* [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5
@ 2022-03-18 18:29 tornaria
2022-03-18 19:45 ` dkwo
` (7 more replies)
0 siblings, 8 replies; 9+ messages in thread
From: tornaria @ 2022-03-18 18:29 UTC (permalink / raw)
To: ml
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There is a new pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages sagemath-lrcalc
https://github.com/void-linux/void-packages/pull/36209
lrcalc: update to 2.1, rebuild sagemath-9.5
This PR updates lrcalc to 2.1, which will be required for sagemath 9.6.
This needs that we rebuild sagemath 9.5 with a few changes:
- add a new python package `python3-lrcalc`
- patch sagemath 9.5 so it can use the new version of lrcalc (via python3-lrcalc)
Unrelated to that, I added two patches to sagemath which fix doctests after upgrades of ipython to 8.0 and scipy to 1.8.
A patch file from https://github.com/void-linux/void-packages/pull/36209.patch is attached
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From 16ce3b48b9ac2f8a47e2713edf6a0e35250d5873 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 28 Feb 2022 12:03:22 -0300
Subject: [PATCH 1/3] lrcalc: update to 2.1.
---
common/shlibs | 2 +-
srcpkgs/lrcalc/patches/includes.patch | 90 ---------------------------
srcpkgs/lrcalc/template | 6 +-
3 files changed, 4 insertions(+), 94 deletions(-)
delete mode 100644 srcpkgs/lrcalc/patches/includes.patch
diff --git a/common/shlibs b/common/shlibs
index 83b5783cb026..4a0a07d366cc 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -4038,7 +4038,7 @@ libarb.so.2 arb-2.20.0_1
libec.so.8 eclib-20210625_1
libsymmetrica.so.2 symmetrica-3.0.1_1
libLfunction.so.1 lcalc-2.0.4_1
-liblrcalc.so.1 lrcalc-1.2_1
+liblrcalc.so.2 lrcalc-2.1_1
libwayland-client++.so.0 libwaylandpp-0.2.8_1
libwayland-cursor++.so.0 libwaylandpp-0.2.8_1
libwayland-egl++.so.0 libwaylandpp-0.2.8_1
diff --git a/srcpkgs/lrcalc/patches/includes.patch b/srcpkgs/lrcalc/patches/includes.patch
deleted file mode 100644
index 707da176a60f..000000000000
--- a/srcpkgs/lrcalc/patches/includes.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-From 4a5e1c8c3c11efdb1cbb4239825a6bf4bf1c52f8 Mon Sep 17 00:00:00 2001
-From: Anders Skovsted Buch <asbuch@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/srcpkgs/lrcalc/template b/srcpkgs/lrcalc/template
index 8b33c3cba6c8..afa889b6d6ad 100644
--- a/srcpkgs/lrcalc/template
+++ b/srcpkgs/lrcalc/template
@@ -1,14 +1,14 @@
# Template file for 'lrcalc'
pkgname=lrcalc
-version=1.2
-revision=2
+version=2.1
+revision=1
build_style=gnu-configure
short_desc="Littlewood-Richardson Calculator"
maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
license="GPL-3.0-or-later"
homepage="https://sites.math.rutgers.edu/~asbuch/lrcalc/"
distfiles="https://sites.math.rutgers.edu/~asbuch/lrcalc/lrcalc-$version.tar.gz"
-checksum=792dd538a0d19698be2c5b8c138730bbb4820e8a44e03b001ae14bd5f1d7040b
+checksum=996ac00e6ea8321ef09b34478f5379f613933c3254aeba624b6419b8afa5df57
lrcalc-devel_package() {
depends="${sourcepkg}>=${version}_${revision} ${makedepends}"
From 0bea3c29ecf5390a728f9c53fae3bc680819583f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 28 Feb 2022 14:06:21 -0300
Subject: [PATCH 2/3] New package: python3-lrcalc-2.1
---
srcpkgs/python3-lrcalc/template | 14 ++++++++++++++
1 file changed, 14 insertions(+)
create mode 100644 srcpkgs/python3-lrcalc/template
diff --git a/srcpkgs/python3-lrcalc/template b/srcpkgs/python3-lrcalc/template
new file mode 100644
index 000000000000..9f335dac35dd
--- /dev/null
+++ b/srcpkgs/python3-lrcalc/template
@@ -0,0 +1,14 @@
+# Template file for 'python3-lrcalc'
+pkgname=python3-lrcalc
+version=2.1
+revision=1
+wrksrc=lrcalc-${version}
+build_style=python3-module
+hostmakedepends="python3-setuptools python3-Cython"
+makedepends="python3-devel lrcalc-devel"
+short_desc="Python bindings for the Littlewood-Richardson Calculator library"
+maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
+license="GPL-3.0-or-later"
+homepage="https://math.rutgers.edu/~asbuch/lrcalc"
+distfiles="${PYPI_SITE}/l/lrcalc/lrcalc-${version}.tar.gz"
+checksum=e3a0509aeda487b412b391a52e817ca36b5c063a8305e09fd54d53259dd6aaa9
From 13ab5c4a1b3453fec6611dbf577816346ea6036c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 28 Feb 2022 14:06:28 -0300
Subject: [PATCH 3/3] sagemath: rebuild for lrcalc 2.1
Also fix doctests for upgrade of ipython 8.0 and scipy 1.8
---
.../trac-31355-upgrade_lrcalc_to_2.1.patch | 670 ++++++++++++++++++
.../trac-33170-fix_doctest_ipython_8.patch | 40 ++
.../trac-33336-fix_doctest_scipy_1.8.patch | 19 +
srcpkgs/sagemath/template | 6 +-
4 files changed, 732 insertions(+), 3 deletions(-)
create mode 100644 srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch
create mode 100644 srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch
create mode 100644 srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch
diff --git a/srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch b/srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch
new file mode 100644
index 000000000000..4bd6f4f4e2dc
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch
@@ -0,0 +1,670 @@
+As produced by `git diff 9.5 9.6.beta3 -- src/sage/libs/lrcalc`
+
+diff --git a/src/sage/libs/lrcalc/lrcalc.pxd b/src/sage/libs/lrcalc/lrcalc.pxd
+deleted file mode 100644
+index 10b88db93f2..00000000000
+--- 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 60%
+rename from src/sage/libs/lrcalc/lrcalc.pyx
+rename to src/sage/libs/lrcalc/lrcalc.py
+index b591081ec4c..b541bfacd89 100644
+--- a/src/sage/libs/lrcalc/lrcalc.pyx
++++ b/src/sage/libs/lrcalc/lrcalc.py
+@@ -10,7 +10,8 @@ fusion products. All of the above are achieved by counting LR
+ appropriate shape and content by iterating through them.
+ Additionally, ``lrcalc`` handles products of Schubert polynomials.
+
+-The web page of ``lrcalc`` is `<http://sites.math.rutgers.edu/~asbuch/lrcalc/>`_.
++The web page of ``lrcalc`` is
++`<http://sites.math.rutgers.edu/~asbuch/lrcalc/>`_.
+
+ The following describes the Sage interface to this library.
+
+@@ -36,12 +37,13 @@ Schur expansion::
+ [4, 2]: 1}
+
+ Same product, but include only partitions with at most 3 rows. This
+-corresponds to computing in the representation ring of gl(3)::
++corresponds to computing in the representation ring of `\mathfrak{gl}(3)`::
+
+ sage: lrcalc.mult([2,1], [2,1], 3)
+ {[2, 2, 2]: 1, [3, 2, 1]: 2, [3, 3]: 1, [4, 1, 1]: 1, [4, 2]: 1}
+
+-We can also compute the fusion product, here for sl(3) and level 2::
++We can also compute the fusion product, here for `\mathfrak{sl}(3)`
++and level 2::
+
+ sage: lrcalc.mult([3,2,1], [3,2,1], 3,2)
+ {[4, 4, 4]: 1, [5, 4, 3]: 1}
+@@ -77,42 +79,38 @@ Multiply two Schubert polynomials::
+ [6, 2, 1, 4, 3, 5]: 1}
+
+ Same product, but include only permutations of 5 elements in the result.
+-This corresponds to computing in the cohomology ring of Fl(5)::
++This corresponds to computing in the cohomology ring of `Fl(5)`::
+
+ sage: lrcalc.mult_schubert([4,2,1,3], [1,4,2,5,3], 5)
+ {[4, 5, 1, 3, 2]: 1, [5, 3, 1, 4, 2]: 1, [5, 4, 1, 2, 3]: 1}
+
+ List all Littlewood-Richardson tableaux of skew shape `\mu/\nu`; in
+ this example `\mu=[3,2,1]` and `\nu=[2,1]`. Specifying a third entry
+-`maxrows` restricts the alphabet to `\{1,2,\ldots,maxrows\}`::
++`M' = ``maxrows`` restricts the alphabet to `\{1,2,\ldots,M\}`::
+
+ sage: list(lrcalc.lrskew([3,2,1],[2,1]))
+ [[[None, None, 1], [None, 1], [1]], [[None, None, 1], [None, 1], [2]],
+ [[None, None, 1], [None, 2], [1]], [[None, None, 1], [None, 2], [3]]]
+
+ sage: list(lrcalc.lrskew([3,2,1],[2,1],maxrows=2))
+- [[[None, None, 1], [None, 1], [1]], [[None, None, 1], [None, 1], [2]], [[None, None, 1], [None, 2], [1]]]
++ [[[None, None, 1], [None, 1], [1]], [[None, None, 1], [None, 1], [2]],
++ [[None, None, 1], [None, 2], [1]]]
+
+ .. TODO::
+
+- use this library in the :class:`SymmetricFunctions` code, to
++ Use this library in the :class:`SymmetricFunctions` code, to
+ make it easy to apply it to linear combinations of Schur functions.
+
+ .. SEEALSO::
+
+ - :func:`lrcoef`
+-
+ - :func:`mult`
+-
+ - :func:`coprod`
+-
+ - :func:`skew`
+-
+ - :func:`lrskew`
+-
+ - :func:`mult_schubert`
+
+-.. rubric:: Underlying algorithmic in lrcalc
++.. RUBRIC:: Underlying algorithmic in lrcalc
+
+ Here is some additional information regarding the main low-level
+ C-functions in `lrcalc`. Given two partitions ``outer`` and ``inner``
+@@ -187,180 +185,24 @@ 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
+-
+-
+-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.
++from sage.combinat.skew_tableau import SemistandardSkewTableaux
++from sage.combinat.skew_partition import SkewPartition
++from sage.rings.integer import Integer
++import lrcalc
+
+- 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"""
+@@ -371,13 +213,11 @@ def lrcoef_unsafe(outer, inner1, inner2):
+
+ INPUT:
+
+- - ``outer`` -- a partition (weakly decreasing list of non-negative integers).
+-
+- - ``inner1`` -- a partition.
++ - ``outer`` -- a partition (weakly decreasing list of non-negative integers)
++ - ``inner1`` -- a partition
++ - ``inner2`` -- a partition
+
+- - ``inner2`` -- a partition.
+-
+- .. warning::
++ .. WARNING::
+
+ This function does not do any check on its input. If you want
+ to use a safer version, use :func:`lrcoef`.
+@@ -392,18 +232,7 @@ 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):
+@@ -415,11 +244,9 @@ def lrcoef(outer, inner1, inner2):
+
+ INPUT:
+
+- - ``outer`` -- a partition (weakly decreasing list of non-negative integers).
+-
+- - ``inner1`` -- a partition.
+-
+- - ``inner2`` -- a partition.
++ - ``outer`` -- a partition (weakly decreasing list of non-negative integers)
++ - ``inner1`` -- a partition
++ - ``inner2`` -- a partition
+
+ .. NOTE::
+
+@@ -436,7 +263,6 @@ def lrcoef(outer, inner1, inner2):
+ 1
+ sage: lrcoef([2,1,1,1,1], [2,1], [2,1])
+ 0
+-
+ """
+ return lrcoef_unsafe(_Partitions(outer), _Partitions(inner1), _Partitions(inner2))
+
+@@ -451,13 +277,9 @@ def mult(part1, part2, maxrows=None, level=None, quantum=None):
+ INPUT:
+
+ - ``part1`` -- a partition
+-
+ - ``part2`` -- a partition
+-
+ - ``maxrows`` -- (optional) an integer
+-
+ - ``level`` -- (optional) an integer
+-
+ - ``quantum`` -- (optional) an element of a ring
+
+ If ``maxrows`` is specified, then only partitions with at most
+@@ -479,7 +301,8 @@ def mult(part1, part2, maxrows=None, level=None, quantum=None):
+ sage: sorted(mult([2],[2]).items())
+ [([2, 2], 1), ([3, 1], 1), ([4], 1)]
+ sage: sorted(mult([2,1],[2,1]).items())
+- [([2, 2, 1, 1], 1), ([2, 2, 2], 1), ([3, 1, 1, 1], 1), ([3, 2, 1], 2), ([3, 3], 1), ([4, 1, 1], 1), ([4, 2], 1)]
++ [([2, 2, 1, 1], 1), ([2, 2, 2], 1), ([3, 1, 1, 1], 1),
++ ([3, 2, 1], 2), ([3, 3], 1), ([4, 1, 1], 1), ([4, 2], 1)]
+ sage: sorted(mult([2,1],[2,1],maxrows=2).items())
+ [([3, 3], 1), ([4, 2], 1)]
+ sage: mult([2,1],[3,2,1],3)
+@@ -510,44 +333,24 @@ 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.
+
+@@ -557,11 +360,9 @@ def skew(outer, inner, maxrows=0):
+
+ INPUT:
+
+- - ``outer`` -- a partition.
+-
+- - ``inner`` -- a partition.
+-
+- - ``maxrows`` -- an integer or ``None``.
++ - ``outer`` -- a partition
++ - ``inner`` -- a partition
++ - ``maxrows`` -- an integer or ``None``
+
+ If ``maxrows`` is specified, then only partitions with at most
+ this number of rows are included in the result.
+@@ -572,14 +373,7 @@ 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):
+@@ -592,9 +386,8 @@ def coprod(part, all=0):
+
+ INPUT:
+
+- - ``part`` -- a partition.
+-
+- - ``all`` -- an integer.
++ - ``part`` -- a partition
++ - ``all`` -- an integer
+
+ If ``all`` is non-zero then all terms are included in the result.
+ If ``all`` is zero, then only pairs of partitions ``(part1,
+@@ -609,12 +402,9 @@ 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):
+@@ -627,11 +417,9 @@ def mult_schubert(w1, w2, rank=0):
+
+ INPUT:
+
+- - ``w1`` -- a permutation.
+-
+- - ``w2`` -- a permutation.
+-
+- - ``rank`` -- an integer.
++ - ``w1`` -- a permutation
++ - ``w2`` -- a permutation
++ - ``rank`` -- an integer
+
+ If ``rank`` is non-zero, then only permutations from the symmetric
+ group `S(\mathrm{rank})` are included in the result.
+@@ -646,33 +434,24 @@ 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``.
+
+ INPUT:
+
+ - ``outer`` -- a partition
+-
+ - ``inner`` -- a partition
+-
+ - ``weight`` -- a partition (optional)
+-
+- - ``maxrows`` -- an integer (optional)
++ - ``maxrows`` -- a positive integer (optional)
+
+ OUTPUT: an iterator of :class:`SkewTableau`
+
+- Specifying ``maxrows`` restricts the alphabet to `\{1,2,\ldots,maxrows\}`.
++ Specifying ``maxrows`` = `M` restricts the alphabet to `\{1,2,\ldots,M\}`.
+
+ Specifying ``weight`` returns only those tableaux of given content/weight.
+
+@@ -702,22 +481,40 @@ def lrskew(outer, inner, weight=None, maxrows=0):
+
+ sage: list(lrskew([3,2,1],[2], weight=[3,1]))
+ [[[None, None, 1], [1, 1], [2]]]
++
++ TESTS::
++
++ sage: from sage.libs.lrcalc.lrcalc import lrskew
++ sage: list(lrskew([3,2,1],[2], weight=[]))
++ []
++ sage: list(lrskew([3,2,1],[2], weight=[0]))
++ []
++ sage: list(lrskew([3,2,1],[3,2,1], weight=[]))
++ [[[None, None, None], [None, None], [None]]]
++ sage: list(lrskew([3,2,1],[3,2,1], weight=[0]))
++ [[[None, None, None], [None, None], [None]]]
++ sage: list(lrskew([3,2,1],[3,2,1], weight=[1]))
++ []
+ """
+- 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 = SemistandardSkewTableaux(shape)
++ 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 = SemistandardSkewTableaux(shape, wt)
++ m = len(wt)
++ for data in iterator:
++ w = [0] * m
++ for j in data:
++ if j >= m:
++ # We know they are not equal, so make the check below quick
++ w = None
++ break
++ w[j] += 1
++ if w == wt:
++ yield ST.from_shape_and_word(shape, [i+1 for i in data])
++
diff --git a/srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch b/srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch
new file mode 100644
index 000000000000..1e2e0ba90742
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch
@@ -0,0 +1,40 @@
+As produced by `git diff a90a3146{^^,}`
+
+diff --git a/src/sage/repl/interface_magic.py b/src/sage/repl/interface_magic.py
+index 8a455b69b0e..a93e1c9e04c 100644
+--- a/src/sage/repl/interface_magic.py
++++ b/src/sage/repl/interface_magic.py
+@@ -260,7 +260,7 @@ class InterfaceMagic(object):
+ 2
+ 120
+ sage: shell.run_cell('%%gap foo\n1+1;\n')
+- ...File "<string>", line unknown
++ ...File...<string>...
+ SyntaxError: Interface magics have no options, got "foo"
+ <BLANKLINE>
+ sage: shell.run_cell('%%gap?')
+diff --git a/src/sage/repl/interpreter.py b/src/sage/repl/interpreter.py
+index 7468afe52d7..06c47b7374a 100644
+--- a/src/sage/repl/interpreter.py
++++ b/src/sage/repl/interpreter.py
+@@ -78,9 +78,9 @@ Check that Cython source code appears in tracebacks::
+ dummy line
+ ...
+ ZeroDivisionError...Traceback (most recent call last)
+- <ipython-input-...> in <module>...
++ ...in <module>...
+ ----> 1 Integer(1)/Integer(0)
+- .../sage/rings/integer.pyx in sage.rings.integer.Integer...div...
++ .../sage/rings/integer.pyx... in sage.rings.integer.Integer...div...
+ ...
+ -> ... raise ZeroDivisionError("rational division by zero")
+ ....: x = <Rational> Rational.__new__(Rational)
+@@ -423,7 +423,7 @@ def SagePreparseTransformer(lines):
+ sage: from sage.repl.interpreter import get_test_shell
+ sage: shell = get_test_shell()
+ sage: shell.run_cell(bad_syntax)
+- File "<string>", line unknown
++ File...<string>...
+ SyntaxError: Mismatched ']'
+ <BLANKLINE>
+ sage: shell.quit()
diff --git a/srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch b/srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch
new file mode 100644
index 000000000000..19b69700a4f6
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch
@@ -0,0 +1,19 @@
+commit 9c8235e44ffb509efa8a3ca6cdb55154e2b5066d
+Author: Antonio Rojas <arojas@archlinux.org>
+Date: Sun Feb 13 19:53:14 2022 +0100
+
+ Fix deprecation warning with scipy 1.8
+
+diff --git a/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py b/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py
+index e9b60dae5ec..7932167b41d 100644
+--- a/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py
++++ b/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py
+@@ -356,7 +356,7 @@ Sage example in ./linsolve.tex, line 2230::
+
+ Sage example in ./linsolve.tex, line 2609::
+
+- sage: from scipy.sparse.linalg.dsolve import *
++ sage: from scipy.sparse.linalg import factorized
+ sage: from scipy.sparse import lil_matrix
+ sage: from numpy import array
+ sage: n = 200
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 710a9e80c052..02d4333fa545 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
# Template file for 'sagemath'
pkgname=sagemath
version=9.5
-revision=1
+revision=2
wrksrc=sage-$version
build_wrksrc=pkgs/sagemath-standard
build_style=python3-module
@@ -12,7 +12,7 @@ hostmakedepends="m4 pkg-config python3-Cython python3-Jinja2 python3-pkgconfig
makedepends="arb-devel boost-devel brial-devel cliquer-devel ecl eclib-devel
ecm-devel fflas-ffpack flintlib-devel gap-devel gd-devel giac-devel glpk-devel
gsl-devel iml-devel lcalc-devel libbraiding-devel libhomfly-devel libmpc-devel
- libpng-devel linbox-devel lrcalc-devel m4ri-devel m4rie-devel mpfi-devel
+ libpng-devel linbox-devel m4ri-devel m4rie-devel mpfi-devel
mpfr-devel ntl-devel openblas-devel pari-devel planarity-devel python3-cypari2
python3-cysignals python3-devel python3-gmpy2 python3-memory_allocator
python3-numpy rankwidth-devel singular symmetrica-devel zn_poly"
@@ -20,7 +20,7 @@ depends="FlintQS eclib-devel fflas-ffpack flintlib-devel gcc-fortran gd-devel
gfan giac gsl-devel gzip libpng-devel linbox-devel m4ri-devel maxima-ecl
mpfr-devel nauty ntl-devel palp pari-devel pari-elldata-small pari-galdata
pari-galpol-small pari-seadata-small pkg-config python3-Cython python3-cypari2
- python3-cysignals python3-devel python3-fpylll python3-ipython
+ python3-cysignals python3-devel python3-fpylll python3-ipython python3-lrcalc
python3-ipython_ipykernel python3-jupyter_ipywidgets python3-matplotlib
python3-memory_allocator python3-networkx python3-pip python3-pkgconfig
python3-pplpy python3-primecountpy python3-requests python3-scipy
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
@ 2022-03-18 19:45 ` dkwo
2022-03-18 20:24 ` tornaria
` (6 subsequent siblings)
7 siblings, 0 replies; 9+ messages in thread
From: dkwo @ 2022-03-18 19:45 UTC (permalink / raw)
To: ml
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New comment by dkwo on void-packages repository
https://github.com/void-linux/void-packages/pull/36209#issuecomment-1072747803
Comment:
May I suggest that we split off a package like
```
sagemath-devel_package() { # or whatever you want to call it
depends = "sagemath"
depends += "move here all the -devel that is in sagemath depends, the compilers etc"
desc += "development stuff, needed to pass all doctests, compile cython code etc."
```
Do you see any drawbacks?
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
2022-03-18 19:45 ` dkwo
@ 2022-03-18 20:24 ` tornaria
2022-03-18 20:41 ` dkwo
` (5 subsequent siblings)
7 siblings, 0 replies; 9+ messages in thread
From: tornaria @ 2022-03-18 20:24 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 2179 bytes --]
New comment by tornaria on void-packages repository
https://github.com/void-linux/void-packages/pull/36209#issuecomment-1072771825
Comment:
> May I suggest that we split off a package like
>
> ```
> sagemath-devel_package() { # or whatever you want to call it
> depends = "sagemath"
> depends += "move here all the -devel that is in sagemath depends, the compilers etc"
> desc += "development stuff, needed to pass all doctests, compile cython code etc."
> ```
>
> Do you see any drawbacks?
What you suggest seems to ill-defined or at least very difficult to determine. What are some example packages that are now listed as runtime dependencies but you would move to `sagemath-devel`? What is the gain (say in installed-size) vs. what is to loose (as in what would stop working). If you are worried about download or installed size, we could have some `sagemath-minimal` which leaves out some functionality, e.g. some of the large databases. But the difference in size has to be worth it.
On a different note I was thinking to have a meta-package `sagemath-builddeps` which depends on all packages that are needed to `build` sagemath from the official source release (i.e. using all possible packages from system). This would *not* depend on `sagemath`, so it's a user choice to install from source.
I'm also working on a `sagemath-beta` package that will install current beta of sagemath -- the catch is that I want this to be installable side-by-side with the main `sagemath` package so we can test new releases as they come out.
In fact, the current PR (update of lrcalc) is motivated by this. In order to have `sagemath` and `sagemath-beta` installed at the same time we need both to use the same dependencies. Since sagemath-9.6.beta5 works only with lrcalc-2.1, we need to have sagemath-9.5 work with lrcalc-2.1 as well.
There are annoying doctest failures triggered by updates to python packages -- I thought I had all covered for the updates to ipython 8.0 and scipy 1.8 but it seems ipython 8.1 has another change. This is the failure we are seeing in CI, it should be easy to fix and push upstream if it's not already fixed in 9.6.beta5.
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
2022-03-18 19:45 ` dkwo
2022-03-18 20:24 ` tornaria
@ 2022-03-18 20:41 ` dkwo
2022-03-18 21:08 ` [PR PATCH] [Updated] " tornaria
` (4 subsequent siblings)
7 siblings, 0 replies; 9+ messages in thread
From: dkwo @ 2022-03-18 20:41 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1017 bytes --]
New comment by dkwo on void-packages repository
https://github.com/void-linux/void-packages/pull/36209#issuecomment-1072781626
Comment:
I was thinking:
depends="FlintQS eclib fflas-ffpack flintlib gd
gfan giac gsl gzip libpng linbox m4ri maxima-ecl
mpfr nauty ntl palp pari pari-elldata-small pari-galdata
pari-galpol-small pari-seadata-small pkg-config python3-Cython python3-cypari2
python3-cysignals python3 python3-fpylll python3-ipython python3-lrcalc
python3-ipython_ipykernel python3-jupyter_ipywidgets python3-matplotlib
python3-memory_allocator python3-networkx python3-pip python3-pkgconfig
python3-pplpy python3-primecountpy python3-requests python3-scipy
python3-sympy python3-traitlets sage-data-combinatorial_designs
sage-data-conway_polynomials sage-data-elliptic_curves sage-data-graphs
sage-data-polytopes_db sympow tachyon"
while
depends+="eclib-devel flintlib-devel gcc-fortran gd-devel gsl-devel libpng-devel
linbox-devel m4ri-devel mpfr-devel ntl-devel pari-devel python3-devel"
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [PR PATCH] [Updated] lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
` (2 preceding siblings ...)
2022-03-18 20:41 ` dkwo
@ 2022-03-18 21:08 ` tornaria
2022-03-18 21:35 ` tornaria
` (3 subsequent siblings)
7 siblings, 0 replies; 9+ messages in thread
From: tornaria @ 2022-03-18 21:08 UTC (permalink / raw)
To: ml
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There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages sagemath-lrcalc
https://github.com/void-linux/void-packages/pull/36209
lrcalc: update to 2.1, rebuild sagemath-9.5
This PR updates lrcalc to 2.1, which will be required for sagemath 9.6.
This needs that we rebuild sagemath 9.5 with a few changes:
- add a new python package `python3-lrcalc`
- patch sagemath 9.5 so it can use the new version of lrcalc (via python3-lrcalc)
Unrelated to that, I added two patches to sagemath which fix doctests after upgrades of ipython to 8.0 and scipy to 1.8.
A patch file from https://github.com/void-linux/void-packages/pull/36209.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-lrcalc-36209.patch --]
[-- Type: text/x-diff, Size: 34999 bytes --]
From 16ce3b48b9ac2f8a47e2713edf6a0e35250d5873 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 28 Feb 2022 12:03:22 -0300
Subject: [PATCH 1/4] lrcalc: update to 2.1.
---
common/shlibs | 2 +-
srcpkgs/lrcalc/patches/includes.patch | 90 ---------------------------
srcpkgs/lrcalc/template | 6 +-
3 files changed, 4 insertions(+), 94 deletions(-)
delete mode 100644 srcpkgs/lrcalc/patches/includes.patch
diff --git a/common/shlibs b/common/shlibs
index 83b5783cb026..4a0a07d366cc 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -4038,7 +4038,7 @@ libarb.so.2 arb-2.20.0_1
libec.so.8 eclib-20210625_1
libsymmetrica.so.2 symmetrica-3.0.1_1
libLfunction.so.1 lcalc-2.0.4_1
-liblrcalc.so.1 lrcalc-1.2_1
+liblrcalc.so.2 lrcalc-2.1_1
libwayland-client++.so.0 libwaylandpp-0.2.8_1
libwayland-cursor++.so.0 libwaylandpp-0.2.8_1
libwayland-egl++.so.0 libwaylandpp-0.2.8_1
diff --git a/srcpkgs/lrcalc/patches/includes.patch b/srcpkgs/lrcalc/patches/includes.patch
deleted file mode 100644
index 707da176a60f..000000000000
--- a/srcpkgs/lrcalc/patches/includes.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-From 4a5e1c8c3c11efdb1cbb4239825a6bf4bf1c52f8 Mon Sep 17 00:00:00 2001
-From: Anders Skovsted Buch <asbuch@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/srcpkgs/lrcalc/template b/srcpkgs/lrcalc/template
index 8b33c3cba6c8..afa889b6d6ad 100644
--- a/srcpkgs/lrcalc/template
+++ b/srcpkgs/lrcalc/template
@@ -1,14 +1,14 @@
# Template file for 'lrcalc'
pkgname=lrcalc
-version=1.2
-revision=2
+version=2.1
+revision=1
build_style=gnu-configure
short_desc="Littlewood-Richardson Calculator"
maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
license="GPL-3.0-or-later"
homepage="https://sites.math.rutgers.edu/~asbuch/lrcalc/"
distfiles="https://sites.math.rutgers.edu/~asbuch/lrcalc/lrcalc-$version.tar.gz"
-checksum=792dd538a0d19698be2c5b8c138730bbb4820e8a44e03b001ae14bd5f1d7040b
+checksum=996ac00e6ea8321ef09b34478f5379f613933c3254aeba624b6419b8afa5df57
lrcalc-devel_package() {
depends="${sourcepkg}>=${version}_${revision} ${makedepends}"
From 0bea3c29ecf5390a728f9c53fae3bc680819583f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 28 Feb 2022 14:06:21 -0300
Subject: [PATCH 2/4] New package: python3-lrcalc-2.1
---
srcpkgs/python3-lrcalc/template | 14 ++++++++++++++
1 file changed, 14 insertions(+)
create mode 100644 srcpkgs/python3-lrcalc/template
diff --git a/srcpkgs/python3-lrcalc/template b/srcpkgs/python3-lrcalc/template
new file mode 100644
index 000000000000..9f335dac35dd
--- /dev/null
+++ b/srcpkgs/python3-lrcalc/template
@@ -0,0 +1,14 @@
+# Template file for 'python3-lrcalc'
+pkgname=python3-lrcalc
+version=2.1
+revision=1
+wrksrc=lrcalc-${version}
+build_style=python3-module
+hostmakedepends="python3-setuptools python3-Cython"
+makedepends="python3-devel lrcalc-devel"
+short_desc="Python bindings for the Littlewood-Richardson Calculator library"
+maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
+license="GPL-3.0-or-later"
+homepage="https://math.rutgers.edu/~asbuch/lrcalc"
+distfiles="${PYPI_SITE}/l/lrcalc/lrcalc-${version}.tar.gz"
+checksum=e3a0509aeda487b412b391a52e817ca36b5c063a8305e09fd54d53259dd6aaa9
From 13ab5c4a1b3453fec6611dbf577816346ea6036c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 28 Feb 2022 14:06:28 -0300
Subject: [PATCH 3/4] sagemath: rebuild for lrcalc 2.1
Also fix doctests for upgrade of ipython 8.0 and scipy 1.8
---
.../trac-31355-upgrade_lrcalc_to_2.1.patch | 670 ++++++++++++++++++
.../trac-33170-fix_doctest_ipython_8.patch | 40 ++
.../trac-33336-fix_doctest_scipy_1.8.patch | 19 +
srcpkgs/sagemath/template | 6 +-
4 files changed, 732 insertions(+), 3 deletions(-)
create mode 100644 srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch
create mode 100644 srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch
create mode 100644 srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch
diff --git a/srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch b/srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch
new file mode 100644
index 000000000000..4bd6f4f4e2dc
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-31355-upgrade_lrcalc_to_2.1.patch
@@ -0,0 +1,670 @@
+As produced by `git diff 9.5 9.6.beta3 -- src/sage/libs/lrcalc`
+
+diff --git a/src/sage/libs/lrcalc/lrcalc.pxd b/src/sage/libs/lrcalc/lrcalc.pxd
+deleted file mode 100644
+index 10b88db93f2..00000000000
+--- 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 60%
+rename from src/sage/libs/lrcalc/lrcalc.pyx
+rename to src/sage/libs/lrcalc/lrcalc.py
+index b591081ec4c..b541bfacd89 100644
+--- a/src/sage/libs/lrcalc/lrcalc.pyx
++++ b/src/sage/libs/lrcalc/lrcalc.py
+@@ -10,7 +10,8 @@ fusion products. All of the above are achieved by counting LR
+ appropriate shape and content by iterating through them.
+ Additionally, ``lrcalc`` handles products of Schubert polynomials.
+
+-The web page of ``lrcalc`` is `<http://sites.math.rutgers.edu/~asbuch/lrcalc/>`_.
++The web page of ``lrcalc`` is
++`<http://sites.math.rutgers.edu/~asbuch/lrcalc/>`_.
+
+ The following describes the Sage interface to this library.
+
+@@ -36,12 +37,13 @@ Schur expansion::
+ [4, 2]: 1}
+
+ Same product, but include only partitions with at most 3 rows. This
+-corresponds to computing in the representation ring of gl(3)::
++corresponds to computing in the representation ring of `\mathfrak{gl}(3)`::
+
+ sage: lrcalc.mult([2,1], [2,1], 3)
+ {[2, 2, 2]: 1, [3, 2, 1]: 2, [3, 3]: 1, [4, 1, 1]: 1, [4, 2]: 1}
+
+-We can also compute the fusion product, here for sl(3) and level 2::
++We can also compute the fusion product, here for `\mathfrak{sl}(3)`
++and level 2::
+
+ sage: lrcalc.mult([3,2,1], [3,2,1], 3,2)
+ {[4, 4, 4]: 1, [5, 4, 3]: 1}
+@@ -77,42 +79,38 @@ Multiply two Schubert polynomials::
+ [6, 2, 1, 4, 3, 5]: 1}
+
+ Same product, but include only permutations of 5 elements in the result.
+-This corresponds to computing in the cohomology ring of Fl(5)::
++This corresponds to computing in the cohomology ring of `Fl(5)`::
+
+ sage: lrcalc.mult_schubert([4,2,1,3], [1,4,2,5,3], 5)
+ {[4, 5, 1, 3, 2]: 1, [5, 3, 1, 4, 2]: 1, [5, 4, 1, 2, 3]: 1}
+
+ List all Littlewood-Richardson tableaux of skew shape `\mu/\nu`; in
+ this example `\mu=[3,2,1]` and `\nu=[2,1]`. Specifying a third entry
+-`maxrows` restricts the alphabet to `\{1,2,\ldots,maxrows\}`::
++`M' = ``maxrows`` restricts the alphabet to `\{1,2,\ldots,M\}`::
+
+ sage: list(lrcalc.lrskew([3,2,1],[2,1]))
+ [[[None, None, 1], [None, 1], [1]], [[None, None, 1], [None, 1], [2]],
+ [[None, None, 1], [None, 2], [1]], [[None, None, 1], [None, 2], [3]]]
+
+ sage: list(lrcalc.lrskew([3,2,1],[2,1],maxrows=2))
+- [[[None, None, 1], [None, 1], [1]], [[None, None, 1], [None, 1], [2]], [[None, None, 1], [None, 2], [1]]]
++ [[[None, None, 1], [None, 1], [1]], [[None, None, 1], [None, 1], [2]],
++ [[None, None, 1], [None, 2], [1]]]
+
+ .. TODO::
+
+- use this library in the :class:`SymmetricFunctions` code, to
++ Use this library in the :class:`SymmetricFunctions` code, to
+ make it easy to apply it to linear combinations of Schur functions.
+
+ .. SEEALSO::
+
+ - :func:`lrcoef`
+-
+ - :func:`mult`
+-
+ - :func:`coprod`
+-
+ - :func:`skew`
+-
+ - :func:`lrskew`
+-
+ - :func:`mult_schubert`
+
+-.. rubric:: Underlying algorithmic in lrcalc
++.. RUBRIC:: Underlying algorithmic in lrcalc
+
+ Here is some additional information regarding the main low-level
+ C-functions in `lrcalc`. Given two partitions ``outer`` and ``inner``
+@@ -187,180 +185,24 @@ 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
+-
+-
+-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.
++from sage.combinat.skew_tableau import SemistandardSkewTableaux
++from sage.combinat.skew_partition import SkewPartition
++from sage.rings.integer import Integer
++import lrcalc
+
+- 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"""
+@@ -371,13 +213,11 @@ def lrcoef_unsafe(outer, inner1, inner2):
+
+ INPUT:
+
+- - ``outer`` -- a partition (weakly decreasing list of non-negative integers).
+-
+- - ``inner1`` -- a partition.
++ - ``outer`` -- a partition (weakly decreasing list of non-negative integers)
++ - ``inner1`` -- a partition
++ - ``inner2`` -- a partition
+
+- - ``inner2`` -- a partition.
+-
+- .. warning::
++ .. WARNING::
+
+ This function does not do any check on its input. If you want
+ to use a safer version, use :func:`lrcoef`.
+@@ -392,18 +232,7 @@ 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):
+@@ -415,11 +244,9 @@ def lrcoef(outer, inner1, inner2):
+
+ INPUT:
+
+- - ``outer`` -- a partition (weakly decreasing list of non-negative integers).
+-
+- - ``inner1`` -- a partition.
+-
+- - ``inner2`` -- a partition.
++ - ``outer`` -- a partition (weakly decreasing list of non-negative integers)
++ - ``inner1`` -- a partition
++ - ``inner2`` -- a partition
+
+ .. NOTE::
+
+@@ -436,7 +263,6 @@ def lrcoef(outer, inner1, inner2):
+ 1
+ sage: lrcoef([2,1,1,1,1], [2,1], [2,1])
+ 0
+-
+ """
+ return lrcoef_unsafe(_Partitions(outer), _Partitions(inner1), _Partitions(inner2))
+
+@@ -451,13 +277,9 @@ def mult(part1, part2, maxrows=None, level=None, quantum=None):
+ INPUT:
+
+ - ``part1`` -- a partition
+-
+ - ``part2`` -- a partition
+-
+ - ``maxrows`` -- (optional) an integer
+-
+ - ``level`` -- (optional) an integer
+-
+ - ``quantum`` -- (optional) an element of a ring
+
+ If ``maxrows`` is specified, then only partitions with at most
+@@ -479,7 +301,8 @@ def mult(part1, part2, maxrows=None, level=None, quantum=None):
+ sage: sorted(mult([2],[2]).items())
+ [([2, 2], 1), ([3, 1], 1), ([4], 1)]
+ sage: sorted(mult([2,1],[2,1]).items())
+- [([2, 2, 1, 1], 1), ([2, 2, 2], 1), ([3, 1, 1, 1], 1), ([3, 2, 1], 2), ([3, 3], 1), ([4, 1, 1], 1), ([4, 2], 1)]
++ [([2, 2, 1, 1], 1), ([2, 2, 2], 1), ([3, 1, 1, 1], 1),
++ ([3, 2, 1], 2), ([3, 3], 1), ([4, 1, 1], 1), ([4, 2], 1)]
+ sage: sorted(mult([2,1],[2,1],maxrows=2).items())
+ [([3, 3], 1), ([4, 2], 1)]
+ sage: mult([2,1],[3,2,1],3)
+@@ -510,44 +333,24 @@ 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.
+
+@@ -557,11 +360,9 @@ def skew(outer, inner, maxrows=0):
+
+ INPUT:
+
+- - ``outer`` -- a partition.
+-
+- - ``inner`` -- a partition.
+-
+- - ``maxrows`` -- an integer or ``None``.
++ - ``outer`` -- a partition
++ - ``inner`` -- a partition
++ - ``maxrows`` -- an integer or ``None``
+
+ If ``maxrows`` is specified, then only partitions with at most
+ this number of rows are included in the result.
+@@ -572,14 +373,7 @@ 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):
+@@ -592,9 +386,8 @@ def coprod(part, all=0):
+
+ INPUT:
+
+- - ``part`` -- a partition.
+-
+- - ``all`` -- an integer.
++ - ``part`` -- a partition
++ - ``all`` -- an integer
+
+ If ``all`` is non-zero then all terms are included in the result.
+ If ``all`` is zero, then only pairs of partitions ``(part1,
+@@ -609,12 +402,9 @@ 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):
+@@ -627,11 +417,9 @@ def mult_schubert(w1, w2, rank=0):
+
+ INPUT:
+
+- - ``w1`` -- a permutation.
+-
+- - ``w2`` -- a permutation.
+-
+- - ``rank`` -- an integer.
++ - ``w1`` -- a permutation
++ - ``w2`` -- a permutation
++ - ``rank`` -- an integer
+
+ If ``rank`` is non-zero, then only permutations from the symmetric
+ group `S(\mathrm{rank})` are included in the result.
+@@ -646,33 +434,24 @@ 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``.
+
+ INPUT:
+
+ - ``outer`` -- a partition
+-
+ - ``inner`` -- a partition
+-
+ - ``weight`` -- a partition (optional)
+-
+- - ``maxrows`` -- an integer (optional)
++ - ``maxrows`` -- a positive integer (optional)
+
+ OUTPUT: an iterator of :class:`SkewTableau`
+
+- Specifying ``maxrows`` restricts the alphabet to `\{1,2,\ldots,maxrows\}`.
++ Specifying ``maxrows`` = `M` restricts the alphabet to `\{1,2,\ldots,M\}`.
+
+ Specifying ``weight`` returns only those tableaux of given content/weight.
+
+@@ -702,22 +481,40 @@ def lrskew(outer, inner, weight=None, maxrows=0):
+
+ sage: list(lrskew([3,2,1],[2], weight=[3,1]))
+ [[[None, None, 1], [1, 1], [2]]]
++
++ TESTS::
++
++ sage: from sage.libs.lrcalc.lrcalc import lrskew
++ sage: list(lrskew([3,2,1],[2], weight=[]))
++ []
++ sage: list(lrskew([3,2,1],[2], weight=[0]))
++ []
++ sage: list(lrskew([3,2,1],[3,2,1], weight=[]))
++ [[[None, None, None], [None, None], [None]]]
++ sage: list(lrskew([3,2,1],[3,2,1], weight=[0]))
++ [[[None, None, None], [None, None], [None]]]
++ sage: list(lrskew([3,2,1],[3,2,1], weight=[1]))
++ []
+ """
+- 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 = SemistandardSkewTableaux(shape)
++ 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 = SemistandardSkewTableaux(shape, wt)
++ m = len(wt)
++ for data in iterator:
++ w = [0] * m
++ for j in data:
++ if j >= m:
++ # We know they are not equal, so make the check below quick
++ w = None
++ break
++ w[j] += 1
++ if w == wt:
++ yield ST.from_shape_and_word(shape, [i+1 for i in data])
++
diff --git a/srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch b/srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch
new file mode 100644
index 000000000000..1e2e0ba90742
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-33170-fix_doctest_ipython_8.patch
@@ -0,0 +1,40 @@
+As produced by `git diff a90a3146{^^,}`
+
+diff --git a/src/sage/repl/interface_magic.py b/src/sage/repl/interface_magic.py
+index 8a455b69b0e..a93e1c9e04c 100644
+--- a/src/sage/repl/interface_magic.py
++++ b/src/sage/repl/interface_magic.py
+@@ -260,7 +260,7 @@ class InterfaceMagic(object):
+ 2
+ 120
+ sage: shell.run_cell('%%gap foo\n1+1;\n')
+- ...File "<string>", line unknown
++ ...File...<string>...
+ SyntaxError: Interface magics have no options, got "foo"
+ <BLANKLINE>
+ sage: shell.run_cell('%%gap?')
+diff --git a/src/sage/repl/interpreter.py b/src/sage/repl/interpreter.py
+index 7468afe52d7..06c47b7374a 100644
+--- a/src/sage/repl/interpreter.py
++++ b/src/sage/repl/interpreter.py
+@@ -78,9 +78,9 @@ Check that Cython source code appears in tracebacks::
+ dummy line
+ ...
+ ZeroDivisionError...Traceback (most recent call last)
+- <ipython-input-...> in <module>...
++ ...in <module>...
+ ----> 1 Integer(1)/Integer(0)
+- .../sage/rings/integer.pyx in sage.rings.integer.Integer...div...
++ .../sage/rings/integer.pyx... in sage.rings.integer.Integer...div...
+ ...
+ -> ... raise ZeroDivisionError("rational division by zero")
+ ....: x = <Rational> Rational.__new__(Rational)
+@@ -423,7 +423,7 @@ def SagePreparseTransformer(lines):
+ sage: from sage.repl.interpreter import get_test_shell
+ sage: shell = get_test_shell()
+ sage: shell.run_cell(bad_syntax)
+- File "<string>", line unknown
++ File...<string>...
+ SyntaxError: Mismatched ']'
+ <BLANKLINE>
+ sage: shell.quit()
diff --git a/srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch b/srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch
new file mode 100644
index 000000000000..19b69700a4f6
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-33336-fix_doctest_scipy_1.8.patch
@@ -0,0 +1,19 @@
+commit 9c8235e44ffb509efa8a3ca6cdb55154e2b5066d
+Author: Antonio Rojas <arojas@archlinux.org>
+Date: Sun Feb 13 19:53:14 2022 +0100
+
+ Fix deprecation warning with scipy 1.8
+
+diff --git a/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py b/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py
+index e9b60dae5ec..7932167b41d 100644
+--- a/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py
++++ b/src/sage/tests/books/computational-mathematics-with-sagemath/linsolve_doctest.py
+@@ -356,7 +356,7 @@ Sage example in ./linsolve.tex, line 2230::
+
+ Sage example in ./linsolve.tex, line 2609::
+
+- sage: from scipy.sparse.linalg.dsolve import *
++ sage: from scipy.sparse.linalg import factorized
+ sage: from scipy.sparse import lil_matrix
+ sage: from numpy import array
+ sage: n = 200
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 710a9e80c052..02d4333fa545 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
# Template file for 'sagemath'
pkgname=sagemath
version=9.5
-revision=1
+revision=2
wrksrc=sage-$version
build_wrksrc=pkgs/sagemath-standard
build_style=python3-module
@@ -12,7 +12,7 @@ hostmakedepends="m4 pkg-config python3-Cython python3-Jinja2 python3-pkgconfig
makedepends="arb-devel boost-devel brial-devel cliquer-devel ecl eclib-devel
ecm-devel fflas-ffpack flintlib-devel gap-devel gd-devel giac-devel glpk-devel
gsl-devel iml-devel lcalc-devel libbraiding-devel libhomfly-devel libmpc-devel
- libpng-devel linbox-devel lrcalc-devel m4ri-devel m4rie-devel mpfi-devel
+ libpng-devel linbox-devel m4ri-devel m4rie-devel mpfi-devel
mpfr-devel ntl-devel openblas-devel pari-devel planarity-devel python3-cypari2
python3-cysignals python3-devel python3-gmpy2 python3-memory_allocator
python3-numpy rankwidth-devel singular symmetrica-devel zn_poly"
@@ -20,7 +20,7 @@ depends="FlintQS eclib-devel fflas-ffpack flintlib-devel gcc-fortran gd-devel
gfan giac gsl-devel gzip libpng-devel linbox-devel m4ri-devel maxima-ecl
mpfr-devel nauty ntl-devel palp pari-devel pari-elldata-small pari-galdata
pari-galpol-small pari-seadata-small pkg-config python3-Cython python3-cypari2
- python3-cysignals python3-devel python3-fpylll python3-ipython
+ python3-cysignals python3-devel python3-fpylll python3-ipython python3-lrcalc
python3-ipython_ipykernel python3-jupyter_ipywidgets python3-matplotlib
python3-memory_allocator python3-networkx python3-pip python3-pkgconfig
python3-pplpy python3-primecountpy python3-requests python3-scipy
From 22cbd7277ba6ee3cdd053337742ee9d2f57e55af Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Fri, 18 Mar 2022 18:07:43 -0300
Subject: [PATCH 4/4] sagemath: fix doctest for ipython 8.1
---
.../trac-33170b-fix_doctest_ipython_8.1.patch | 13 +++++++++++++
1 file changed, 13 insertions(+)
create mode 100644 srcpkgs/sagemath/patches/trac-33170b-fix_doctest_ipython_8.1.patch
diff --git a/srcpkgs/sagemath/patches/trac-33170b-fix_doctest_ipython_8.1.patch b/srcpkgs/sagemath/patches/trac-33170b-fix_doctest_ipython_8.1.patch
new file mode 100644
index 000000000000..853813b0f5bd
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-33170b-fix_doctest_ipython_8.1.patch
@@ -0,0 +1,13 @@
+Fix for ipython 8.1
+
+--- a/src/sage/repl/interpreter.py
++++ b/src/sage/repl/interpreter.py
+@@ -78,7 +78,7 @@ Check that Cython source code appears in tracebacks::
+ dummy line
+ ...
+ ZeroDivisionError...Traceback (most recent call last)
+- ...in <module>...
++ ...
+ ----> 1 Integer(1)/Integer(0)
+ .../sage/rings/integer.pyx... in sage.rings.integer.Integer...div...
+ ...
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
` (3 preceding siblings ...)
2022-03-18 21:08 ` [PR PATCH] [Updated] " tornaria
@ 2022-03-18 21:35 ` tornaria
2022-03-19 8:14 ` dkwo
` (2 subsequent siblings)
7 siblings, 0 replies; 9+ messages in thread
From: tornaria @ 2022-03-18 21:35 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 938 bytes --]
New comment by tornaria on void-packages repository
https://github.com/void-linux/void-packages/pull/36209#issuecomment-1072834030
Comment:
> depends+="eclib-devel flintlib-devel gcc-fortran gd-devel gsl-devel libpng-devel linbox-devel m4ri-devel mpfr-devel ntl-devel pari-devel python3-devel"
Granted, there are some large packages there. I'd like to have a look at what extent these are used in sage, etc. Ideally there should be a feature flag that indicates that a doctest only works when a working C compiler is installed, etc. That needs to be done with upstream.
What would happen to doctesting in CI? I guess that would still work since it's done in the masterdir...
Let me think about it... We need some good workflow to play with bare-bones void so we can test dependencies are ok, because an xbps-src chroot always contain gcc, etc. which will may not be installed (gcc is pulled in as a dependency of gcc-fortran).
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
` (4 preceding siblings ...)
2022-03-18 21:35 ` tornaria
@ 2022-03-19 8:14 ` dkwo
2022-04-04 1:31 ` tornaria
2022-04-04 1:31 ` [PR PATCH] [Closed]: " tornaria
7 siblings, 0 replies; 9+ messages in thread
From: dkwo @ 2022-03-19 8:14 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 415 bytes --]
New comment by dkwo on void-packages repository
https://github.com/void-linux/void-packages/pull/36209#issuecomment-1072966952
Comment:
Ok, think about it.
I agree doctest in ci should still work.
Indeed, one can test with a different chroot, with only base installed.
This is the one I was using on musl
https://git.disroot.org/tuxliban/tutoriales_void/src/branch/master/Gu%C3%ADas/Container%20Void/Guide.md
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
` (5 preceding siblings ...)
2022-03-19 8:14 ` dkwo
@ 2022-04-04 1:31 ` tornaria
2022-04-04 1:31 ` [PR PATCH] [Closed]: " tornaria
7 siblings, 0 replies; 9+ messages in thread
From: tornaria @ 2022-04-04 1:31 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 292 bytes --]
New comment by tornaria on void-packages repository
https://github.com/void-linux/void-packages/pull/36209#issuecomment-1087020031
Comment:
This was superseded by #36420, so I'm closing now.
The proposal to split a `sagemath-devel` subpkg seems useful, I will consider for sagemath-9.6.
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [PR PATCH] [Closed]: lrcalc: update to 2.1, rebuild sagemath-9.5
2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
` (6 preceding siblings ...)
2022-04-04 1:31 ` tornaria
@ 2022-04-04 1:31 ` tornaria
7 siblings, 0 replies; 9+ messages in thread
From: tornaria @ 2022-04-04 1:31 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 571 bytes --]
There's a closed pull request on the void-packages repository
lrcalc: update to 2.1, rebuild sagemath-9.5
https://github.com/void-linux/void-packages/pull/36209
Description:
This PR updates lrcalc to 2.1, which will be required for sagemath 9.6.
This needs that we rebuild sagemath 9.5 with a few changes:
- add a new python package `python3-lrcalc`
- patch sagemath 9.5 so it can use the new version of lrcalc (via python3-lrcalc)
Unrelated to that, I added two patches to sagemath which fix doctests after upgrades of ipython to ~8.0~ 8.1 and scipy to 1.8.
^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2022-04-04 1:31 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz / follow: Atom feed)
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2022-03-18 18:29 [PR PATCH] lrcalc: update to 2.1, rebuild sagemath-9.5 tornaria
2022-03-18 19:45 ` dkwo
2022-03-18 20:24 ` tornaria
2022-03-18 20:41 ` dkwo
2022-03-18 21:08 ` [PR PATCH] [Updated] " tornaria
2022-03-18 21:35 ` tornaria
2022-03-19 8:14 ` dkwo
2022-04-04 1:31 ` tornaria
2022-04-04 1:31 ` [PR PATCH] [Closed]: " tornaria
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