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sage: 9.8 -> 10.0

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This commit is contained in:
Mauricio Collares 2023-02-16 14:26:09 +01:00
parent 19bf4ba0e0
commit 0edaaae3ff
9 changed files with 135 additions and 469 deletions
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2
pkgs/applications/science/math/sage/default.nix
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@ -128,7 +128,7 @@ let
singular = pkgs.singular.override { inherit flint; };
maxima = pkgs.maxima-ecl-5_45.override {
maxima = pkgs.maxima-ecl.override {
lisp-compiler = pkgs.ecl.override {
# "echo syntax error | ecl > /dev/full 2>&1" segfaults in
# ECL. We apply a patch to fix it (write_error.patch), but it

19
pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
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@ -1,19 +0,0 @@
diff --git a/src/sage/repl/configuration.py b/src/sage/repl/configuration.py
index 67d7d2accf..18279581e2 100644
--- a/src/sage/repl/configuration.py
+++ b/src/sage/repl/configuration.py
@@ -9,10 +9,11 @@ the IPython simple prompt is being used::
sage: cmd = 'print([sys.stdin.isatty(), sys.stdout.isatty()])'
sage: import pexpect
sage: output = pexpect.run(
- ....: 'bash -c \'echo "{0}" | sage\''.format(cmd),
+ ....: 'bash -c \'export SAGE_BANNER=no; echo "{0}" | sage\''.format(cmd),
....: ).decode('utf-8', 'surrogateescape')
- sage: 'sage: [False, True]' in output
- True
+ sage: print(output)
+ sage...[False, True]
+ ...
"""
#*****************************************************************************

87
pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
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@ -1,87 +0,0 @@
diff --git a/src/sage/env.py b/src/sage/env.py
index c4953cfa65..47b880f9ad 100644
--- a/src/sage/env.py
+++ b/src/sage/env.py
@@ -244,81 +244,8 @@ os.environ['MPMATH_SAGE'] = '1'
SAGE_BANNER = var("SAGE_BANNER", "")
SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes")
-
-def _get_shared_lib_path(*libnames: str) -> Optional[str]:
- """
- Return the full path to a shared library file installed in
- ``$SAGE_LOCAL/lib`` or the directories associated with the
- Python sysconfig.
-
- This can also be passed more than one library name (e.g. for cases where
- some library may have multiple names depending on the platform) in which
- case the first one found is returned.
-
- This supports most *NIX variants (in which ``lib<libname>.so`` is found
- under ``$SAGE_LOCAL/lib``), macOS (same, but with the ``.dylib``
- extension), and Cygwin (under ``$SAGE_LOCAL/bin/cyg<libname>.dll``,
- or ``$SAGE_LOCAL/bin/cyg<libname>-*.dll`` for versioned DLLs).
-
- For distributions like Debian that use a multiarch layout, we also try the
- multiarch lib paths (i.e. ``/usr/lib/<arch>/``).
-
- This returns ``None`` if no matching library file could be found.
-
- EXAMPLES::
-
- sage: from sage.env import _get_shared_lib_path
- sage: "gap" in _get_shared_lib_path("gap")
- True
- sage: _get_shared_lib_path("an_absurd_lib") is None
- True
-
- """
-
- for libname in libnames:
- search_directories: List[Path] = []
- patterns: List[str] = []
- if sys.platform == 'cygwin':
- # Later down we take the first matching DLL found, so search
- # SAGE_LOCAL first so that it takes precedence
- if SAGE_LOCAL:
- search_directories.append(Path(SAGE_LOCAL) / 'bin')
- search_directories.append(Path(sysconfig.get_config_var('BINDIR')))
- # Note: The following is not very robust, since if there are multible
- # versions for the same library this just selects one more or less
- # at arbitrary. However, practically speaking, on Cygwin, there
- # will only ever be one version
- patterns = [f'cyg{libname}.dll', f'cyg{libname}-*.dll']
- else:
- if sys.platform == 'darwin':
- ext = 'dylib'
- else:
- ext = 'so'
-
- if SAGE_LOCAL:
- search_directories.append(Path(SAGE_LOCAL) / 'lib')
- libdir = sysconfig.get_config_var('LIBDIR')
- if libdir is not None:
- libdir = Path(libdir)
- search_directories.append(libdir)
-
- multiarchlib = sysconfig.get_config_var('MULTIARCH')
- if multiarchlib is not None:
- search_directories.append(libdir / multiarchlib),
-
- patterns = [f'lib{libname}.{ext}']
-
- for directory in search_directories:
- for pattern in patterns:
- path = next(directory.glob(pattern), None)
- if path is not None:
- return str(path.resolve())
-
- # Just return None if no files were found
- return None
-
# locate libgap shared object
-GAP_SO = var("GAP_SO", _get_shared_lib_path("gap", ""))
+GAP_SO = var("GAP_SO", '/default')
# post process
if DOT_SAGE is not None and ' ' in DOT_SAGE:

19
pkgs/applications/science/math/sage/patches/fix-ecl-race.patch
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@ -1,19 +0,0 @@
diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
index 02e18e67e7..2ebf6eb35f 100644
--- a/src/sage/doctest/forker.py
+++ b/src/sage/doctest/forker.py
@@ -1075,6 +1075,14 @@ class SageDocTestRunner(doctest.DocTestRunner, object):
sage: set(ex2.predecessors) == set([ex0,ex1])
True
"""
+
+ # Fix ECL dir race conditions by using a separate dir for each process
+ # (https://trac.sagemath.org/ticket/26968)
+ os.environ['MAXIMA_USERDIR'] = "{}/sage-maxima-{}".format(
+ tempfile.gettempdir(),
+ os.getpid()
+ )
+
if isinstance(globs, RecordingDict):
globs.start()
example.sequence_number = len(self.history)

58
pkgs/applications/science/math/sage/patches/numpy-1.24-upgrade.patch
View File

@ -1,58 +0,0 @@
diff --git a/src/sage/misc/persist.pyx b/src/sage/misc/persist.pyx
index 3ac5f1cc2b..cb1f327c19 100644
--- a/src/sage/misc/persist.pyx
+++ b/src/sage/misc/persist.pyx
@@ -157,7 +157,7 @@ def load(*filename, compress=True, verbose=True, **kwargs):
....: _ = f.write(code)
sage: load(t)
sage: hello
- <fortran object>
+ <fortran ...>
"""
import sage.repl.load
if len(filename) != 1:
diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
index 6f0aeab87a..b77c69b2f7 100644
--- a/src/sage/plot/complex_plot.pyx
+++ b/src/sage/plot/complex_plot.pyx
@@ -461,6 +461,8 @@ def complex_to_rgb(z_values, contoured=False, tiled=False,
rgb[i, j, 2] = b
sig_off()
+ nan_indices = np.isnan(rgb).any(-1) # Mask for undefined points
+ rgb[nan_indices] = 1 # Make nan_indices white
return rgb
diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
index 3bc2b76b58..388c2d1391 100644
--- a/src/sage/plot/histogram.py
+++ b/src/sage/plot/histogram.py
@@ -87,13 +87,8 @@ class Histogram(GraphicPrimitive):
TESTS::
- sage: h = histogram([10,3,5], normed=True)[0]
- doctest:warning...:
- DeprecationWarning: the 'normed' option is deprecated. Use 'density' instead.
- See https://trac.sagemath.org/25260 for details.
+ sage: h = histogram([10,3,5], density=True)[0]
sage: h.get_minmax_data()
- doctest:warning ...
- ...VisibleDeprecationWarning: Passing `normed=True` on non-uniform bins has always been broken, and computes neither the probability density function nor the probability mass function. The result is only correct if the bins are uniform, when density=True will produce the same result anyway. The argument will be removed in a future version of numpy.
{'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
"""
import numpy
diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 798671aab4..cad6a47ca8 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -405,7 +405,7 @@ class SageMagics(Magics):
....: C END FILE FIB1.F
....: ''')
sage: fib
- <fortran object>
+ <fortran ...>
sage: from numpy import array
sage: a = array(range(10), dtype=float)
sage: fib(a, 10)

82
pkgs/applications/science/math/sage/patches/tachyon-renamed-focallength.patch
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@ -1,82 +0,0 @@
diff --git a/src/sage/interfaces/tachyon.py b/src/sage/interfaces/tachyon.py
index 23671e5089..a5604a643c 100644
--- a/src/sage/interfaces/tachyon.py
+++ b/src/sage/interfaces/tachyon.py
@@ -74,14 +74,14 @@ Camera projection modes
The ``PROJECTION`` keyword must be followed by one of the supported
camera projection mode identifiers ``PERSPECTIVE``, ``PERSPECTIVE_DOF``,
``ORTHOGRAPHIC``, or ``FISHEYE``. The ``FISHEYE`` projection mode
-requires two extra parameters ``FOCALLENGTH`` and ``APERTURE`` which
+requires two extra parameters ``FOCALDIST`` and ``APERTURE`` which
precede the regular camera options.
::
Camera
projection perspective_dof
- focallength 0.75
+ focaldist 0.75
aperture 0.02
Zoom 0.666667
Aspectratio 1.000000
diff --git a/src/sage/plot/plot3d/tachyon.py b/src/sage/plot/plot3d/tachyon.py
index 88c8eba2d5..c4427dd484 100644
--- a/src/sage/plot/plot3d/tachyon.py
+++ b/src/sage/plot/plot3d/tachyon.py
@@ -92,7 +92,7 @@ angle, right angle)::
Finally there is the ``projection='perspective_dof'`` option. ::
sage: T = Tachyon(xres=800, antialiasing=4, raydepth=10,
- ....: projection='perspective_dof', focallength='1.0', aperture='.0025')
+ ....: projection='perspective_dof', focaldist='1.0', aperture='.0025')
sage: T.light((0,5,7), 1.0, (1,1,1))
sage: T.texture('t1', opacity=1, specular=.3)
sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
@@ -186,7 +186,7 @@ class Tachyon(WithEqualityById, SageObject):
or ``'fisheye'``.
- ``frustum`` - (default ''), otherwise list of four numbers. Only
used with projection='fisheye'.
- - ``focallength`` - (default ''), otherwise a number. Only used
+ - ``focaldist`` - (default ''), otherwise a number. Only used
with projection='perspective_dof'.
- ``aperture`` - (default ''), otherwise a number. Only used
with projection='perspective_dof'.
@@ -331,7 +331,7 @@ class Tachyon(WithEqualityById, SageObject):
Use of the ``projection='perspective_dof'`` option. This may not be
implemented correctly. ::
- sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focallength='1.0', aperture='.0025')
+ sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focaldist='1.0', aperture='.0025')
sage: T.light((0,5,7), 1.0, (1,1,1))
sage: T.texture('t1', opacity=1, specular=.3)
sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
@@ -365,7 +365,7 @@ class Tachyon(WithEqualityById, SageObject):
look_at=[0, 0, 0],
viewdir=None,
projection='PERSPECTIVE',
- focallength='',
+ focaldist='',
aperture='',
frustum=''):
r"""
@@ -391,7 +391,7 @@ class Tachyon(WithEqualityById, SageObject):
self._camera_position = (-3, 0, 0) # default value
self._updir = updir
self._projection = projection
- self._focallength = focallength
+ self._focaldist = focaldist
self._aperture = aperture
self._frustum = frustum
self._objects = []
@@ -624,9 +624,9 @@ class Tachyon(WithEqualityById, SageObject):
camera_out = r"""
camera
projection %s""" % (tostr(self._projection))
- if self._focallength != '':
+ if self._focaldist != '':
camera_out = camera_out + r"""
- focallength %s""" % (float(self._focallength))
+ focaldist %s""" % (float(self._focaldist))
if self._aperture != '':
camera_out = camera_out + r"""
aperture %s""" % (float(self._aperture))

6
pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix
View File

@ -1,8 +1,9 @@
{ lib
, buildPythonPackage
, sage-src
, sphinx
, jupyter-sphinx
, sphinx
, sphinx-copybutton
}:
buildPythonPackage rec {
@ -11,8 +12,9 @@ buildPythonPackage rec {
src = sage-src;
propagatedBuildInputs = [
sphinx
jupyter-sphinx
sphinx
sphinx-copybutton
];
preBuild = ''

156
pkgs/applications/science/math/sage/sage-src.nix
View File

@ -8,87 +8,41 @@
# This is done because multiple derivations rely on these sources and they should
# all get the same sources with the same patches applied.
let
# Fetch a diff between `base` and `rev` on sage's git server.
# Used to fetch trac tickets by setting the `base` to the last release and the
# `rev` to the last commit of the ticket.
#
# We don't use sage's own build system (which builds all its
# dependencies), so we exclude changes to "build/" from patches by
# default to avoid conflicts.
fetchSageDiff = { base, name, rev, sha256, squashed ? false, excludes ? [ "build/*" ]
, ...}@args: (
fetchpatch ({
inherit name sha256 excludes;
# There are three places to get changes from:
#
# 1) From Sage's Trac. Contains all release tags (like "9.4") and all developer
# branches (wip patches from tickets), but exports each commit as a separate
# patch, so merge commits can lead to conflicts. Used if squashed == false.
#
# The above is the preferred option. To use it, find a Trac ticket and pass the
# "Commit" field from the ticket as "rev", choosing "base" as an appropriate
# release tag, i.e. a tag that doesn't cause the patch to include a lot of
# unrelated changes. If there is no such tag (due to nonlinear history, for
# example), there are two other options, listed below.
#
# 2) From GitHub's sagemath/sage repo. This lets us use a GH feature that allows
# us to choose between a .patch file, with one patch per commit, or a .diff file,
# which squashes all commits into a single diff. This is used if squashed ==
# true. This repo has all release tags. However, it has no developer branches, so
# this option can't be used if a change wasn't yet shipped in a (possibly beta)
# release.
#
# 3) From GitHub's sagemath/sagetrac-mirror repo. Mirrors all developer branches,
# but has no release tags. The only use case not covered by 1 or 2 is when we need
# to apply a patch from an open ticket that contains merge commits.
#
# Item 3 could cover all use cases if the sagemath/sagetrack-mirror repo had
# release tags, but it requires a sha instead of a release number in "base", which
# is inconvenient.
urls = if squashed
then [
"https://github.com/sagemath/sage/compare/${base}...${rev}.diff"
"https://github.com/sagemath/sagetrac-mirror/compare/${base}...${rev}.diff"
]
else [ "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}" ];
} // builtins.removeAttrs args [ "rev" "base" "sha256" "squashed" "excludes" ])
);
in
stdenv.mkDerivation rec {
version = "9.8";
version = "10.0";
pname = "sage-src";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "sha256-dDbrzJXsOBARYfJz0r7n3LbaoXHnx7Acz6HBa95NV9o=";
sha256 = "sha256-zN/Lo/GBCjYGemuaYpgG3laufN8te3wPjXMQ+Me9zgY=";
};
# 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 = [
# Fixes a potential race condition which can lead to transient doctest failures.
./patches/fix-ecl-race.patch
# Not necessary since library location is set explicitly
# https://trac.sagemath.org/ticket/27660#ticket
./patches/do-not-test-find-library.patch
# Parallelize docubuild using subprocesses, fixing an isolation issue. See
# https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
./patches/sphinx-docbuild-subprocesses.patch
# After updating smypow to (https://github.com/sagemath/sage/issues/3360)
# we can now set the cache dir to be within the .sage directory. This is
# not strictly necessary, but keeps us from littering in the user's HOME.
./patches/sympow-cache.patch
];
# Since sage unfortunately does not release bugfix releases, packagers must
# fix those bugs themselves. This is for critical bugfixes, where "critical"
# == "causes (transient) doctest failures / somebody complained".
bugfixPatches = [
# To help debug the transient error in
# https://trac.sagemath.org/ticket/23087 when it next occurs.
./patches/configurationpy-error-verbose.patch
# Sage uses mixed integer programs (MIPs) to find edge disjoint
# spanning trees. For some reason, aarch64 glpk takes much longer
# than x86_64 glpk to solve such MIPs. Since the MIP formulation
# has "numerous problems" and will be replaced by a polynomial
# algorithm soon, disable this test for now.
# https://github.com/sagemath/sage/issues/34575
./patches/disable-slow-glpk-test.patch
];
# Patches needed because of package updates. We could just pin the versions of
@ -98,73 +52,33 @@ stdenv.mkDerivation rec {
# should come from or be proposed to upstream. This list will probably never
# be empty since dependencies update all the time.
packageUpgradePatches = [
# After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
# now set the cache dir to be within the .sage directory. This is not
# strictly necessary, but keeps us from littering in the user's HOME.
./patches/sympow-cache.patch
# Upstream will wait until Sage 9.7 to upgrade to linbox 1.7 because it
# does not support gcc 6. We can upgrade earlier.
# https://trac.sagemath.org/ticket/32959
./patches/linbox-1.7-upgrade.patch
# adapted from https://trac.sagemath.org/ticket/23712#comment:22
./patches/tachyon-renamed-focallength.patch
# https://trac.sagemath.org/ticket/34391
(fetchSageDiff {
name = "gap-4.12-upgrade.patch";
base = "9.8.beta7";
rev = "dd4a17281adcda74e11f998ef519b6bd0dafb043";
sha256 = "sha256-UQT9DO9xd5hh5RucvUkIm+rggPKu8bc1YaSI6LVYH98=";
})
# https://trac.sagemath.org/ticket/34701
(fetchSageDiff {
name = "libgap-fix-gc-crashes-on-aarch64.patch";
base = "eb8cd42feb58963adba67599bf6e311e03424328"; # TODO: update when #34391 lands
rev = "90acc7f1c13a80b8aa673469a2668feb9cd4207f";
sha256 = "sha256-9BhQLFB3wUhiXRQsK9L+I62lSjvTfrqMNi7QUIQvH4U=";
})
# https://github.com/sagemath/sage/pull/35235
# https://github.com/sagemath/sage/pull/35584, positively reviewed
(fetchpatch {
name = "ipython-8.11-upgrade.patch";
url = "https://github.com/sagemath/sage/commit/23471e2d242c4de8789d7b1fc8b07a4b1d1e595a.diff";
sha256 = "sha256-wvH4BvDiaBv7jbOP8LvOE5Vs16Kcwz/C9jLpEMohzLQ=";
name = "networkx-3.1-upgrade.patch";
url = "https://github.com/sagemath/sage/compare/10.0.rc2..e599562cf5fdfb9799a5412fac40c2f8e9f97341.diff";
sha256 = "sha256-3A90kXqNR0c7+k8xrZXAt5wqWg/VFAPNhQujwTdOyhI=";
})
# positively reviewed
# https://github.com/sagemath/sage/pull/35612, positively reviewed
(fetchpatch {
name = "matplotlib-3.7.0-upgrade.patch";
url = "https://github.com/sagemath/sage/pull/35177.diff";
sha256 = "sha256-YdPnMsjXBm9ZRm6a8hH8rSynkrABjLoIzqwp3F/rKAw=";
name = "linbox-1.7-upgrade.patch";
url = "https://github.com/sagemath/sage/compare/10.0.rc2..9c8796c7b677e3a056348e3510331ea8b8c3c42e.diff";
sha256 = "sha256-/TpvIQZUqmbUuz6wvp3ni9oRir5LBA2FKDJcmnHI1r4=";
})
# https://github.com/sagemath/sage/pull/35336, merged in 10.0.beta8
# https://github.com/sagemath/sage/pull/35619
(fetchpatch {
name = "ipywidgets-8.0.5-upgrade.patch";
url = "https://github.com/sagemath/sage/commit/7ab3e3aa81d47a35d09161b965bba8ab16fd5c9e.diff";
sha256 = "sha256-WjdsPTui6uv92RerlV0mqltmLaxADvz+3aqSvxBFmfU=";
name = "maxima-5.46.0-upgrade.patch";
url = "https://github.com/sagemath/sage/compare/10.0.rc3..7e86af5dae8f89868b25a6f57189bb5ca618da89.diff";
sha256 = "sha256-pxSxdJ2lyHoMUIxhlIn1nTHaddRxGvvTj9IbwFCTBFU=";
})
# https://github.com/sagemath/sage/pull/35499
# https://github.com/sagemath/sage/pull/35635, positively reviewed
(fetchpatch {
name = "ipywidgets-8.0.5-upgrade-part-deux.patch";
url = "https://github.com/sagemath/sage/pull/35499.diff";
sha256 = "sha256-uNCjLs9qrARTQNsq1+kTdvuV2A1M4xx5b1gWh5c55X0=";
name = "sympy-1.12-upgrade.patch";
url = "https://github.com/sagemath/sage/compare/10.0.rc2..aa4193cdc8ec9fb7bd7c49696b7f914668f7913a.diff";
sha256 = "sha256-UAmYCxHvnE5p+H2DySNZTPFVm915jHtOEoG+tZz5n7I=";
})
# rebased from https://github.com/sagemath/sage/pull/34994, merged in sage 10.0.beta2
./patches/numpy-1.24-upgrade.patch
# Sage uses mixed integer programs (MIPs) to find edge disjoint
# spanning trees. For some reason, aarch64 glpk takes much longer
# than x86_64 glpk to solve such MIPs. Since the MIP formulation
# has "numerous problems" and will be replaced by a polynomial
# algorithm soon, disable this test for now.
# https://trac.sagemath.org/ticket/34575
./patches/disable-slow-glpk-test.patch
];
patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
@ -179,12 +93,10 @@ stdenv.mkDerivation rec {
"s|var(\"SAGE_ROOT\".*|var(\"SAGE_ROOT\", \"$out\")|" \
src/sage/env.py
# src/doc/en/reference/spkg/conf.py expects index.rst in its directory,
# a list of external packages in the sage distribution (build/pkgs)
# generated by the bootstrap script (which we don't run). this is not
# relevant for other distributions, so remove it.
rm src/doc/en/reference/spkg/conf.py
sed -i "/spkg/d" src/doc/en/reference/index.rst
# docbuilding expects a spkg index generated by the doc/bootstrap script (which
# we don't run) to exist. the spkg list includes nix package names, but it's not
# worth the hassle of running the bootstrap script, so just create a dummy index.
touch src/doc/en/reference/spkg/index.rst
# the bootstrap script also generates installation instructions for
# arch, debian, fedora, cygwin and homebrew using data from build/pkgs.

175
pkgs/applications/science/math/sage/sagelib.nix
View File

@ -1,76 +1,83 @@
{ sage-src
, env-locations
, perl
, python
, buildPythonPackage
, m4
, perl
, pkg-config
, sage-setup
, gd
, iml
, libpng
, readline
, arb
, blas
, lapack
, boost
, brial
, cliquer
, cypari2
, cysignals
, cython
, lisp-compiler
, eclib
, ecm
, fflas-ffpack
, flint
, gd
, gap
, giac
, givaro
, glpk
, gsl
, iml
, jinja2
, libpng
, lapack
, lcalc
, lrcalc
, gap
, libbraiding
, libhomfly
, libmpc
, linbox
, lisp-compiler
, lrcalc
, m4ri
, m4rie
, memory-allocator
, libmpc
, mpfi
, mpfr
, ntl
, numpy
, pari
, pkgconfig # the python module, not the pkg-config alias
, pkg-config
, planarity
, ppl
, primecountpy
, python
, ratpoints
, readline
, rankwidth
, symmetrica
, zn_poly
, fflas-ffpack
, boost
, ratpoints
, singular
, pip
, jupyter-core
, sage-setup
, libhomfly
, libbraiding
, gmpy2
, pplpy
, sqlite
, jupyter-client
, ipywidgets
, mpmath
, rpy2
, symmetrica
, cvxopt
, cypari2
, cysignals
, cython
, fpylll
, scipy
, sympy
, matplotlib
, pillow
, gmpy2
, importlib-metadata
, importlib-resources
, ipykernel
, networkx
, ptyprocess
, ipython
, ipywidgets
, jinja2
, jupyter-client
, jupyter-core
, lrcalc-python
, sphinx # TODO: this is in setup.cfg, should we override it?
, matplotlib
, memory-allocator
, mpmath
, networkx
, numpy
, pexpect
, pillow
, pip
, pkgconfig
, pplpy
, primecountpy
, ptyprocess
, requests
, rpy2
, scipy
, sphinx
, sympy
, typing-extensions
}:
assert (!blas.isILP64) && (!lapack.isILP64);
@ -87,83 +94,93 @@ buildPythonPackage rec {
nativeBuildInputs = [
iml
perl
jupyter-core
pkg-config
sage-setup
pip # needed to query installed packages
lisp-compiler
m4
perl
pip # needed to query installed packages
pkg-config
sage-setup
];
buildInputs = [
gd
readline
iml
libpng
readline
];
propagatedBuildInputs = [
cypari2
jinja2
numpy
pkgconfig
boost
# native dependencies (TODO: determine which ones need to be propagated)
arb
blas
boost
brial
cliquer
lisp-compiler
eclib
ecm
fflas-ffpack
flint
gap
giac
givaro
glpk
gsl
lapack
lcalc
gap
libbraiding
libhomfly
libmpc
linbox
lisp-compiler
lrcalc
m4ri
m4rie
memory-allocator
mpfi
mpfr
ntl
blas
lapack
pari
planarity
ppl
primecountpy
rankwidth
ratpoints
singular
symmetrica
zn_poly
pip
cython
cysignals
libhomfly
libbraiding
gmpy2
pplpy
sqlite
symmetrica
# from src/sage/setup.cfg and requirements.txt
cvxopt
cypari2
cysignals
cython
fpylll
gmpy2
importlib-metadata
importlib-resources
ipykernel
ipython
ipywidgets
jinja2
jupyter-client
jupyter-core
lrcalc-python
matplotlib
memory-allocator
mpmath
networkx
numpy
pexpect
pillow
pip
pkgconfig
pplpy
primecountpy
ptyprocess
requests
rpy2
scipy
sympy
matplotlib
pillow
ipykernel
fpylll
networkx
jupyter-client
ipywidgets
ptyprocess
lrcalc-python
sphinx
sympy
typing-extensions
];
preBuild = ''