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sage: 9.4 -> 9.5

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This commit is contained in:
Mauricio Collares 2021-09-13 22:56:34 -03:00
parent 0aef6270cd
commit cecbb55fb0
13 changed files with 156 additions and 108 deletions
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19
pkgs/applications/science/math/sage/default.nix
View file

@ -14,13 +14,17 @@ let
# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
sagelib = self.callPackage ./sagelib.nix {
inherit flint arb;
inherit sage-src env-locations pynac singular;
inherit sage-src env-locations singular;
inherit (maxima) lisp-compiler;
linbox = pkgs.linbox.override { withSage = true; };
pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
};
sage_docbuild = self.callPackage ./sage_docbuild.nix {
sage-docbuild = self.callPackage ./python-modules/sage-docbuild.nix {
inherit sage-src;
};
sage-setup = self.callPackage ./python-modules/sage-setup.nix {
inherit sage-src;
};
};
@ -58,9 +62,9 @@ let
# the env-locations file.
sage-env = callPackage ./sage-env.nix {
sagelib = python3.pkgs.sagelib;
sage_docbuild = python3.pkgs.sage_docbuild;
sage-docbuild = python3.pkgs.sage-docbuild;
inherit env-locations;
inherit python3 singular palp flint pynac pythonEnv maxima;
inherit python3 singular palp flint pythonEnv maxima;
pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
};
@ -74,7 +78,7 @@ let
sage-with-env = callPackage ./sage-with-env.nix {
inherit python3 pythonEnv;
inherit sage-env;
inherit pynac singular maxima;
inherit singular maxima;
inherit three;
pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
};
@ -91,7 +95,7 @@ let
pythonRuntimeDeps = with python3.pkgs; [
sagelib
sage_docbuild
sage-docbuild
cvxopt
networkx
service-identity
@ -132,9 +136,6 @@ let
};
};
# *not* to confuse with the python package "pynac"
pynac = pkgs.pynac.override { inherit singular flint; };
# With openblas (64 bit), the tests fail the same way as when sage is build with
# openblas instead of openblasCompat. Apparently other packages somehow use flints
# blas when it is available. Alternative would be to override flint to use

21
pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
View file

@ -1,8 +1,8 @@
diff --git a/src/sage/env.py b/src/sage/env.py
index 95980cc2df..37107a30e1 100644
index c4953cfa65..47b880f9ad 100644
--- a/src/sage/env.py
+++ b/src/sage/env.py
@@ -227,93 +227,12 @@ OPENMP_CXXFLAGS = var("OPENMP_CXXFLAGS", "")
@@ -244,81 +244,8 @@ os.environ['MPMATH_SAGE'] = '1'
SAGE_BANNER = var("SAGE_BANNER", "")
SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes")
@ -29,20 +29,12 @@ index 95980cc2df..37107a30e1 100644
-
- EXAMPLES::
-
- sage: import sys
- sage: from fnmatch import fnmatch
- sage: from sage.env import _get_shared_lib_path
- sage: lib_filename = _get_shared_lib_path("Singular", "singular-Singular")
- sage: if sys.platform == 'cygwin':
- ....: pattern = "*/cygSingular-*.dll"
- ....: elif sys.platform == 'darwin':
- ....: pattern = "*/libSingular-*.dylib"
- ....: else:
- ....: pattern = "*/lib*Singular-*.so"
- sage: fnmatch(str(lib_filename), pattern)
- sage: "gap" in _get_shared_lib_path("gap")
- True
- sage: _get_shared_lib_path("an_absurd_lib") is None
- True
-
- """
-
- for libname in libnames:
@ -87,11 +79,6 @@ index 95980cc2df..37107a30e1 100644
- # Just return None if no files were found
- return None
-
# locate singular shared object
# On Debian it's libsingular-Singular so try that as well
-SINGULAR_SO = var("SINGULAR_SO", _get_shared_lib_path("Singular", "singular-Singular"))
+SINGULAR_SO = var("SINGULAR_SO", '/default')
# locate libgap shared object
-GAP_SO = var("GAP_SO", _get_shared_lib_path("gap", ""))
+GAP_SO = var("GAP_SO", '/default')

58
pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch Normal file
View file

@ -0,0 +1,58 @@
diff --git a/src/sage/libs/linbox/conversion.pxd b/src/sage/libs/linbox/conversion.pxd
index 7794c9edc3..1753277b1f 100644
--- a/src/sage/libs/linbox/conversion.pxd
+++ b/src/sage/libs/linbox/conversion.pxd
@@ -177,9 +177,8 @@ cdef inline Vector_integer_dense new_sage_vector_integer_dense(P, DenseVector_in
- v -- linbox vector
"""
cdef Vector_integer_dense res = P()
- cdef cppvector[Integer] * vec = &v.refRep()
cdef size_t i
for i in range(<size_t> res._degree):
- mpz_set(res._entries[i], vec[0][i].get_mpz_const())
+ mpz_set(res._entries[i], v.getEntry(i).get_mpz_const())
return res
diff --git a/src/sage/libs/linbox/linbox.pxd b/src/sage/libs/linbox/linbox.pxd
index 9112d151f8..dcc482960c 100644
--- a/src/sage/libs/linbox/linbox.pxd
+++ b/src/sage/libs/linbox/linbox.pxd
@@ -32,7 +32,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
ctypedef Modular_double Field
ctypedef double Element
DenseMatrix_Modular_double(Field F, size_t m, size_t n)
- DenseMatrix_Modular_double(Field F, Element*, size_t m, size_t n)
+ DenseMatrix_Modular_double(Field F, size_t m, size_t n, Element*)
void setEntry(size_t i, size_t j, Element& a)
Element &getEntry(size_t i, size_t j)
@@ -42,7 +42,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
ctypedef Modular_float Field
ctypedef float Element
DenseMatrix_Modular_float(Field F, size_t m, size_t n)
- DenseMatrix_Modular_float(Field F, Element*, size_t m, size_t n)
+ DenseMatrix_Modular_float(Field F, size_t m, size_t n, Element*)
void setEntry(size_t i, size_t j, Element& a)
Element &getEntry(size_t i, size_t j)
@@ -101,7 +101,6 @@ cdef extern from "linbox/vector/vector.h":
DenseVector_integer (Field &F)
DenseVector_integer (Field &F, long& m)
DenseVector_integer (Field &F, cppvector[Integer]&)
- cppvector[Element]& refRep()
size_t size()
void resize(size_t)
void resize(size_t n, const Element&)
diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi
index 010365d76f..3d60726ff9 100644
--- a/src/sage/matrix/matrix_modn_dense_template.pxi
+++ b/src/sage/matrix/matrix_modn_dense_template.pxi
@@ -219,7 +219,7 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_
return 0,[]
cdef ModField *F = new ModField(<long>modulus)
- cdef DenseMatrix *A = new DenseMatrix(F[0], <ModField.Element*>entries,<Py_ssize_t>nrows, <Py_ssize_t>ncols)
+ cdef DenseMatrix *A = new DenseMatrix(F[0], <Py_ssize_t>nrows, <Py_ssize_t>ncols, <ModField.Element*>entries)
cdef Py_ssize_t r = reducedRowEchelonize(A[0])
cdef Py_ssize_t i,j
for i in range(nrows):

12
pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
View file

@ -1,8 +1,8 @@
diff --git a/src/sage_docbuild/__init__.py b/src/sage_docbuild/__init__.py
index 79005b903a..fbe6fe2595 100644
index 8a5c1a19d2..21fd192642 100644
--- a/src/sage_docbuild/__init__.py
+++ b/src/sage_docbuild/__init__.py
@@ -85,27 +85,6 @@ def builder_helper(type):
@@ -89,27 +89,6 @@ def builder_helper(type):
"""
Returns a function which builds the documentation for
output type ``type``.
@ -12,7 +12,7 @@ index 79005b903a..fbe6fe2595 100644
- Check that :trac:`25161` has been resolved::
-
- sage: from sage_docbuild import DocBuilder, setup_parser
- sage: DocBuilder._options = setup_parser().parse_args([])[0] # builder_helper needs _options to be set
- sage: DocBuilder._options = setup_parser().parse_args([]) # builder_helper needs _options to be set
-
- sage: import sage_docbuild.sphinxbuild
- sage: def raiseBaseException():
@ -30,7 +30,7 @@ index 79005b903a..fbe6fe2595 100644
"""
def f(self, *args, **kwds):
output_dir = self._output_dir(type)
@@ -127,10 +106,9 @@ def builder_helper(type):
@@ -131,10 +110,9 @@ def builder_helper(type):
logger.debug(build_command)
# Run Sphinx with Sage's special logger
@ -44,10 +44,10 @@ index 79005b903a..fbe6fe2595 100644
if ABORT_ON_ERROR:
raise
diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py
index f58f6c61d7..ef51a55411 100644
index d917c3e9d4..551cc8028a 100644
--- a/src/sage_docbuild/sphinxbuild.py
+++ b/src/sage_docbuild/sphinxbuild.py
@@ -326,3 +326,8 @@ def runsphinx():
@@ -327,3 +327,8 @@ def runsphinx():
sys.stderr = saved_stderr
sys.stdout.flush()
sys.stderr.flush()

28
pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix Normal file
View file

@ -0,0 +1,28 @@
{ lib
, buildPythonPackage
, sage-src
, sphinx
}:
buildPythonPackage rec {
version = src.version;
pname = "sage-docbuild";
src = sage-src;
propagatedBuildInputs = [
sphinx
];
preBuild = ''
cd pkgs/sage-docbuild
'';
doCheck = false; # we will run tests in sagedoc.nix
meta = with lib; {
description = "Build system of the Sage documentation";
homepage = "https://www.sagemath.org";
license = licenses.gpl2Plus;
maintainers = teams.sage.members;
};
}

28
pkgs/applications/science/math/sage/python-modules/sage-setup.nix Normal file
View file

@ -0,0 +1,28 @@
{ lib
, buildPythonPackage
, sage-src
, pkgconfig # the python module, not the pkg-config alias
}:
buildPythonPackage rec {
version = src.version;
pname = "sage-setup";
src = sage-src;
buildInputs = [
pkgconfig
];
preBuild = ''
cd pkgs/sage-setup
'';
doCheck = false; # sagelib depends on sage-setup, but sage-setup's tests depend on sagelib
meta = with lib; {
description = "Build system of the Sage library";
homepage = "https://www.sagemath.org";
license = licenses.gpl2Plus;
maintainers = teams.sage.members;
};
}

11
pkgs/applications/science/math/sage/sage-env.nix
View file

@ -2,7 +2,7 @@
, lib
, writeTextFile
, sagelib
, sage_docbuild
, sage-docbuild
, env-locations
, gfortran
, bash
@ -45,11 +45,10 @@
, flint
, gmp
, mpfr
, pynac
, zlib
, gsl
, ntl
, jdk8
, jdk
, less
}:
@ -60,8 +59,6 @@ assert (!blas.isILP64) && (!lapack.isILP64);
# dependencies.
let
jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
runtimepath = (lib.makeBinPath ([
"@sage-local@"
"@sage-local@/build"
@ -163,7 +160,6 @@ writeTextFile rec {
gmp
mpfr
pari
pynac
zlib
eclib
gsl
@ -179,7 +175,6 @@ writeTextFile rec {
glpk
flint
gap
pynac
mpfr.dev
])
}'
@ -193,5 +188,5 @@ writeTextFile rec {
'';
} // { # equivalent of `passthru`, which `writeTextFile` doesn't support
lib = sagelib;
docbuild = sage_docbuild;
docbuild = sage-docbuild;
}

49
pkgs/applications/science/math/sage/sage-src.nix
View file

@ -57,14 +57,14 @@ let
);
in
stdenv.mkDerivation rec {
version = "9.4";
version = "9.5";
pname = "sage-src";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "sha256-jqkr4meG02KbTCMsGvyr1UbosS4ZuUJhPXU/InuS+9A=";
sha256 = "sha256-uOsLpsGpcIGs8Xr82X82MElnTB2E908gytyNJ8WVD5w=";
};
# Patches needed because of particularities of nix or the way this is packaged.
@ -117,46 +117,6 @@ stdenv.mkDerivation rec {
# Let's just assume warnings are expected until we update to 4.27.0.
./patches/fonttools-deprecation-warnings.patch
# https://trac.sagemath.org/ticket/32305
(fetchSageDiff {
base = "9.4";
name = "networkx-2.6-upgrade.patch";
rev = "9808325853ba9eb035115e5b056305a1c9d362a0";
sha256 = "sha256-gJSqycCtbAVr5qnVEbHFUvIuTOvaxFIeffpzd6nH4DE=";
})
# https://trac.sagemath.org/ticket/32420
(fetchSageDiff {
base = "9.5.beta2";
name = "sympy-1.9-update.patch";
rev = "beed4e16aff32e47d0c3b1c58cb1e2f4c38590f8";
sha256 = "sha256-3eJPfWfCrCAQ5filIn7FbzjRQeO9QyTIVl/HyRuqFtE=";
})
# https://trac.sagemath.org/ticket/32567
(fetchSageDiff {
base = "9.5.beta2";
name = "arb-2.21.0-update.patch";
rev = "eb3304dd521a3d5a9334e747a08e234bbf16b4eb";
sha256 = "sha256-XDkaY4VQGyESXI6zuD7nCNzyQOl/fmBFvAESH9+RRvk=";
})
# https://trac.sagemath.org/ticket/32797
(fetchSageDiff {
base = "9.5.beta7";
name = "pari-2.13.3-update.patch";
rev = "f5f7a86908daf60b25e66e6a189c51ada7e0a732";
sha256 = "sha256-H/caGx3q4KcdsyGe+ojV9bUTQ5y0siqM+QHgDbeEnbw=";
})
# https://trac.sagemath.org/ticket/32909
(fetchSageDiff {
base = "9.5.beta7";
name = "matplotlib-3.5-deprecation-warnings.patch";
rev = "a5127dc56fdf5c2e82f6bc781cfe78dbd04e97b7";
sha256 = "sha256-p23qUu9mgEUbdbX6cy7ArxZAtpcFjCKbgyxN4jWvj1o=";
})
# https://trac.sagemath.org/ticket/32968
(fetchSageDiff {
base = "9.5.beta8";
@ -164,6 +124,11 @@ stdenv.mkDerivation rec {
rev = "fc84f82f52b6f05f512cb359ec7c100f93cf8841";
sha256 = "sha256-bBbfdcnw/9LUOlY8rHJRbFJEdMXK4shosqTNaobTS1Q=";
})
# Upstream has not upgraded to linbox 1.7 yet because it conflicts with
# pre-4.2.1p3 versions of Singular, but we don't have this problem.
# https://trac.sagemath.org/ticket/32959
./patches/linbox-1.7-upgrade.patch
];
patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

6
pkgs/applications/science/math/sage/sage-with-env.nix
View file

@ -18,7 +18,6 @@
, eclib
, ntl
, ecm
, pynac
, pythonEnv
}:
@ -36,7 +35,6 @@ let
blas lapack
singular
three
pynac
giac
gap
pari
@ -126,6 +124,10 @@ stdenv.mkDerivation rec {
cp -r src/bin "$out/bin"
cp -r build/bin "$out/build/bin"
# sage assumes the existence of sage-src-env-config.in means it's being executed in-tree. in this case, it
# adds SAGE_SRC/bin to PATH, breaking our wrappers
rm "$out/bin"/*.in "$out/build/bin"/*.in
cp -f '${sage-env}/sage-env' "$out/bin/sage-env"
substituteInPlace "$out/bin/sage-env" \
--subst-var-by sage-local "$out"

3
pkgs/applications/science/math/sage/sage.nix
View file

@ -62,7 +62,8 @@ stdenv.mkDerivation rec {
meta = with lib; {
description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
license = licenses.gpl2;
homepage = "https://www.sagemath.org";
license = licenses.gpl2Plus;
maintainers = teams.sage.members;
};
}

20
pkgs/applications/science/math/sage/sage_docbuild.nix
View file

@ -1,20 +0,0 @@
{ buildPythonPackage
, sage-src
, sphinx
}:
buildPythonPackage rec {
version = src.version;
pname = "sage_docbuild";
src = sage-src;
propagatedBuildInputs = [
sphinx
];
preBuild = ''
cd build/pkgs/sage_docbuild/src
'';
doCheck = false; # we will run tests in sagedoc.nix
}

2
pkgs/applications/science/math/sage/sagedoc.nix
View file

@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
jmol
cddlib
] ++ (with python3.pkgs; [
sage_docbuild
sage-docbuild
psutil
future
sphinx

7
pkgs/applications/science/math/sage/sagelib.nix
View file

@ -38,7 +38,7 @@
, pkg-config
, planarity
, ppl
, pynac
, primecountpy
, python
, ratpoints
, readline
@ -50,6 +50,7 @@
, singular
, pip
, jupyter_core
, sage-setup
, libhomfly
, libbraiding
, gmpy2
@ -86,6 +87,7 @@ buildPythonPackage rec {
perl
jupyter_core
pkg-config
sage-setup
pip # needed to query installed packages
lisp-compiler
m4
@ -130,7 +132,7 @@ buildPythonPackage rec {
pari
planarity
ppl
pynac
primecountpy
rankwidth
ratpoints
singular
@ -181,6 +183,7 @@ buildPythonPackage rec {
# build/pkgs, either directly or via sage-get-system-packages.
sed -i 's/==2.1.0rc1/>=2.1.1/' ../gmpy2/install-requires.txt
sed -i 's/, <3.4//' ../rpy2/install-requires.txt
sed -i 's/, <4.3//' ../sphinx/install-requires.txt
sed -i '/sage_conf/d' src/setup.cfg.m4
sed -i '/sage_conf/d' src/requirements.txt.m4
for infile in src/*.m4; do