sage: 8.9 -> 9.2

This commit is contained in:
Masanori Ogino 2020-10-22 17:20:17 +09:00 committed by Mauricio Collares
parent dd95aa337e
commit 5c4136daf7
20 changed files with 66 additions and 437 deletions

View file

@ -9,30 +9,11 @@
let
inherit (pkgs) symlinkJoin callPackage nodePackages;
# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
python = pkgs.python2.override {
python = pkgs.python3.override {
packageOverrides = self: super: {
# python packages that appear unmaintained and were not accepted into the nixpkgs
# tree because of that. These packages are only dependencies of the more-or-less
# deprecated sagenb. However sagenb is still a default dependency and the doctests
# depend on it.
# See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
# The dependency on the sage notebook (and therefore these packages) will be
# removed in the future:
# https://trac.sagemath.org/ticket/25837
flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
flask-openid = self.callPackage ./flask-openid.nix {};
python-openid = self.callPackage ./python-openid.nix {};
sagenb = self.callPackage ./sagenb.nix {
mathjax = nodePackages.mathjax;
};
# Package with a cyclic dependency with sage
pybrial = self.callPackage ./pybrial.nix {};
# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
sagelib = self.callPackage ./sagelib.nix {
inherit flint ecl arb;
inherit flint arb;
inherit sage-src env-locations pynac singular;
linbox = pkgs.linbox.override { withSage = true; };
pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
@ -59,7 +40,7 @@ let
# A bash script setting various environment variables to tell sage where
# the files its looking fore are located. Also see `sage-env`.
env-locations = callPackage ./env-locations.nix {
inherit pari_data ecl;
inherit pari_data;
inherit singular maxima-ecl;
cysignals = python.pkgs.cysignals;
three = nodePackages.three;
@ -71,7 +52,7 @@ let
sage-env = callPackage ./sage-env.nix {
sagelib = python.pkgs.sagelib;
inherit env-locations;
inherit python ecl singular palp flint pynac pythonEnv maxima-ecl;
inherit python singular palp flint pynac pythonEnv maxima-ecl;
pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};
@ -102,8 +83,6 @@ let
pythonRuntimeDeps = with python.pkgs; [
sagelib
pybrial
sagenb
cvxopt
networkx
service-identity
@ -129,7 +108,6 @@ let
singular = pkgs.singular.override { inherit flint; };
# https://trac.sagemath.org/ticket/26625
maxima-ecl = pkgs.maxima-ecl;
# *not* to confuse with the python package "pynac"
@ -161,9 +139,6 @@ let
pari-seadata-small
];
};
# https://trac.sagemath.org/ticket/22191
ecl = pkgs.ecl_16_1_2;
in
# A wrapper around sage that makes sure sage finds its docs (if they were build).
callPackage ./sage.nix {

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@ -1,36 +0,0 @@
{ stdenv
, buildPythonPackage
, fetchFromGitHub
, python
, flask
}:
buildPythonPackage rec {
pname = "Flask-OldSessions";
version = "0.10";
# no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1
src = fetchFromGitHub {
owner = "mitsuhiko";
repo = "flask-oldsessions";
rev = version;
sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn";
};
propagatedBuildInputs = [
flask
];
# missing module flask.testsuite, probably assumes an old version of flask
doCheck = false;
checkPhase = ''
${python.interpreter} run-tests.py
'';
meta = with stdenv.lib; {
description = "Provides a session class that works like the one in Flask before 0.10.";
license = licenses.bsd2;
maintainers = teams.sage.members;
homepage = "https://github.com/mitsuhiko/flask-oldsessions";
};
}

View file

@ -1,28 +0,0 @@
{ stdenv
, buildPythonPackage
, fetchPypi
, flask
, python-openid
}:
buildPythonPackage rec {
pname = "Flask-OpenID";
version = "1.2.5";
src = fetchPypi {
inherit pname version;
sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss";
};
propagatedBuildInputs = [
flask
python-openid
];
meta = with stdenv.lib; {
description = "Adds openid support to flask applications";
license = licenses.bsd2;
maintainers = teams.sage.members;
homepage = "https://pythonhosted.org/Flask-OpenID/";
};
}

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@ -1,17 +1,17 @@
From 8218bd4fdeb4c92de8af0d3aabec55980fc4fb3d Mon Sep 17 00:00:00 2001
From f5ea42a7aaed7611fb55b65897b9fcf2b7bcf97e Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Sun, 21 Oct 2018 17:52:40 +0200
Subject: [PATCH] Only test py2/py3 optional tests when all of sage is tested
---
src/sage/doctest/control.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
src/sage/doctest/control.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
index bf18df8b2b..935c67abf7 100644
index 2d93841e50..6d156e29a1 100644
--- a/src/sage/doctest/control.py
+++ b/src/sage/doctest/control.py
@@ -362,7 +362,8 @@ class DocTestController(SageObject):
@@ -375,7 +375,8 @@ class DocTestController(SageObject):
if not optionaltag_regex.search(o):
raise ValueError('invalid optional tag {!r}'.format(o))
@ -21,15 +21,6 @@ index bf18df8b2b..935c67abf7 100644
self.options = options
@@ -765,7 +766,7 @@ class DocTestController(SageObject):
sage: DC = DocTestController(DD, [dirname])
sage: DC.expand_files_into_sources()
sage: sorted(DC.sources[0].options.optional) # abs tol 1
- ['guava', 'magma', 'py2']
+ ['guava', 'magma']
We check that files are skipped appropriately::
--
2.18.1
2.28.0

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@ -1,17 +1,17 @@
diff --git a/src/sage/env.py b/src/sage/env.py
index 061b94f3f1..67cd091540 100644
index 1ddfc7cfb9..45033d6328 100644
--- a/src/sage/env.py
+++ b/src/sage/env.py
@@ -189,88 +189,13 @@ var('MAXIMA_FAS')
@@ -203,97 +203,13 @@ var('ARB_LIBRARY', 'arb')
var('SAGE_BANNER', '')
var('SAGE_IMPORTALL', 'yes')
-
-def _get_shared_lib_filename(libname, *additional_libnames):
- """
- Return the full path to a shared library file installed in the standard
- location for the system within the ``LIBDIR`` prefix (or
- ``$SAGE_LOCAL/lib`` in the case of manual build of Sage).
- Return the full path to a shared library file installed in
- ``$SAGE_LOCAL/lib`` or the directories associated with the
- Python sysconfig.
-
- This can also be passed more than one library name (e.g. for cases where
- some library may have multiple names depending on the platform) in which
@ -25,7 +25,7 @@ index 061b94f3f1..67cd091540 100644
- For distributions like Debian that use a multiarch layout, we also try the
- multiarch lib paths (i.e. ``/usr/lib/<arch>/``).
-
- Returns ``None`` if the file does not exist.
- This returns ``None`` if the file does not exist.
-
- EXAMPLES::
-
@ -48,11 +48,17 @@ index 061b94f3f1..67cd091540 100644
-
- for libname in (libname,) + additional_libnames:
- if sys.platform == 'cygwin':
- bindir = sysconfig.get_config_var('BINDIR')
- # Later down we take the last matching DLL found, so search
- # SAGE_LOCAL second so that it takes precedence
- bindirs = [
- sysconfig.get_config_var('BINDIR'),
- os.path.join(SAGE_LOCAL, 'bin')
- ]
- pats = ['cyg{}.dll'.format(libname), 'cyg{}-*.dll'.format(libname)]
- filenames = []
- for pat in pats:
- filenames += glob.glob(os.path.join(bindir, pat))
- for bindir in bindirs:
- for pat in pats:
- filenames += glob.glob(os.path.join(bindir, pat))
-
- # Note: This is not very robust, since if there are multi DLL
- # versions for the same library this just selects one more or less
@ -66,10 +72,13 @@ index 061b94f3f1..67cd091540 100644
- else:
- ext = 'so'
-
- libdirs = [sysconfig.get_config_var('LIBDIR')]
- libdirs = [
- os.path.join(SAGE_LOCAL, 'lib'),
- sysconfig.get_config_var('LIBDIR')
- ]
- multilib = sysconfig.get_config_var('MULTILIB')
- if multilib:
- libdirs.insert(0, os.path.join(libdirs[0], multilib))
- libdirs.insert(1, os.path.join(libdirs[0], multilib))
-
- for libdir in libdirs:
- basename = 'lib{}.{}'.format(libname, ext)
@ -89,7 +98,7 @@ index 061b94f3f1..67cd091540 100644
# locate libgap shared object
-GAP_SO= _get_shared_lib_filename('gap','')
+GAP_SO= '/default'
+GAP_SO = '/default'
var('GAP_SO', GAP_SO)
# post process

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@ -1,24 +0,0 @@
diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py
index 4849c2bffa..76b7bc8602 100644
--- a/src/sage/misc/sphinxify.py
+++ b/src/sage/misc/sphinxify.py
@@ -25,6 +25,7 @@ from __future__ import absolute_import, print_function
import os
import re
import shutil
+import warnings
from tempfile import mkdtemp
from sphinx.application import Sphinx
@@ -120,7 +121,10 @@ smart_quotes = no""")
# buildername, confoverrides, status, warning, freshenv).
sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format,
confoverrides, None, None, True)
- sphinx_app.build(None, [rst_name])
+ with warnings.catch_warnings():
+ # Quick and dirty workaround for https://trac.sagemath.org/ticket/28856#comment:19
+ warnings.simplefilter("ignore")
+ sphinx_app.build(None, [rst_name])
sys.path = old_sys_path
# We need to remove "_" from __builtin__ that the gettext module installs

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@ -1,24 +1,24 @@
diff --git a/src/sage/tests/cmdline.py b/src/sage/tests/cmdline.py
index bd6b76ab82..ccf1203dec 100644
index 6e034dcb5a..8ec60ec72b 100644
--- a/src/sage/tests/cmdline.py
+++ b/src/sage/tests/cmdline.py
@@ -837,8 +837,6 @@ def test_executable(args, input="", timeout=100.0, **kwds):
@@ -660,8 +660,8 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False
sage: with open(input, 'w') as F:
....: _ = F.write(s)
sage: L = ["sage", "--rst2ipynb", input, output]
- sage: test_executable(L) # optional - rst2ipynb
- ('', '', 0)
+ sage: test_executable(L)[2] # optional - rst2ipynb
+ 0
sage: import json # optional - rst2ipynb
sage: d = json.load(open(output,'r')) # optional - rst2ipynb
sage: type(d) # optional - rst2ipynb
@@ -757,8 +757,6 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False
///
4
}}}
- sage: err # py2
- sage: err # py2 # optional -- sagenb
- ''
sage: ret
sage: ret # py2 # optional -- sagenb
0
@@ -871,8 +869,8 @@ def test_executable(args, input="", timeout=100.0, **kwds):
sage: output = tmp_filename(ext='.sws')
sage: with open(input, 'w') as F:
....: _ = F.write(s)
- sage: test_executable(["sage", "--rst2sws", input, output]) # py2
- ('', '', 0)
+ sage: test_executable(["sage", "--rst2sws", input, output])[2] # py2
+ 0
sage: import tarfile # py2
sage: f = tarfile.open(output, 'r') # py2
sage: print(f.extractfile('sage_worksheet/worksheet.html').read()) # py2

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@ -1,12 +0,0 @@
diff --git a/src/sage/all.py b/src/sage/all.py
index c87c9372e9..862fca4fcc 100644
--- a/src/sage/all.py
+++ b/src/sage/all.py
@@ -306,6 +306,7 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0))
# Ignore all deprecations from IPython etc.
warnings.filterwarnings('ignore', category=DeprecationWarning,
module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)')
+warnings.filterwarnings('ignore', category=DeprecationWarning, message=r".*The import 'werkzeug.ImmutableDict' is deprecated")
# Ignore collections.abc warnings, there are a lot of them but they are
# harmless.
warnings.filterwarnings('ignore', category=DeprecationWarning,

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@ -1,20 +0,0 @@
diff --git a/src/sage/doctest/parsing.py b/src/sage/doctest/parsing.py
index 6bdc9a0..31fc780 100644
--- a/src/sage/doctest/parsing.py
+++ b/src/sage/doctest/parsing.py
@@ -40,6 +40,7 @@ from .external import available_software
float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)')
optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
+pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.')
find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
random_marker = re.compile('.*random', re.I)
@@ -935,6 +936,7 @@ class SageOutputChecker(doctest.OutputChecker):
<type 'float'>
"""
got = self.human_readable_escape_sequences(got)
+ got = pari_stack_warning_regex.sub('', got)
if isinstance(want, MarkedOutput):
if want.random:
return True

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@ -1,28 +0,0 @@
diff --git a/src/sage/all.py b/src/sage/all.py
index ca309ef..be3186b 100644
--- a/src/sage/all.py
+++ b/src/sage/all.py
@@ -298,6 +298,23 @@ warnings.filterwarnings('ignore', module='matplotlib[.]font_manager')
warnings.filterwarnings('default',
'[\s\S]*See http://trac.sagemath.org/[0-9]* for details.')
+# Hotpatch around https://bugs.python.org/issue5755 which won't be fixed for
+# python 2.7. Idea by https://stackoverflow.com/a/36293331.
+from distutils.command.build_ext import build_ext
+from distutils.sysconfig import customize_compiler
+
+_build_extensions = build_ext.build_extensions
+
+def build_extensions_patched(self):
+ customize_compiler(self.compiler)
+ try:
+ self.compiler.compiler_so.remove("-Wstrict-prototypes")
+ except (AttributeError, ValueError):
+ pass
+ _build_extensions(self)
+
+build_ext.build_extensions = build_extensions_patched
+
# Set a new random number seed as the very last thing
# (so that printing initial_seed() and using that seed

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@ -1,13 +0,0 @@
diff --git a/sagenb/__init__.py b/sagenb/__init__.py
index 4db0d2cb..2fc5f01e 100644
--- a/sagenb/__init__.py
+++ b/sagenb/__init__.py
@@ -1,3 +1,8 @@
# -*- coding: utf-8 -*
# init
+import warnings
from . import storage
+
+# deprecation in attrs, needs to be fixed in twisted
+warnings.filterwarnings('ignore', category=DeprecationWarning,
+ message=r'The usage of `cmp` is deprecated and will be removed.*')

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@ -1,5 +1,5 @@
diff --git a/src/sage/lfunctions/sympow.py b/src/sage/lfunctions/sympow.py
index 1640ac4f6a..03578be7b8 100644
index 92cb01fd73..b123e6accc 100644
--- a/src/sage/lfunctions/sympow.py
+++ b/src/sage/lfunctions/sympow.py
@@ -50,6 +50,7 @@ from __future__ import print_function, absolute_import
@ -8,14 +8,14 @@ index 1640ac4f6a..03578be7b8 100644
+from sage.env import DOT_SAGE
from sage.structure.sage_object import SageObject
from sage.misc.all import pager, verbose
import sage.rings.all
@@ -76,7 +77,7 @@ class Sympow(SageObject):
from sage.misc.all import pager
from sage.misc.verbose import verbose
@@ -78,7 +79,7 @@ class Sympow(SageObject):
"""
Used to call sympow with given args
"""
- cmd = 'sympow %s'%args
- cmd = 'sympow %s' % args
+ cmd = 'env SYMPOW_CACHEDIR="%s/sympow///" sympow %s' % (DOT_SAGE, args)
v = os.popen(cmd).read().strip()
with os.popen(cmd) as f:
v = f.read().strip()
verbose(v, level=2)
return v

View file

@ -1,25 +0,0 @@
{ stdenv
, fetchFromGitHub
, buildPythonPackage
, brial
}:
# This has a cyclic dependency with sage. I don't include sage in the
# buildInputs and let python figure it out at runtime. Because of this,
# I don't include the package in the main nipxkgs tree. It wouldn't be useful
# outside of sage anyways (as you could just directly depend on sage and use
# it).
buildPythonPackage rec {
pname = "pyBRiAl";
version = brial.version;
# included with BRiAl source
src = brial.src;
sourceRoot = "source/sage-brial";
meta = with stdenv.lib; {
description = "python implementation of BRiAl";
license = licenses.gpl2;
maintainers = teams.sage.members;
};
}

View file

@ -1,40 +0,0 @@
{ stdenv
, buildPythonPackage
, fetchPypi
, isPy3k
, django
, nose
, twill
, pycrypto
}:
buildPythonPackage rec {
pname = "python-openid";
version = "2.2.5";
disabled = isPy3k;
src = fetchPypi {
inherit pname version;
sha256 = "1vvhxlghjan01snfdc4k7ykd80vkyjgizwgg9bncnin8rqz1ricj";
};
propagatedBuildInputs = [
pycrypto
];
# Cannot access the djopenid example module.
# I don't know how to fix that (adding the examples dir to PYTHONPATH doesn't work)
doCheck = false;
checkInputs = [ nose django twill ];
checkPhase = ''
nosetests
'';
meta = with stdenv.lib; {
description = "OpenID library for Python";
license = licenses.asl20;
maintainers = teams.sage.members;
homepage = "https://github.com/openid/python-openid/";
};
}

View file

@ -10,44 +10,23 @@
# all get the same sources with the same patches applied.
stdenv.mkDerivation rec {
version = "8.9";
version = "9.2";
pname = "sage-src";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "1bwga58x3s8z42w5h51c232f91ndsc1861dlb1glhax3pn0rhn3a";
sha256 = "103j8d5x6szl9fxaz0dvdi4y47q1af9h9y5hmjh2xayi62qmp5ql";
};
# Patches needed because of particularities of nix or the way this is packaged.
# The goal is to upstream all of them and get rid of this list.
nixPatches = [
# https://trac.sagemath.org/ticket/25358
(fetchpatch {
name = "safe-directory-test-without-patch.patch";
url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=dc673c17555efca611f68398d5013b66e9825463";
sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7";
})
# `is_unitary` test in `matrix_double_dense.pyx` fails with some BLAS implementations
# https://trac.sagemath.org/ticket/29297 should be included in 9.1
(fetchpatch {
name = "is_unitary-special-case.patch";
url = "https://git.sagemath.org/sage.git/patch?id=cc3eb9ffa991e328b09028d32aab7e7cc2ddbb6a";
sha256 = "0jq4w8hnp5c9q99011ldr4n3knvm1rx2g85z0hidv3i9x868p0ay";
})
# Unfortunately inclusion in upstream sage was rejected. Instead the bug was
# fixed in python, but of course not backported to 2.7. So we'll probably
# have to keep this around until 2.7 is deprecated.
# https://trac.sagemath.org/ticket/25316
# https://github.com/python/cpython/pull/7476
./patches/python-5755-hotpatch.patch
# Make sure py2/py3 tests are only run when their expected context (all "sage"
# tests) are also run. That is necessary to test dochtml individually. See
# https://trac.sagemath.org/ticket/26110 for an upstream discussion.
# TODO: Determine if it is still necessary.
./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
# Fixes a potential race condition which can lead to transient doctest failures.
@ -60,11 +39,6 @@ stdenv.mkDerivation rec {
# Parallelize docubuild using subprocesses, fixing an isolation issue. See
# https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
./patches/sphinx-docbuild-subprocesses.patch
# Fix doctest failures with docutils 0.15:
# https://nix-cache.s3.amazonaws.com/log/dzmzrb2zvardsmpy7idg7djkizmkzdhs-sage-tests-8.9.drv
# https://trac.sagemath.org/ticket/28856#comment:19
./patches/docutils-0.15.patch
];
# Since sage unfortunately does not release bugfix releases, packagers must
@ -96,55 +70,13 @@ stdenv.mkDerivation rec {
} // builtins.removeAttrs args [ "rev" "base" ])
);
in [
# New glpk version has new warnings, filter those out until upstream sage has found a solution
# Should be fixed with glpk > 4.65.
# https://trac.sagemath.org/ticket/24824
./patches/pari-stackwarn.patch # not actually necessary since the pari upgrade, but necessary for the glpk patch to apply
(fetchpatch {
url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/dt-version-glpk-4.65-ignore-warnings.patch";
sha256 = "0b9293v73wb4x13wv5zwyjgclc01zn16msccfzzi6znswklgvddp";
stripLen = 1;
})
# After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
# now set the cache dir to be withing the .sage directory. This is not
# strictly necessary, but keeps us from littering in the user's HOME.
./patches/sympow-cache.patch
# https://trac.sagemath.org/ticket/28472
(fetchpatch {
name = "eclib-20190909.patch";
url = "https://git.sagemath.org/sage.git/patch?id=d27dc479a5772d59e4bc85d805b6ffd595284f1d";
sha256 = "1nf1s9y7n30lhlbdnam7sghgaq9nasmv96415gl5jlcf7a3hlxk3";
})
# ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests
./patches/ignore-cmp-deprecation.patch
# Werkzeug has deprecated ImmutableDict, but it is still used in legacy
# sagenb. That's no big issue since sagenb will be removed soon anyways.
./patches/ignore-werkzeug-immutable-dict-deprecation.patch
# threejs r109 (#28560)
(fetchpatch {
name = "threejs-r109.patch";
url = "https://git.sagemath.org/sage.git/patch?id=fcc11d6effa39f375bc5f4ea5831fb7a2f2767da";
sha256 = "0hnmc8ld3bblks0hcjvjjaydkgwdr1cs3dbl2ys4gfq964pjgqwc";
})
# https://trac.sagemath.org/ticket/28911
(fetchpatch {
name = "sympy-1.5.patch";
url = "https://git.sagemath.org/sage.git/patch/?h=c6d0308db15efd611211d26cfcbefbd180fc0831";
sha256 = "0nwai2jr22h49km4hx3kwafs3mzsc5kwsv7mqwjf6ibwfx2bbgyq";
})
# https://trac.sagemath.org/ticket/29313 (patch from ArchLinux)
(fetchpatch {
name = "pari-2.11.3.patch";
url = "https://aur.archlinux.org/cgit/aur.git/plain/sagemath-pari-2.11.3.patch?h=sagemath-git&id=02e1d58bd1cd70935d69a4990469d18be6bd2c43";
sha256 = "0z07444zvijyw96d11q7j81pvg7ysd6ycf1bbbjr6za9y74hv7d2";
})
];
patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

View file

@ -13,7 +13,7 @@
, pari
, gmp
, gfan
, python2
, python3
, flintqs
, eclib
, ntl
@ -54,7 +54,7 @@ let
pkg_to_spkg_name = pkg: patch_names: let
parts = lib.splitString "-" pkg.name;
# remove python2.7-
stripped_parts = if (builtins.head parts) == python2.libPrefix then builtins.tail parts else parts;
stripped_parts = if (builtins.head parts) == python3.libPrefix then builtins.tail parts else parts;
version = lib.last stripped_parts;
orig_pkgname = lib.init stripped_parts;
pkgname = patch_names (lib.concatStringsSep "_" orig_pkgname);
@ -126,6 +126,8 @@ stdenv.mkDerivation rec {
cp -r src/bin "$out/bin"
cp -r build/bin "$out/build/bin"
ln -s "${python3}/bin/python3" "$out/bin/python3"
cp -f '${sage-env}/sage-env' "$out/bin/sage-env"
substituteInPlace "$out/bin/sage-env" \
--subst-var-by sage-local "$out"

View file

@ -61,7 +61,6 @@ stdenv.mkDerivation rec {
};
meta = with stdenv.lib; {
broken = true;
description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
license = licenses.gpl2;
maintainers = teams.sage.members;

View file

@ -26,7 +26,6 @@ stdenv.mkDerivation rec {
psutil
future
sphinx
sagenb
scipy
sympy
matplotlib
@ -36,7 +35,6 @@ stdenv.mkDerivation rec {
ipywidgets
jupyter_client
typing
pybrial
]);
unpackPhase = ''

View file

@ -15,6 +15,7 @@
, ecm
, flint
, gd
, giac
, givaro
, glpk
, gsl
@ -51,6 +52,8 @@
, libbraiding
, gmpy2
, pplpy
, sqlite
, boehmgc # FIXME
}:
assert (!blas.isILP64) && (!lapack.isILP64);
@ -94,6 +97,7 @@ buildPythonPackage rec {
ecm
fflas-ffpack
flint
giac
givaro
glpk
gsl
@ -124,6 +128,8 @@ buildPythonPackage rec {
libbraiding
gmpy2
pplpy
sqlite
boehmgc # FIXME
];
buildPhase = ''

View file

@ -1,57 +0,0 @@
{ stdenv
, python
, buildPythonPackage
, fetchFromGitHub
, mathjax
, twisted
, flask
, flask-oldsessions
, flask-openid
, flask-autoindex
, flask-babel
}:
# Has a cyclic dependency with sage (not expressed here) and is not useful outside of sage.
# Deprecated, hopefully soon to be removed. See
# https://trac.sagemath.org/ticket/25837
buildPythonPackage rec {
pname = "sagenb";
version = "1.1.2";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sagenb";
rev = version;
sha256 = "0bxvhr03qh2nsjdfc4pyfiqrn9jhp3vf7irsc9gqx0185jlblbxs";
};
patches = [
# cmp deprecation in attrs needs to be handled in twisted
./patches/sagenb-cmp-deprecation.patch
];
propagatedBuildInputs = [
twisted
flask
flask-oldsessions
flask-openid
flask-autoindex
flask-babel
];
# tests depend on sage
doCheck = false;
meta = with stdenv.lib; {
description = "Sage Notebook";
license = licenses.gpl3Plus;
maintainers = teams.sage.members;
};
# let sagenb use mathjax
postInstall = ''
mkdir -p "$out/${python.sitePackages}/sagenb/data"
ln -s ${mathjax}/lib/node_modules/mathjax "$out/${python.sitePackages}/sagenb/data/mathjax"
'';
}