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guix-mirrors/gnu/packages/patches/sage-update-eclib.patch
Andreas Enge b58c78093e
gnu: Add sage. 
* gnu/packages/sagemath.scm (sage): New variable.
(conway-polynomials, graphs, polytopes-db): Make packages private.
* gnu/packages/patches/sage-update-eclib.patch,
gnu/packages/patches/sage-update-pari-gp.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register patches.

Change-Id: I1cf647760ea3af2dd01d11eedbf1e847a2175365
2025-02-15 21:17:46 +01:00

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From 6dfc26b805d2fb0cafa60f0d778db3d68188b724 Mon Sep 17 00:00:00 2001
From: John Cremona <john.cremona@gmail.com>
Date: Wed, 13 Nov 2024 14:46:51 +0000
Subject: [PATCH 1/4] #38960-eclib-upgrade-20241112
---
build/pkgs/eclib/SPKG.rst | 2 +-
build/pkgs/eclib/checksums.ini | 4 ++--
build/pkgs/eclib/package-version.txt | 2 +-
build/pkgs/eclib/spkg-configure.m4 | 2 +-
4 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/build/pkgs/eclib/SPKG.rst b/build/pkgs/eclib/SPKG.rst
index 5627fdcb57c..ac8b27b3606 100644
--- a/build/pkgs/eclib/SPKG.rst
+++ b/build/pkgs/eclib/SPKG.rst
@@ -30,5 +30,5 @@ Upstream Contact
- Author: John Cremona
- Email: john.cremona@gmail.com
- Website:
- http://homepages.warwick.ac.uk/staff/J.E.Cremona/mwrank/index.html
+ https://johncremona.github.io/mwrank/index.html
- Repository: https://github.com/JohnCremona/eclib
diff --git a/build/pkgs/eclib/checksums.ini b/build/pkgs/eclib/checksums.ini
index fde4faaee15..b046783341d 100644
--- a/build/pkgs/eclib/checksums.ini
+++ b/build/pkgs/eclib/checksums.ini
@@ -1,4 +1,4 @@
tarball=eclib-VERSION.tar.bz2
-sha1=3028ac95e1b76699f5f9e871ac706cda363ab842
-sha256=32d116a3e359b0de4f6486c2bb6188bb8b553c8b833f618cc2596484e8b6145a
+sha1=749e4fda3660006a9459f129148d05ba482daa29
+sha256=30765c27ca1420141f83517897119d0185fea9b31132392170ddae40b060e46f
upstream_url=https://github.com/JohnCremona/eclib/releases/download/vVERSION/eclib-VERSION.tar.bz2
diff --git a/build/pkgs/eclib/package-version.txt b/build/pkgs/eclib/package-version.txt
index 190b92f716b..353869c3cba 100644
--- a/build/pkgs/eclib/package-version.txt
+++ b/build/pkgs/eclib/package-version.txt
@@ -1 +1 @@
-20231212
+20241112
diff --git a/build/pkgs/eclib/spkg-configure.m4 b/build/pkgs/eclib/spkg-configure.m4
index ba5c22fa090..23771dad1bd 100644
--- a/build/pkgs/eclib/spkg-configure.m4
+++ b/build/pkgs/eclib/spkg-configure.m4
@@ -1,7 +1,7 @@
SAGE_SPKG_CONFIGURE([eclib], [
SAGE_SPKG_DEPCHECK([ntl pari flint], [
dnl use existing eclib only if the version reported by pkg-config is recent enough
- m4_pushdef([SAGE_ECLIB_VER],["20231212"])
+ m4_pushdef([SAGE_ECLIB_VER],["20241112"])
PKG_CHECK_MODULES([ECLIB], [eclib >= SAGE_ECLIB_VER], [
AC_CACHE_CHECK([for mwrank version == SAGE_ECLIB_VER], [ac_cv_path_MWRANK], [
AC_PATH_PROGS_FEATURE_CHECK([MWRANK], [mwrank], [
From d38cb48c67c7565572064fd29748c1e8da3b3271 Mon Sep 17 00:00:00 2001
From: John Cremona <john.cremona@gmail.com>
Date: Tue, 19 Nov 2024 13:51:49 +0000
Subject: [PATCH 2/4] #38960 fix eclib interface after upgrade
---
src/sage/libs/eclib/__init__.pxd | 4 ++--
src/sage/libs/eclib/mat.pyx | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/sage/libs/eclib/__init__.pxd b/src/sage/libs/eclib/__init__.pxd
index d44d4fba865..84d1fc92275 100644
--- a/src/sage/libs/eclib/__init__.pxd
+++ b/src/sage/libs/eclib/__init__.pxd
@@ -55,7 +55,7 @@ cdef extern from "eclib/matrix.h":
cdef cppclass mat:
mat()
mat(mat m)
- scalar* get_entries()
+ vector[scalar] get_entries()
scalar sub(long, long)
long nrows()
long ncols()
@@ -67,7 +67,7 @@ cdef extern from "eclib/smatrix.h":
cdef cppclass smat:
smat()
smat(smat m)
- scalar* get_entries()
+ vector[scalar] get_entries()
scalar sub(long, long)
long nrows()
long ncols()
diff --git a/src/sage/libs/eclib/mat.pyx b/src/sage/libs/eclib/mat.pyx
index bfdeb6ae5c1..e7abe369b2b 100644
--- a/src/sage/libs/eclib/mat.pyx
+++ b/src/sage/libs/eclib/mat.pyx
@@ -10,7 +10,7 @@ from sage.rings.integer_ring import ZZ
from sage.matrix.matrix_integer_sparse cimport Matrix_integer_sparse
from sage.matrix.matrix_integer_dense cimport Matrix_integer_dense
from sage.rings.integer cimport Integer
-
+from libcpp.vector cimport vector
cdef class Matrix:
"""
@@ -213,7 +213,7 @@ cdef class Matrix:
"""
cdef long n = self.nrows()
cdef long i, j, k
- cdef scalar* v = <scalar*> self.M.get_entries() # coercion needed to deal with const
+ cdef vector[scalar] v = <vector[scalar]> self.M.get_entries() # coercion needed to deal with const
cdef Matrix_integer_dense Td
cdef Matrix_integer_sparse Ts
From 4f2cb3f7a943aefd05d4baf7b5845a6fc3dba779 Mon Sep 17 00:00:00 2001
From: John Cremona <john.cremona@gmail.com>
Date: Wed, 4 Dec 2024 08:35:58 +0000
Subject: [PATCH 3/4] #38960 simplify eclib interface
---
src/sage/libs/eclib/__init__.pxd | 2 --
src/sage/libs/eclib/mat.pyx | 18 +++++++-----------
2 files changed, 7 insertions(+), 13 deletions(-)
diff --git a/src/sage/libs/eclib/__init__.pxd b/src/sage/libs/eclib/__init__.pxd
index 84d1fc92275..2673af0613f 100644
--- a/src/sage/libs/eclib/__init__.pxd
+++ b/src/sage/libs/eclib/__init__.pxd
@@ -55,7 +55,6 @@ cdef extern from "eclib/matrix.h":
cdef cppclass mat:
mat()
mat(mat m)
- vector[scalar] get_entries()
scalar sub(long, long)
long nrows()
long ncols()
@@ -67,7 +66,6 @@ cdef extern from "eclib/smatrix.h":
cdef cppclass smat:
smat()
smat(smat m)
- vector[scalar] get_entries()
scalar sub(long, long)
long nrows()
long ncols()
diff --git a/src/sage/libs/eclib/mat.pyx b/src/sage/libs/eclib/mat.pyx
index e7abe369b2b..5dbb39faa0e 100644
--- a/src/sage/libs/eclib/mat.pyx
+++ b/src/sage/libs/eclib/mat.pyx
@@ -10,7 +10,6 @@ from sage.rings.integer_ring import ZZ
from sage.matrix.matrix_integer_sparse cimport Matrix_integer_sparse
from sage.matrix.matrix_integer_dense cimport Matrix_integer_dense
from sage.rings.integer cimport Integer
-from libcpp.vector cimport vector
cdef class Matrix:
"""
@@ -212,8 +211,7 @@ cdef class Matrix:
<class 'sage.matrix.matrix_integer_dense.Matrix_integer_dense'>
"""
cdef long n = self.nrows()
- cdef long i, j, k
- cdef vector[scalar] v = <vector[scalar]> self.M.get_entries() # coercion needed to deal with const
+ cdef long i, j
cdef Matrix_integer_dense Td
cdef Matrix_integer_sparse Ts
@@ -221,21 +219,19 @@ cdef class Matrix:
# Ugly code...
if sparse:
Ts = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
- k = 0
for i from 0 <= i < n:
for j from 0 <= j < n:
- if v[k]:
- Ts.set_unsafe(i, j, Integer(v[k]))
- k += 1
+ Mij = Integer(self.M.sub(i+1,j+1));
+ if Mij:
+ Ts.set_unsafe(i, j, Mij)
return Ts
else:
Td = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
- k = 0
for i from 0 <= i < n:
for j from 0 <= j < n:
- if v[k]:
- Td.set_unsafe(i, j, Integer(v[k]))
- k += 1
+ Mij = Integer(self.M.sub(i+1,j+1));
+ if Mij:
+ Td.set_unsafe(i, j, Mij)
return Td
From 8754c7052084043209c8332d3d1154c26c25ae91 Mon Sep 17 00:00:00 2001
From: John Cremona <john.cremona@gmail.com>
Date: Wed, 4 Dec 2024 09:20:07 +0000
Subject: [PATCH 4/4] #38960: fix lint issue
---
src/sage/libs/eclib/mat.pyx | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/sage/libs/eclib/mat.pyx b/src/sage/libs/eclib/mat.pyx
index 5dbb39faa0e..989d9d1a70c 100644
--- a/src/sage/libs/eclib/mat.pyx
+++ b/src/sage/libs/eclib/mat.pyx
@@ -221,7 +221,7 @@ cdef class Matrix:
Ts = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
for i from 0 <= i < n:
for j from 0 <= j < n:
- Mij = Integer(self.M.sub(i+1,j+1));
+ Mij = Integer(self.M.sub(i+1,j+1))
if Mij:
Ts.set_unsafe(i, j, Mij)
return Ts
@@ -229,7 +229,7 @@ cdef class Matrix:
Td = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
for i from 0 <= i < n:
for j from 0 <= j < n:
- Mij = Integer(self.M.sub(i+1,j+1));
+ Mij = Integer(self.M.sub(i+1,j+1))
if Mij:
Td.set_unsafe(i, j, Mij)
return Td
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