -DUSE_GMP=OFF -DCMAKE_VERBOSE_MAKEFILE=ON
sdh_make
--sdh_make_install
-+sdh_install src/*.hh $SAGE_LOCAL/include/bliss/
-+sdh_install libbliss.so $SAGE_LOCAL/lib/
-+sdh_install bliss $SAGE_LOCAL/bin/
+ sdh_make_install
diff --git a/build/pkgs/bliss/spkg-src b/build/pkgs/bliss/spkg-src
deleted file mode 100755
index 90073233b7..0000000000
@@ -77,18 +143,16 @@
-
-
diff --git a/src/sage/graphs/bliss.pyx b/src/sage/graphs/bliss.pyx
-index 22e861a587..fa426e3d11 100644
+index bf15833664..4f4e0ee3ca 100644
--- a/src/sage/graphs/bliss.pyx
+++ b/src/sage/graphs/bliss.pyx
-@@ -47,22 +47,27 @@ cdef extern from "bliss/graph.hh" namespace "bliss":
+@@ -47,22 +47,23 @@ cdef extern from "bliss/graph.hh" namespace "bliss":
cdef cppclass Graph(AbstractGraph):
Graph(const unsigned int)
void add_edge(const unsigned int, const unsigned int)
- void find_automorphisms(Stats&, void (*)(void* , unsigned int,
- const unsigned int*), void*)
-+ #void find_automorphisms(Stats&, void (*)(void* , unsigned int,
-+ #const unsigned int*), void*)
- void change_color(const unsigned int, const unsigned int);
+ void change_color(const unsigned int, const unsigned int)
- const unsigned int* canonical_form(Stats&, void (*)(void*,unsigned int,
- const unsigned int*), void*)
+ const unsigned int* canonical_form(Stats&)
@@ -100,9 +164,7 @@
void add_edge(const unsigned int, const unsigned int)
- void find_automorphisms(Stats&, void (*)(void* , unsigned int,
- const unsigned int*), void*)
-+ #void find_automorphisms(Stats&, void (*)(void* , unsigned int,
-+ #const unsigned int*), void*)
- void change_color(const unsigned int, const unsigned int);
+ void change_color(const unsigned int, const unsigned int)
- const unsigned int* canonical_form(Stats&, void (*)(void*,unsigned int,
- const unsigned int*), void*)
+ const unsigned int* canonical_form(Stats&)
@@ -116,7 +178,7 @@
cdef int encoding_numbits(int n):
r"""
-@@ -124,9 +129,6 @@ cdef void add_gen(void *user_param, unsigned int n, const unsigned int *aut):
+@@ -124,9 +125,6 @@ cdef void add_gen(void *user_param, unsigned int n, const unsigned int *aut):
sig_free(done)
@@ -126,7 +188,7 @@
#####################################################
# constructing bliss graphs from edge lists
#####################################################
-@@ -345,10 +347,10 @@ cdef canonical_form_from_edge_list(int Vnr, list Vout, list Vin, int Lnr=1, list
+@@ -345,10 +343,10 @@ cdef canonical_form_from_edge_list(int Vnr, list Vout, list Vin, int Lnr=1, list
if directed:
d = bliss_digraph_from_labelled_edges(Vnr, Lnr, Vout, Vin, labels, partition)
@@ -139,7 +201,7 @@
for i in range(len(Vout)):
x = Vout[i]
-@@ -640,11 +642,11 @@ cdef automorphism_group_gens_from_edge_list(int Vnr, Vout, Vin, int Lnr=1, label
+@@ -640,11 +638,11 @@ cdef automorphism_group_gens_from_edge_list(int Vnr, Vout, Vin, int Lnr=1, label
if directed:
d = bliss_digraph_from_labelled_edges(Vnr, Lnr, Vout, Vin, labels, partition)
Deleted: sagemath-doc-sphinx4.3.patch
===================================================================
--- sagemath-doc-sphinx4.3.patch 2022-05-16 06:50:08 UTC (rev 1207510)
+++ sagemath-doc-sphinx4.3.patch 2022-05-16 06:50:35 UTC (rev 1207511)
@@ -1,12 +0,0 @@
-diff --git a/src/sage/docs/conf.py b/src/sage/docs/conf.py
-index c788623..dd92d4c 100644
---- a/src/sage/docs/conf.py
-+++ b/src/sage/docs/conf.py
-@@ -911,6 +911,7 @@ def setup(app):
- if app.srcdir.startswith(SAGE_DOC_SRC):
- app.add_config_value('intersphinx_mapping', {}, False)
- app.add_config_value('intersphinx_cache_limit', 5, False)
-+ app.add_config_value('intersphinx_disabled_reftypes', [], False)
- app.connect('config-inited', set_intersphinx_mappings)
- app.connect('builder-inited', intersphinx.load_mappings)
- # We do *not* fully initialize intersphinx since we call it by hand
Deleted: sagemath-lrcalc2.patch
===================================================================
--- sagemath-lrcalc2.patch 2022-05-16 06:50:08 UTC (rev 1207510)
+++ sagemath-lrcalc2.patch 2022-05-16 06:50:35 UTC (rev 1207511)
@@ -1,685 +0,0 @@
-diff --git a/build/pkgs/lrcalc/checksums.ini b/build/pkgs/lrcalc/checksums.ini
-index 7a0e6a1b96..8b8620ba52 100644
---- a/build/pkgs/lrcalc/checksums.ini
-+++ b/build/pkgs/lrcalc/checksums.ini
-@@ -1,4 +1,5 @@
--tarball=lrcalc-VERSION.tar.gz
--sha1=89c288875bc3e3e2919876cb645bdfd7316b5965
--md5=6bba16c0cca9debccd0af847bd3d4a23
--cksum=3738483656
-+tarball=liblrcalc-VERSION.tar.gz
-+sha1=2a98661eb39c7ef526c932f7886fc3142fd639ab
-+md5=7cfa8f67287f2b70a15a833b94bc24b6
-+cksum=2250996027
-+upstream_url=https://sites.math.rutgers.edu/~asbuch/lrcalc/lrcalc-VERSION.tar.gz
-diff --git a/build/pkgs/lrcalc/package-version.txt b/build/pkgs/lrcalc/package-version.txt
-index 92ab3427e8..879b416e60 100644
---- a/build/pkgs/lrcalc/package-version.txt
-+++ b/build/pkgs/lrcalc/package-version.txt
-@@ -1 +1 @@
--1.2.p1
-+2.1
-diff --git a/build/pkgs/lrcalc/patches/includes.patch b/build/pkgs/lrcalc/patches/includes.patch
-deleted file mode 100644
-index 707da176a6..0000000000
---- a/build/pkgs/lrcalc/patches/includes.patch
-+++ /dev/null
-@@ -1,90 +0,0 @@
--From 4a5e1c8c3c11efdb1cbb4239825a6bf4bf1c52f8 Mon Sep 17 00:00:00 2001
--From: Anders Skovsted Buch <asbuch at math.rutgers.edu>
--Date: Sun, 29 Nov 2015 16:25:56 -0500
--Subject: [PATCH] Patch by Jeroen Demeyer to change include <vector.h> to
-- "vector.h", plus similar cases.
--
-----
-- src/lrcalc.c | 2 +-
-- src/maple.c | 4 ++--
-- src/schublib.h | 2 +-
-- src/symfcn.c | 6 +++---
-- src/symfcn.h | 4 ++--
-- 5 files changed, 9 insertions(+), 9 deletions(-)
--
--diff --git a/src/lrcalc.c b/src/lrcalc.c
--index aff3f75..60df49e 100644
----- a/src/lrcalc.c
--+++ b/src/lrcalc.c
--@@ -8,7 +8,7 @@
-- #include <stdlib.h>
-- extern char *optarg;
--
---#include <vectarg.h>
--+#include "vectarg.h"
--
-- #include "symfcn.h"
-- #include "maple.h"
--diff --git a/src/maple.c b/src/maple.c
--index fdc0768..a5f4d14 100644
----- a/src/maple.c
--+++ b/src/maple.c
--@@ -4,8 +4,8 @@
-- */
--
-- #include <stdio.h>
---#include <vector.h>
---#include <hashtab.h>
--+#include "vector.h"
--+#include "hashtab.h"
-- #include "maple.h"
--
--
--diff --git a/src/schublib.h b/src/schublib.h
--index a8e8511..864850c 100644
----- a/src/schublib.h
--+++ b/src/schublib.h
--@@ -1,7 +1,7 @@
-- #ifndef _SCHUBLIB_H
-- #define _SCHUBLIB_H
--
---#include <hashtab.h>
--+#include "hashtab.h"
--
-- hashtab *trans(vector *w, int vars, hashtab *res);
-- hashtab *monk(int i, hashtab *slc, int rank);
--diff --git a/src/symfcn.c b/src/symfcn.c
--index 4ffbe4b..fd5df5d 100644
----- a/src/symfcn.c
--+++ b/src/symfcn.c
--@@ -5,9 +5,9 @@
--
-- #include <stdio.h>
--
---#include <alloc.h>
---#include <vector.h>
---#include <hashtab.h>
--+#include "alloc.h"
--+#include "vector.h"
--+#include "hashtab.h"
--
-- #include "symfcn.h"
--
--diff --git a/src/symfcn.h b/src/symfcn.h
--index b8543b1..29bb00d 100644
----- a/src/symfcn.h
--+++ b/src/symfcn.h
--@@ -1,8 +1,8 @@
-- #ifndef _SYMFCN_H
-- #define _SYMFCN_H
--
---#include <hashtab.h>
---#include <vector.h>
--+#include "hashtab.h"
--+#include "vector.h"
--
-- int part_itr_sz(vector *part);
-- int part_itr_sub(vector *part, vector *outer);
----
--2.1.1.1.g1fb337f
--
-diff --git a/build/pkgs/lrcalc/spkg-configure.m4 b/build/pkgs/lrcalc/spkg-configure.m4
-index f2f8b74f8f..b8171ce23f 100644
---- a/build/pkgs/lrcalc/spkg-configure.m4
-+++ b/build/pkgs/lrcalc/spkg-configure.m4
-@@ -1,9 +1,10 @@
- SAGE_SPKG_CONFIGURE([lrcalc], [
-- AC_CHECK_HEADERS([lrcalc/schublib.h], [
-+ AC_LANG_PUSH([C])
-+ AC_CHECK_HEADERS([lrcalc/schublib.h] [lrcalc/lrcoef.h], [
- AC_SEARCH_LIBS([mult_poly_schubert], [lrcalc], [], [sage_spkg_install_lrcalc=yes])
- ], [sage_spkg_install_lrcalc=yes],
-- [[#ifndef _HASHTAB_H
-- #include <lrcalc/hashtab.h>
-- #include <lrcalc/vector.h>
-+ [[#ifndef _IVECTOR_H
-+ #include <lrcalc/ivector.h>
- #endif]])
-+ AC_LANG_POP
- ])
-diff --git a/build/pkgs/lrcalc/spkg-install.in b/build/pkgs/lrcalc/spkg-install.in
-index d6665bfb42..a863950189 100644
---- a/build/pkgs/lrcalc/spkg-install.in
-+++ b/build/pkgs/lrcalc/spkg-install.in
-@@ -1,9 +1,5 @@
- cd src
-
--# Use newer version of config.guess and config.sub (see Trac #19725)
--cp "$SAGE_ROOT"/config/config.guess .
--cp "$SAGE_ROOT"/config/config.sub .
--
- sdh_configure
- sdh_make
- sdh_make_install
-diff --git a/build/pkgs/lrcalc_python/SPKG.rst b/build/pkgs/lrcalc_python/SPKG.rst
-new file mode 100644
-index 0000000000..3a98d556ca
---- /dev/null
-+++ b/build/pkgs/lrcalc_python/SPKG.rst
-@@ -0,0 +1,22 @@
-+lrcalc_python: Littlewood-Richardson calculator
-+===============================================
-+
-+Description
-+-----------
-+
-+Python bindings for the Littlewood-Richardson Calculator
-+
-+http://sites.math.rutgers.edu/~asbuch/lrcalc/
-+
-+License
-+-------
-+
-+GNU General Public License V3
-+
-+
-+Upstream Contact
-+----------------
-+
-+Anders S. Buch (asbuch at math.rutgers.edu)
-+
-+https://bitbucket.org/asbuch/lrcalc
-diff --git a/build/pkgs/lrcalc_python/checksums.ini b/build/pkgs/lrcalc_python/checksums.ini
-new file mode 100644
-index 0000000000..bdfef8711e
---- /dev/null
-+++ b/build/pkgs/lrcalc_python/checksums.ini
-@@ -0,0 +1,5 @@
-+tarball=lrcalc-VERSION.tar.gz
-+sha1=3e9366d9e8b8beccec70b07d174b8f6683c01574
-+md5=4ae444d12ed8e0dd770594ea3ef4a208
-+cksum=2741305196
-+upstream_url=https://pypi.io/packages/source/l/lrcalc/lrcalc-VERSION.tar.gz
-diff --git a/build/pkgs/lrcalc_python/dependencies b/build/pkgs/lrcalc_python/dependencies
-new file mode 100644
-index 0000000000..63e5177ae0
---- /dev/null
-+++ b/build/pkgs/lrcalc_python/dependencies
-@@ -0,0 +1,5 @@
-+$(PYTHON) lrcalc | $(PYTHON_TOOLCHAIN) cython
-+
-+----------
-+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.
-diff --git a/build/pkgs/lrcalc_python/install-requires.txt b/build/pkgs/lrcalc_python/install-requires.txt
-new file mode 100644
-index 0000000000..8b44d97f4b
---- /dev/null
-+++ b/build/pkgs/lrcalc_python/install-requires.txt
-@@ -0,0 +1 @@
-+lrcalc ~=2.1
-diff --git a/build/pkgs/lrcalc_python/package-version.txt b/build/pkgs/lrcalc_python/package-version.txt
-new file mode 100644
-index 0000000000..879b416e60
---- /dev/null
-+++ b/build/pkgs/lrcalc_python/package-version.txt
-@@ -0,0 +1 @@
-+2.1
-diff --git a/build/pkgs/lrcalc_python/spkg-install.in b/build/pkgs/lrcalc_python/spkg-install.in
-new file mode 100644
-index 0000000000..deba1bb42b
---- /dev/null
-+++ b/build/pkgs/lrcalc_python/spkg-install.in
-@@ -0,0 +1 @@
-+cd src && sdh_pip_install .
-diff --git a/build/pkgs/lrcalc_python/type b/build/pkgs/lrcalc_python/type
-new file mode 100644
-index 0000000000..a6a7b9cd72
---- /dev/null
-+++ b/build/pkgs/lrcalc_python/type
-@@ -0,0 +1 @@
-+standard
-diff --git a/build/pkgs/sagelib/dependencies b/build/pkgs/sagelib/dependencies
-index 9c7797b1f4..3369d4d905 100644
---- a/build/pkgs/sagelib/dependencies
-+++ b/build/pkgs/sagelib/dependencies
-@@ -1,4 +1,4 @@
--FORCE $(SCRIPTS) arb boost_cropped $(BLAS) brial cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml jinja2 jupyter_core lcalc lrcalc libbraiding libhomfly libpng linbox m4ri m4rie memory_allocator mpc mpfi mpfr $(MP_LIBRARY) ntl numpy pari pip pkgconfig planarity ppl pplpy primesieve primecount primecountpy pycygwin $(PYTHON) ratpoints requests rw sage_conf singular symmetrica zn_poly $(PCFILES) | $(PYTHON_TOOLCHAIN) sage_setup
-+FORCE $(SCRIPTS) arb boost_cropped $(BLAS) brial cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml jinja2 jupyter_core lcalc lrcalc_python libbraiding libhomfly libpng linbox m4ri m4rie memory_allocator mpc mpfi mpfr $(MP_LIBRARY) ntl numpy pari pip pkgconfig planarity ppl pplpy primesieve primecount primecountpy pycygwin $(PYTHON) ratpoints requests rw sage_conf singular symmetrica zn_poly $(PCFILES) | $(PYTHON_TOOLCHAIN) sage_setup
-
- ----------
- All lines of this file are ignored except the first.
-diff --git a/src/sage/libs/lrcalc/lrcalc.pxd b/src/sage/libs/lrcalc/lrcalc.pxd
-deleted file mode 100644
-index 10b88db93f..0000000000
---- a/src/sage/libs/lrcalc/lrcalc.pxd
-+++ /dev/null
-@@ -1,77 +0,0 @@
--# distutils: libraries = lrcalc
--
--cdef extern from "lrcalc/hashtab.h":
-- ctypedef struct hashtab:
-- pass
--
-- ctypedef struct hash_itr:
-- pass
--
-- ctypedef unsigned long hashkey_t
-- ctypedef int (*cmp_t) (void* a, void* b)
-- ctypedef hashkey_t (*hash_t) (void* a)
--
-- hashtab* hash_new(cmp_t cm, hash_t hsh)
-- void hash_free(hashtab *ht)
--
-- void* hash_lookup(hashtab *ht, void *key)
-- void* hash_insert(hashtab *ht, void *key, void *value)
--
-- bint hash_good(hash_itr)
-- void hash_first(hashtab* s, hash_itr itr)
-- void hash_next(hash_itr itr)
-- void* hash_key(hash_itr itr)
-- void* hash_value(hash_itr itr)
-- int hash_intvalue(hash_itr itr)
--
--cdef extern from "lrcalc/vector.h":
-- ctypedef struct vector:
-- size_t length
-- int* array
--
-- vector* v_new(int length)
-- void v_free(vector* v)
-- void v_print(vector *v)
-- int v_length(vector* v)
-- int v_elem(vector* v, int i)
--
-- ctypedef struct vecpair:
-- vector *first
-- vector *second
--
-- vector* vp_first(vecpair* vp)
-- vector* vp_second(vecpair* vp)
--
--cdef extern from "lrcalc/list.h":
-- cdef struct _list:
-- void **array
-- size_t allocated
-- size_t length
-- void l_free(_list *lst)
--
--cdef extern from "lrcalc/symfcn.h":
-- long long lrcoef_c "lrcoef"(vector* outer, vector* inner1, vector* inner2)
-- hashtab* mult_c "mult"(vector *sh1, vector *sh2, int maxrows)
-- hashtab* skew_c "skew"(vector *outer, vector *inner, int maxrows)
-- hashtab* coprod_c "coprod"(vector *part, int all)
-- void fusion_reduce_c "fusion_reduce"(hashtab* ht, int rows, int cols, int opt_zero)
-- _list *quantum_reduce_c "quantum_reduce"(hashtab* ht, int rows, int col)
--
-- ctypedef struct skewtab:
-- vector *outer
-- vector *inner
-- vector *conts
-- int maxrows
-- vector *conjugate
-- int rows
-- int cols
-- int matrix[1]
--
-- skewtab *st_new(vector *outer, vector *inner, vector *conts, int maxrows)
-- int st_next(skewtab *st)
-- void st_print(skewtab *st)
-- void st_free(skewtab *st)
--
--
--cdef extern from "lrcalc/schublib.h":
-- hashtab* mult_schubert_c "mult_schubert"(vector *sh1, vector *sh2, int rank)
-diff --git a/src/sage/libs/lrcalc/lrcalc.pyx b/src/sage/libs/lrcalc/lrcalc.py
-similarity index 65%
-rename from src/sage/libs/lrcalc/lrcalc.pyx
-rename to src/sage/libs/lrcalc/lrcalc.py
-index b591081ec4..65db959944 100644
---- a/src/sage/libs/lrcalc/lrcalc.pyx
-+++ b/src/sage/libs/lrcalc/lrcalc.py
-@@ -187,180 +187,24 @@ AUTHORS:
- # https://www.gnu.org/licenses/
- # ****************************************************************************
-
--from sage.rings.integer cimport Integer
--from sage.structure.parent cimport Parent
- from sage.combinat.partition import _Partitions
- from sage.combinat.permutation import Permutation
--from sage.combinat.skew_tableau import SkewTableau
-+from sage.combinat.skew_tableau import SkewTableaux
-+from sage.combinat.skew_partition import SkewPartition
-+from sage.rings.integer import Integer
-+import lrcalc
-
--
--cdef vector* iterable_to_vector(it):
-- """
-- Return an lrcalc vector (which is a list of integers) from a Python iterable.
--
-- TESTS::
--
-- sage: from sage.libs.lrcalc.lrcalc import test_iterable_to_vector
-- sage: x = test_iterable_to_vector(Partition([3,2,1])); x #indirect doctest
-- [3, 2, 1]
-- """
-- cdef vector* v
-- cdef list itr = list(it)
-- cdef int n = len(itr)
-- cdef int i
-- v = v_new(n)
-- for i in range(n):
-- v.array[i] = int(itr[i])
-- return v
--
--
--cdef list vector_to_list(vector *v):
-- """
-- Converts a lrcalc vector to Python list.
--
-- TESTS::
--
-- sage: from sage.libs.lrcalc.lrcalc import test_iterable_to_vector
-- sage: x = test_iterable_to_vector([]); x #indirect doctest
-- []
-- """
-- cdef int i, n
-- n = v_length(v)
-- cdef list result = [None]*n
-- for i in range(n):
-- result[i] = Integer(v_elem(v, i))
-- return result
--
--
--def test_iterable_to_vector(it):
-- """
-- A wrapper function for the cdef function ``iterable_to_vector``
-- and ``vector_to_list``, to test that they are working correctly.
--
-- EXAMPLES::
--
-- sage: from sage.libs.lrcalc.lrcalc import test_iterable_to_vector
-- sage: x = test_iterable_to_vector([3,2,1]); x
-- [3, 2, 1]
-- """
-- cdef vector *v = iterable_to_vector(it)
-- result = vector_to_list(v)
-- v_free(v)
-- return result
--
--
--cdef skewtab_to_SkewTableau(skewtab *st):
-- """
-- A wrapper function which transforms the data set ``st`` used in
-- ``lrcalc`` to a ``SkewTableau`` in Sage.
-+def _lrcalc_dict_to_sage(result):
-+ r"""
-+ Translate from lrcalc output format to Sage expected format.
-
- TESTS::
-
-- sage: from sage.libs.lrcalc.lrcalc import test_skewtab_to_SkewTableau
-- sage: test_skewtab_to_SkewTableau([],[])
-- []
-- """
-- inner = vector_to_list(st.inner)
-- outer = vector_to_list(st.outer)
-- return SkewTableau(expr=[[inner[y] for y in range(len(outer))],
-- [[st.matrix[x + y * st.cols] + 1
-- for x in range(inner[y], outer[y])]
-- for y in range(len(outer) - 1, -1, -1)]])
--
--
--def test_skewtab_to_SkewTableau(outer, inner):
-- """
-- A wrapper function for the cdef function ``skewtab_to_SkewTableau``
-- for testing purposes.
--
-- It constructs the first LR skew tableau of shape ``outer/inner``
-- as an ``lrcalc`` ``skewtab``, and converts it to a
-- :class:`SkewTableau`.
--
-- EXAMPLES::
--
-- sage: from sage.libs.lrcalc.lrcalc import test_skewtab_to_SkewTableau
-- sage: test_skewtab_to_SkewTableau([3,2,1],[])
-- [[1, 1, 1], [2, 2], [3]]
-- sage: test_skewtab_to_SkewTableau([4,3,2,1],[1,1]).pp()
-- . 1 1 1
-- . 2 2
-- 1 3
-- 2
-- """
-- cdef vector* o = iterable_to_vector(outer)
-- cdef vector* i = iterable_to_vector(inner+[0]*(len(outer)-len(inner)))
-- cdef skewtab* st = st_new(o, i, NULL, 0)
-- return skewtab_to_SkewTableau(st)
--
--
--cdef dict sf_hashtab_to_dict(hashtab *ht):
-- """
-- Return a dictionary representing a Schur function. The keys are
-- partitions and the values are integers <class 'sage.rings.integer.Integer'>.
--
-- EXAMPLES::
--
- sage: from sage.libs.lrcalc.lrcalc import mult
-- sage: sorted(mult([1],[1]).items()) #indirect doctest
-- [([1, 1], 1), ([2], 1)]
-- sage: assert isinstance(mult([1],[1]),dict)#indirect doctest
-- """
-- cdef hash_itr itr
-- cdef dict result = {}
-- cdef list p
-- hash_first(ht, itr)
-- while hash_good(itr):
-- p = vector_to_list(<vector*> hash_key(itr))
-- result[_Partitions(p)] = Integer(hash_intvalue(itr))
-- hash_next(itr)
-- return result
--
--
--cdef dict schubert_hashtab_to_dict(hashtab *ht):
-- """
-- Return a dictionary corresponding to a Schubert polynomial whose keys
-- are permutations and whose values are integers <class 'sage.rings.integer.Integer'>.
--
-- EXAMPLES::
--
-- sage: from sage.libs.lrcalc.lrcalc import mult_schubert
-- sage: mult_schubert([3,2,1], [1,2,3]) #indirect doctest
-- {[3, 2, 1]: 1}
-- """
-- cdef hash_itr itr
-- cdef dict result = {}
-- hash_first(ht, itr)
-- while hash_good(itr):
-- p = vector_to_list(<vector*> hash_key(itr))
-- result[Permutation(p)] = Integer(hash_intvalue(itr))
-- hash_next(itr)
-- return result
--
--
--cdef dict vp_hashtab_to_dict(hashtab *ht):
-- """
-- Return a dictionary corresponding to the coproduct of a Schur function whose keys are
-- pairs of partitions and whose values are integers <class 'sage.rings.integer.Integer'>.
--
-- EXAMPLES::
--
-- sage: from sage.libs.lrcalc.lrcalc import coprod
-- sage: coprod([1]) #indirect doctest
-- {([1], []): 1}
-+ sage: mult([2,1],[3,2,1],3) # indirect doctest
-+ {[3, 3, 3]: 1, [4, 3, 2]: 2, [4, 4, 1]: 1, [5, 2, 2]: 1, [5, 3, 1]: 1}
- """
-- cdef hash_itr itr
-- cdef vecpair* vp
-- cdef dict result = {}
-- hash_first(ht, itr)
-- while hash_good(itr):
-- vp = <vecpair*> hash_key(itr)
-- p1 = _Partitions(vector_to_list(vp_first(vp)))
-- p2 = _Partitions(vector_to_list(vp_second(vp)))
-- result[(p1, p2)] = Integer(hash_intvalue(itr))
-- hash_next(itr)
-- return result
--
-+ return {_Partitions(la):Integer(k) for la,k in result.items()}
-
- def lrcoef_unsafe(outer, inner1, inner2):
- r"""
-@@ -392,18 +236,7 @@ def lrcoef_unsafe(outer, inner1, inner2):
- sage: lrcoef_unsafe([2,1,1,1,1], [2,1], [2,1])
- 0
- """
-- cdef long long result
-- cdef vector *o
-- cdef vector *i1
-- cdef vector *i2
-- o = iterable_to_vector(outer)
-- i1 = iterable_to_vector(inner1)
-- i2 = iterable_to_vector(inner2)
-- result = lrcoef_c(o, i1, i2)
-- v_free(o)
-- v_free(i1)
-- v_free(i2)
-- return Integer(result)
-+ return Integer(lrcalc.lrcoef(outer, inner1, inner2))
-
-
- def lrcoef(outer, inner1, inner2):
-@@ -510,44 +343,24 @@ def mult(part1, part2, maxrows=None, level=None, quantum=None):
- if quantum is not None and (level is None or maxrows is None):
- raise ValueError('missing parameters maxrows or level')
-
-- cdef vector* v1 = iterable_to_vector(part1)
-- cdef vector* v2 = iterable_to_vector(part2)
-- if maxrows is None:
-- maxrows = 0
-- cdef hashtab* ht = mult_c(v1, v2, int(maxrows))
-- cdef hashtab* tab
-- cdef dict result
--
- if quantum is None:
- if level is not None:
-- fusion_reduce_c(ht, int(maxrows), int(level), int(0))
-- result = sf_hashtab_to_dict(ht)
-- v_free(v1)
-- v_free(v2)
-- hash_free(ht)
-- return result
-+ return _lrcalc_dict_to_sage(lrcalc.mult_fusion(part1, part2, maxrows, level))
-+ if maxrows is None:
-+ maxrows = -1
-+ return _lrcalc_dict_to_sage(lrcalc.mult(part1, part2, maxrows))
-
- # Otherwise do quantum multiplication
-- cdef _list *qlist
-- cdef dict temp
-- qlist = quantum_reduce_c(ht, int(maxrows), int(level))
-- # The above call frees the memory associated with ht
-- v_free(v1)
-- v_free(v2)
--
-- cdef Parent P = quantum.parent()
-- result = {}
-- for i in range(qlist.length):
-- tab = <hashtab*>(qlist.array[i])
-- temp = sf_hashtab_to_dict(tab)
-- for k in temp:
-- result[k] = result.get(k, P.zero()) + quantum**i * temp[k]
-- hash_free(tab)
-- l_free(qlist)
-- return result
--
--
--def skew(outer, inner, maxrows=0):
-+ result = lrcalc.mult_quantum(part1, part2, maxrows, level, degrees=True)
-+ P = quantum.parent()
-+ output = {}
-+ for i,k in result.items():
-+ la = _Partitions(i[0])
-+ output[la] = output.get(la, P.zero()) + k*quantum**(i[1])
-+ return output
-+
-+
-+def skew(outer, inner, maxrows=-1):
- """
- Compute the Schur expansion of a skew Schur function.
-
-@@ -572,14 +385,7 @@ def skew(outer, inner, maxrows=0):
- sage: sorted(skew([2,1],[1]).items())
- [([1, 1], 1), ([2], 1)]
- """
-- cdef vector* v1 = iterable_to_vector(outer)
-- cdef vector* v2 = iterable_to_vector(inner)
-- cdef hashtab* ht = skew_c(v1, v2, int(maxrows))
-- result = sf_hashtab_to_dict(ht)
-- v_free(v1)
-- v_free(v2)
-- hash_free(ht)
-- return result
-+ return _lrcalc_dict_to_sage(lrcalc.skew(outer, inner, maxrows))
-
-
- def coprod(part, all=0):
-@@ -609,12 +415,8 @@ def coprod(part, all=0):
- sage: sorted(coprod([2,1]).items())
- [(([1, 1], [1]), 1), (([2], [1]), 1), (([2, 1], []), 1)]
- """
-- cdef vector* v1 = iterable_to_vector(part)
-- cdef hashtab* ht = coprod_c(v1, int(all))
-- result = vp_hashtab_to_dict(ht)
-- v_free(v1)
-- hash_free(ht)
-- return result
-+ result = lrcalc.coprod(part, all)
-+ return {tuple(_Partitions(mu) for mu in la):Integer(k) for la,k in result.items()}
-
-
- def mult_schubert(w1, w2, rank=0):
-@@ -646,17 +448,11 @@ def mult_schubert(w1, w2, rank=0):
- ([6, 4, 3, 1, 2, 5], 1), ([6, 5, 2, 1, 3, 4], 1),
- ([7, 3, 4, 1, 2, 5, 6], 1), ([7, 4, 2, 1, 3, 5, 6], 1)]
- """
-- cdef vector* v1 = iterable_to_vector(w1)
-- cdef vector* v2 = iterable_to_vector(w2)
-- cdef hashtab* ht = mult_schubert_c(v1, v2, int(rank))
-- result = schubert_hashtab_to_dict(ht)
-- v_free(v1)
-- v_free(v2)
-- hash_free(ht)
-- return result
-+ result = lrcalc.schubmult(w1, w2, rank)
-+ return {Permutation(list(la)):Integer(k) for la,k in result.items()}
-
-
--def lrskew(outer, inner, weight=None, maxrows=0):
-+def lrskew(outer, inner, weight=None, maxrows=-1):
- r"""
- Iterate over the skew LR tableaux of shape ``outer / inner``.
-
-@@ -703,21 +499,20 @@ def lrskew(outer, inner, weight=None, maxrows=0):
- sage: list(lrskew([3,2,1],[2], weight=[3,1]))
- [[[None, None, 1], [1, 1], [2]]]
- """
-- cdef vector* o = iterable_to_vector(outer)
-- cdef vector* i = iterable_to_vector(inner + [0]*(len(outer) - len(inner)))
-- cdef skewtab* st = st_new(o, i, NULL, int(maxrows))
-+ iterator = lrcalc.lr_iterator(outer, inner, maxrows)
-+ shape = SkewPartition([outer, inner])
-
- if weight is None:
-- yield skewtab_to_SkewTableau(st)
-- while st_next(st):
-- yield skewtab_to_SkewTableau(st)
-+ ST = SkewTableaux()
-+ for data in iterator:
-+ yield ST.from_shape_and_word(shape, [i+1 for i in data])
- else:
- wt = _Partitions(weight)
-- r = skewtab_to_SkewTableau(st)
-- if r.weight() == wt:
-- yield r
-- while st_next(st):
-- r = skewtab_to_SkewTableau(st)
-- if r.weight() == wt:
-- yield r
-- st_free(st)
-+ ST = SkewTableaux()
-+ for data in iterator:
-+ m = max(data) + 1
-+ w = [0] * m
-+ for j in data:
-+ w[j] += 1
-+ if w == wt:
-+ yield ST.from_shape_and_word(shape, [i+1 for i in data])
Modified: sagemath-optional-packages.patch
===================================================================
--- sagemath-optional-packages.patch 2022-05-16 06:50:08 UTC (rev 1207510)
+++ sagemath-optional-packages.patch 2022-05-16 06:50:35 UTC (rev 1207511)
@@ -3,7 +3,7 @@
--- a/pkgs/sagemath-standard/setup.py
+++ b/pkgs/sagemath-standard/setup.py
@@ -81,10 +81,9 @@ else:
- from sage_setup.optional_extension import is_package_installed_and_updated
+ from sage.misc.package import is_package_installed_and_updated
distributions = ['']
optional_packages_with_extensions = ['mcqd', 'bliss', 'tdlib',
- 'coxeter3', 'fes', 'sirocco', 'meataxe']
Modified: test-optional.patch
===================================================================
--- test-optional.patch 2022-05-16 06:50:08 UTC (rev 1207510)
+++ test-optional.patch 2022-05-16 06:50:35 UTC (rev 1207511)
@@ -2,7 +2,7 @@
index 2d93841e50..937e20cd2e 100644
--- a/src/sage/doctest/control.py
+++ b/src/sage/doctest/control.py
-@@ -400,11 +400,6 @@ class DocTestController(SageObject):
+@@ -411,11 +411,6 @@ class DocTestController(SageObject):
# that the package is actually installed).
if 'optional' in options.optional:
options.optional.discard('optional')
@@ -13,5 +13,4 @@
-
from sage.features import package_systems
options.optional.update(system.name
-
-
+ for system in package_systems())
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