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Merge pull request #54690 from timokau/sage-8.7

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sage: 8.6 -> 8.7
This commit is contained in:
Timo Kaufmann 2019-04-18 22:50:45 +02:00 committed by GitHub
commit 0fdd79d0dd
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GPG Key ID: 4AEE18F83AFDEB23
13 changed files with 243 additions and 176 deletions
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1
pkgs/applications/science/math/sage/env-locations.nix
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@ -28,6 +28,7 @@ writeTextFile rec {
export GPDOCDIR="${pari}/share/pari/doc"
export SINGULARPATH='${singular}/share/singular'
export SINGULAR_SO='${singular}/lib/libSingular.so'
export GAP_SO='${gap}/lib/libgap.so'
export SINGULAR_EXECUTABLE='${singular}/bin/Singular'
export MAXIMA_FAS='${maxima-ecl}/lib/maxima/${maxima-ecl.version}/binary-ecl/maxima.fas'
export MAXIMA_PREFIX="${maxima-ecl}"

95
pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch Normal file
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@ -0,0 +1,95 @@
diff --git a/src/sage/env.py b/src/sage/env.py
index 061b94f3f1..67cd091540 100644
--- a/src/sage/env.py
+++ b/src/sage/env.py
@@ -189,88 +189,13 @@ var('MAXIMA_FAS')
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
- ``$SAGE_LOCAL/lib`` in the case of manual build of Sage).
-
- This can also be passed more than one library name (e.g. for cases where
- some library may have multiple names depending on the platform) in which
- case the first one found is returned.
-
- This supports most *NIX variants (in which ``lib<libname>.so`` is found
- under ``$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>/``).
-
- Returns ``None`` if the file does not exist.
-
- EXAMPLES::
-
- sage: import sys
- sage: from fnmatch import fnmatch
- sage: from sage.env import _get_shared_lib_filename
- sage: lib_filename = _get_shared_lib_filename("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(lib_filename, pattern)
- True
- sage: _get_shared_lib_filename("an_absurd_lib") is None
- True
- """
-
- for libname in (libname,) + additional_libnames:
- if sys.platform == 'cygwin':
- bindir = sysconfig.get_config_var('BINDIR')
- pats = ['cyg{}.dll'.format(libname), 'cyg{}-*.dll'.format(libname)]
- filenames = []
- 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
- # at arbitrary. However, practically speaking, on Cygwin, there
- # will only ever be one version
- if filenames:
- return filenames[-1]
- else:
- if sys.platform == 'darwin':
- ext = 'dylib'
- else:
- ext = 'so'
-
- libdirs = [sysconfig.get_config_var('LIBDIR')]
- multilib = sysconfig.get_config_var('MULTILIB')
- if multilib:
- libdirs.insert(0, os.path.join(libdirs[0], multilib))
-
- for libdir in libdirs:
- basename = 'lib{}.{}'.format(libname, ext)
- filename = os.path.join(libdir, basename)
- if os.path.exists(filename):
- return filename
-
- # 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 = _get_shared_lib_filename('Singular', 'singular-Singular')
+SINGULAR_SO = '/default'
var('SINGULAR_SO', SINGULAR_SO)
# locate libgap shared object
-GAP_SO= _get_shared_lib_filename('gap','')
+GAP_SO= '/default'
var('GAP_SO', GAP_SO)
# post process

26
pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch Normal file
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@ -0,0 +1,26 @@
diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py
index 3bca15d53b..7cf04ff8d1 100644
--- a/src/sage/misc/package.py
+++ b/src/sage/misc/package.py
@@ -478,16 +478,16 @@ def package_manifest(package):
EXAMPLES::
- sage: from sage.misc.package import package_manifest
- sage: sagetex_manifest = package_manifest('sagetex')
- sage: sagetex_manifest['package_name'] == 'sagetex'
+ sage: from sage.misc.package import package_manifest # optional - buildsystem
+ sage: sagetex_manifest = package_manifest('sagetex') # optional - buildsystem
+ sage: sagetex_manifest['package_name'] == 'sagetex' # optional - buildsystem
True
- sage: 'files' in sagetex_manifest
+ sage: 'files' in sagetex_manifest # optional - buildsystem
True
Test a nonexistent package::
- sage: package_manifest('dummy-package')
+ sage: package_manifest('dummy-package') # optional - buildsystem
Traceback (most recent call last):
...
KeyError: 'dummy-package'

14
pkgs/applications/science/math/sage/patches/giac-1.5.0.patch
View File

@ -1,14 +0,0 @@
--- a/src/sage/interfaces/giac.py 2018-12-08 22:11:56.285500644 +0100
+++ b/src/sage/interfaces/giac.py 2018-12-08 22:11:56.285500644 +0100
@@ -617,10 +617,7 @@
'4\n3'
sage: s='g(x):={\nx+1;\nx+2;\n}'
sage: giac(s)
- (x)->{
- x+1;
- x+2;
- }
+ (x)->[x+1,x+2]
sage: giac.g(5)
7
"""

22
pkgs/applications/science/math/sage/patches/ignore-pip-deprecation.patch
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@ -1,22 +0,0 @@
diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py
index 689e5a23b9..4e16fe3a8d 100644
--- a/src/sage/misc/package.py
+++ b/src/sage/misc/package.py
@@ -142,9 +142,14 @@ def pip_installed_packages():
sage: d['beautifulsoup'] # optional - beautifulsoup
u'...'
"""
- proc = subprocess.Popen(["pip", "list", "--no-index", "--format", "json"], stdout=subprocess.PIPE)
- stdout = proc.communicate()[0].decode()
- return {package['name'].lower():package['version'] for package in json.loads(stdout)}
+ with open(os.devnull, 'w') as devnull:
+ proc = subprocess.Popen(
+ ["pip", "list", "--no-index", "--format", "json"],
+ stdout=subprocess.PIPE,
+ stderr=devnull,
+ )
+ stdout = proc.communicate()[0].decode()
+ return {package['name'].lower():package['version'] for package in json.loads(stdout)}
def list_packages(*pkg_types, **opts):
r"""

71
pkgs/applications/science/math/sage/patches/revert-sphinx-always-fork.patch
View File

@ -1,71 +0,0 @@
commit f1c59929c3c180ac283334c2b3c901ac8c82f6b1
Author: Timo Kaufmann <timokau@zoho.com>
Date: Sat Oct 20 20:07:41 2018 +0200
Revert "Something related to the sphinxbuild seems to be leaking memory"
This reverts commit 7d85dc796c58c3de57401bc22d3587b94e205091.
diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py
index 0b24b1a60b..084c3f89d7 100644
--- a/src/sage_setup/docbuild/__init__.py
+++ b/src/sage_setup/docbuild/__init__.py
@@ -265,29 +265,35 @@ class DocBuilder(object):
# import the customized builder for object.inv files
inventory = builder_helper('inventory')
-def build_many(target, args):
- # Pool() uses an actual fork() to run each new instance. This is important
- # for performance reasons, i.e., don't use a forkserver when it becomes
- # available with Python 3: Here, sage is already initialized which is quite
- # costly, with a forkserver we would have to reinitialize it for every
- # document we build. At the same time, don't serialize this by taking the
- # pool (and thus the call to fork()) out completely: The call to Sphinx
- # leaks memory, so we need to build each document in its own process to
- # control the RAM usage.
- from multiprocessing import Pool
- pool = Pool(NUM_THREADS, maxtasksperchild=1)
- # map_async handles KeyboardInterrupt correctly. Plain map and
- # apply_async does not, so don't use it.
- x = pool.map_async(target, args, 1)
- try:
- ret = x.get(99999)
- pool.close()
- pool.join()
- except Exception:
- pool.terminate()
- if ABORT_ON_ERROR:
- raise
- return ret
+if NUM_THREADS > 1:
+ def build_many(target, args):
+ from multiprocessing import Pool
+ pool = Pool(NUM_THREADS, maxtasksperchild=1)
+ # map_async handles KeyboardInterrupt correctly. Plain map and
+ # apply_async does not, so don't use it.
+ x = pool.map_async(target, args, 1)
+ try:
+ ret = x.get(99999)
+ pool.close()
+ pool.join()
+ except Exception:
+ pool.terminate()
+ if ABORT_ON_ERROR:
+ raise
+ return ret
+else:
+ def build_many(target, args):
+ results = []
+
+ for arg in args:
+ try:
+ results.append(target(arg))
+ except Exception:
+ if ABORT_ON_ERROR:
+ raise
+
+ return results
+
##########################################
# Parallel Building Ref Manual #

89
pkgs/applications/science/math/sage/sage-src.nix
View File

@ -10,14 +10,14 @@
# all get the same sources with the same patches applied.
stdenv.mkDerivation rec {
version = "8.6";
name = "sage-src-${version}";
version = "8.7";
pname = "sage-src";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "1vs3pbgbqpg0qnwr018bqsdmm7crgjp310cx8zwh7za3mv1cw5j3";
sha256 = "05vvrd6syh0hlmrk6kzjrwd0hpmvxp8vr8p3mkjb0jh5p2kjdd27";
};
# Patches needed because of particularities of nix or the way this is packaged.
@ -37,12 +37,6 @@ stdenv.mkDerivation rec {
# https://github.com/python/cpython/pull/7476
./patches/python-5755-hotpatch.patch
# Revert the commit that made the sphinx build fork even in the single thread
# case. For some yet unknown reason, that breaks the docbuild on nix and archlinux.
# See https://groups.google.com/forum/#!msg/sage-packaging/VU4h8IWGFLA/mrmCMocYBwAJ.
# https://trac.sagemath.org/ticket/26608
./patches/revert-sphinx-always-fork.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.
@ -59,6 +53,21 @@ stdenv.mkDerivation rec {
sha256 = "07p9i0fwjgapmfvmi436yn6v60p8pvmxqjc93wsssqgh5kd8qw3n";
stripLen = 1;
})
# Part of the build system. Should become unnecessary with sage 8.8.
# Upstream discussion here: https://trac.sagemath.org/ticket/27124#comment:33
./patches/do-not-test-package-manifests.patch
# Not necessary since library location is set explicitly
# https://trac.sagemath.org/ticket/27660#ticket
./patches/do-not-test-find-library.patch
# https://trac.sagemath.org/ticket/27697#ticket
(fetchpatch {
name = "pplpy-doc-location-configurable.patch";
url = "https://git.sagemath.org/sage.git/patch/?h=c4d966e7cb0c7b87c55d52dc6f46518433a2a0a2";
sha256 = "0pqbbsx8mriwny422s9mp3z5d095cnam32sm62q4mxk8g8jb9vm9";
})
];
# Since sage unfortunately does not release bugfix releases, packagers must
@ -72,12 +81,6 @@ stdenv.mkDerivation rec {
url = "https://git.sagemath.org/sage.git/patch?id2=10407524b18659e14e184114b61c043fb816f3c2&id=c9b0cc9d0b8748ab85e568f8f57f316c5e8cbe54";
sha256 = "0wgp7yvn9sm1ynlhcr4l0hzmvr2n28llg4xc01p6k1zz4im64c17";
})
# https://trac.sagemath.org/ticket/27224
(fetchpatch {
name = "sig_on_in_matrix_misc.patch";
url = "https://git.sagemath.org/sage.git/patch?id=85d25bf2eb73f7d3c6de4ee6222b0c399be43b07";
sha256 = "1ciwhh57pnb9b4i8m3vb07wfsibsay5sg0jp5giq1pzc5zc79a4p";
})
];
# Patches needed because of package updates. We could just pin the versions of
@ -110,52 +113,12 @@ stdenv.mkDerivation rec {
stripLen = 1;
})
# https://trac.sagemath.org/ticket/26315
./patches/giac-1.5.0.patch
# https://trac.sagemath.org/ticket/26442
(fetchSageDiff {
name = "cypari2-2.0.3.patch";
base = "8.6.rc1";
rev = "cd62d45bcef93fb4f7ed62609a46135e6de07051";
sha256 = "08l2b9w0rn1zrha6188j72f7737xs126gkgmydjd31baa6367np2";
})
# https://trac.sagemath.org/ticket/26949
(fetchpatch {
name = "sphinx-1.8.3-dependency.patch";
url = "https://git.sagemath.org/sage.git/patch?id=d305eda0fedc73fdbe0447b5d6d2b520b8d112c4";
sha256 = "1x3q5j8lq35vlj893gj5gq9fhzs60szm9r9rx6ri79yiy9apabph";
})
# https://trac.sagemath.org/ticket/26451
(fetchpatch {
name = "sphinx-1.8.3.patch";
url = "https://git.sagemath.org/sage.git/patch?id2=0cb494282d7b4cea50aba7f4d100e7932a4c00b1&id=62b989d5ee1d9646db85ea56053cd22e9ffde5ab";
sha256 = "1n5c61mvhalcr2wbp66wzsynwwk59aakvx3xqa5zw9nlkx3rd0h1";
})
# https://trac.sagemath.org/ticket/27061
(fetchpatch {
name = "numpy-1.16-inline-fortran.patch";
url = "https://git.sagemath.org/sage.git/patch?id=a05b6b038e1571ab15464e98f76d1927c0c3fd12";
sha256 = "05yq97pq84xi60wb1p9skrad5h5x770gq98ll4frr7hvvmlwsf58";
})
# https://trac.sagemath.org/ticket/27405
./patches/ignore-pip-deprecation.patch
# https://trac.sagemath.org/ticket/27360
(fetchpatch {
name = "eclib-20190226.patch";
url = "https://git.sagemath.org/sage.git/patch/?id=f570e3a7fc2965764b84c04ce301a88ded2c42df";
sha256 = "0l5c4giixkn15v2a06sfzq5mkxila6l67zkjbacirwprrlpcnmmp";
})
# https://trac.sagemath.org/ticket/27420
(fetchpatch {
name = "cypari-2.1.patch";
url = "https://git.sagemath.org/sage.git/patch/?id=e351bf2f2914e683d5e2028597c45ae8d1b7f855";
sha256 = "00faa7fl0vaqcqbw0bidkhl78qa8l34d3a07zirbcl0vm74bdn1p";
(fetchSageDiff {
name = "sphinx-1.8.patch";
base = "8.7";
rev = "737afd8f314bd1e16feaec562bb4b5efa2effa8b";
sha256 = "0n56ss88ds662bp49j23z5c2i6hsn3jynxw13wv76hyl0h7l1hjh";
})
# https://trac.sagemath.org/ticket/27653
@ -177,6 +140,12 @@ stdenv.mkDerivation rec {
echo '#!${runtimeShell}
python "$@"' > build/bin/sage-python23
# Make sure sage can at least be imported without setting any environment
# variables. It won't be close to feature complete though.
sed -i \
"s|var('SAGE_LOCAL',.*|var('SAGE_LOCAL', '$out/src')|" \
src/sage/env.py
# Do not use sage-env-config (generated by ./configure).
# Instead variables are set manually.
echo '# do nothing' > src/bin/sage-env-config

3
pkgs/applications/science/math/sage/sagedoc.nix
View File

@ -52,6 +52,9 @@ stdenv.mkDerivation rec {
export HOME="$TMPDIR/sage_home"
mkdir -p "$HOME"
# needed to link them in the sage docs using intersphinx
export PPLPY_DOCS=${python.pkgs.pplpy.doc}/share/doc/pplpy
${sage-with-env}/bin/sage -python -m sage_setup.docbuild \
--mathjax \
--no-pdf-links \

4
pkgs/applications/science/math/sage/sagelib.nix
View File

@ -47,6 +47,8 @@
, jupyter_core
, libhomfly
, libbraiding
, gmpy2
, pplpy
}:
# This is the core sage python package. Everything else is just wrappers gluing
@ -115,6 +117,8 @@ buildPythonPackage rec {
cysignals
libhomfly
libbraiding
gmpy2
pplpy
];
buildPhase = ''

9
pkgs/development/python-modules/cysignals/default.nix
View File

@ -31,12 +31,13 @@ buildPythonPackage rec {
export PATH="$out/bin:$PATH"
'';
buildInputs = lib.optionals pariSupport [
pari
];
propagatedBuildInputs = [
cython
] ++ lib.optionals pariSupport [
# When cysignals is built with pari, including cysignals into the
# buildInputs of another python package will cause cython to link against
# pari.
pari
];
enableParallelBuilding = true;

19
pkgs/development/python-modules/gmpy2/default.nix
View File

@ -1,8 +1,15 @@
{ stdenv, buildPythonPackage, fetchurl, isPyPy, gmp, mpfr, libmpc } :
{ stdenv
, buildPythonPackage
, fetchFromGitHub
, isPyPy
, gmp
, mpfr
, libmpc
}:
let
pname = "gmpy2";
version = "2.0.8";
version = "2.1a4";
in
buildPythonPackage {
@ -10,9 +17,11 @@ buildPythonPackage {
disabled = isPyPy;
src = fetchurl {
url = "mirror://pypi/g/gmpy2/${pname}-${version}.zip";
sha256 = "0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx";
src = fetchFromGitHub {
owner = "aleaxit";
repo = "gmpy";
rev = "gmpy2-${version}";
sha256 = "1wg4w4q2l7n26ksrdh4rwqmifgfm32n7x29cgdvmmbv5lmilb5hz";
};
buildInputs = [ gmp mpfr libmpc ];

64
pkgs/development/python-modules/pplpy/default.nix Normal file
View File

@ -0,0 +1,64 @@
{ lib
, python
, fetchPypi
, buildPythonPackage
, gmp
, mpfr
, libmpc
, ppl
, pari
, cython
, cysignals
, gmpy2
, sphinx
}:
buildPythonPackage rec {
pname = "pplpy";
version = "0.8.4";
src = fetchPypi {
inherit pname version;
sha256 = "0dk8l5r3f2jbkkasddvxwvhlq35pjsiirh801lrapv8lb16r2qmr";
};
buildInputs = [
gmp
mpfr
libmpc
ppl
];
nativeBuildInputs = [
sphinx # docbuild, called by make
];
propagatedBuildInputs = [
cython
cysignals
gmpy2
];
outputs = [ "out" "doc" ];
postBuild = ''
# Find the build result in order to put it into PYTHONPATH. The doc
# build needs to import pplpy.
build_result="$PWD/$( find build/ -type d -name 'lib.*' | head -n1 )"
echo "Building documentation"
PYTHONPATH="$build_result:$PYTHONPATH" make -C docs html
'';
postInstall = ''
mkdir -p "$doc/share/doc"
mv docs/build/html "$doc/share/doc/pplpy"
'';
meta = with lib; {
description = "A Python wrapper for ppl";
homepage = https://gitlab.com/videlec/pplpy;
maintainers = with maintainers; [ timokau ];
license = licenses.gpl3;
};
}

2
pkgs/top-level/python-packages.nix
View File

@ -585,6 +585,8 @@ in {
poetry = callPackage ../development/python-modules/poetry { };
pplpy = callPackage ../development/python-modules/pplpy { };
pprintpp = callPackage ../development/python-modules/pprintpp { };
progress = callPackage ../development/python-modules/progress { };