From 68233970a2de5d1b1e2c23cd698d1b576326ca7f Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Tue, 9 Apr 2019 11:40:00 +0200
Subject: [PATCH 1/4] gmpy2: 2.0.8 -> 2.1a4
---
.../python-modules/gmpy2/default.nix | 19 ++++++++++++++-----
1 file changed, 14 insertions(+), 5 deletions(-)
diff --git a/pkgs/development/python-modules/gmpy2/default.nix b/pkgs/development/python-modules/gmpy2/default.nix
index a03188bb8f2..edca1d30d8e 100644
--- a/pkgs/development/python-modules/gmpy2/default.nix
+++ b/pkgs/development/python-modules/gmpy2/default.nix
@@ -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-${version}";
+ sha256 = "1wg4w4q2l7n26ksrdh4rwqmifgfm32n7x29cgdvmmbv5lmilb5hz";
};
buildInputs = [ gmp mpfr libmpc ];
From 1f643b9c49154d55e56adb26a684303294e504e9 Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Tue, 5 Mar 2019 21:59:18 +0100
Subject: [PATCH 2/4] python.pkgs.pplpy: init at 0.8.4
This is a new dependency for the upcoming sage version.
---
.../python-modules/pplpy/default.nix | 64 +++++++++++++++++++
pkgs/top-level/python-packages.nix | 2 +
2 files changed, 66 insertions(+)
create mode 100644 pkgs/development/python-modules/pplpy/default.nix
diff --git a/pkgs/development/python-modules/pplpy/default.nix b/pkgs/development/python-modules/pplpy/default.nix
new file mode 100644
index 00000000000..6f118a51c87
--- /dev/null
+++ b/pkgs/development/python-modules/pplpy/default.nix
@@ -0,0 +1,64 @@
+{ lib
+, python
+, fetchPypi
+, buildPythonPackage
+, gmp
+, mpfr
+, libmpc
+, ppl
+, pari
+, cython
+, cysignals
+, gmpy2
+, sphinx
+}:
+
+buildPythonPackage rec {
+ pname = "pplpy";
+ version = "0.8.4";
+
+ src = fetchPypi {
+ inherit pname version;
+ sha256 = "0dk8l5r3f2jbkkasddvxwvhlq35pjsiirh801lrapv8lb16r2qmr";
+ };
+
+ buildInputs = [
+ gmp
+ mpfr
+ libmpc
+ ppl
+ ];
+
+ nativeBuildInputs = [
+ sphinx # docbuild, called by make
+ ];
+
+ propagatedBuildInputs = [
+ cython
+ cysignals
+ gmpy2
+ ];
+
+ outputs = [ "out" "doc" ];
+
+ postBuild = ''
+ # Find the build result in order to put it into PYTHONPATH. The doc
+ # build needs to import pplpy.
+ build_result="$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 "$doc/share/doc/pplpy"
+ '';
+
+ meta = with lib; {
+ description = "A Python wrapper for ppl";
+ homepage = https://gitlab.com/videlec/pplpy;
+ maintainers = with maintainers; [ timokau ];
+ license = licenses.gpl3;
+ };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 1572eb7f654..eb53f2dd5e0 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -585,6 +585,8 @@ in {
poetry = callPackage ../development/python-modules/poetry { };
+ pplpy = callPackage ../development/python-modules/pplpy { };
+
pprintpp = callPackage ../development/python-modules/pprintpp { };
progress = callPackage ../development/python-modules/progress { };
From 930fa9b92ed8fcd8e976eeb3c519b6ce7c2a96bc Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Tue, 5 Mar 2019 21:55:51 +0100
Subject: [PATCH 3/4] python.pkgs.cysignals: propagate pari
This didn't cause issues earlier since all packages that depend on
cysignals have a pari dependency anyways.
---
pkgs/development/python-modules/cysignals/default.nix | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/pkgs/development/python-modules/cysignals/default.nix b/pkgs/development/python-modules/cysignals/default.nix
index c1f85ce75ac..1cd55acdbeb 100644
--- a/pkgs/development/python-modules/cysignals/default.nix
+++ b/pkgs/development/python-modules/cysignals/default.nix
@@ -31,12 +31,13 @@ buildPythonPackage rec {
export PATH="$out/bin:$PATH"
'';
- buildInputs = lib.optionals pariSupport [
- pari
- ];
-
propagatedBuildInputs = [
cython
+ ] ++ lib.optionals pariSupport [
+ # When cysignals is built with pari, including cysignals into the
+ # buildInputs of another python package will cause cython to link against
+ # pari.
+ pari
];
enableParallelBuilding = true;
From 49b8efcb841fd8f4896f1ac83e7ee672e82a18cf Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Sun, 27 Jan 2019 11:28:39 +0100
Subject: [PATCH 4/4] sage: 8.6 -> 8.7
https://groups.google.com/forum/#!topic/sage-release/3m8PV9JkFro
---
.../science/math/sage/env-locations.nix | 1 +
.../patches/do-not-test-find-library.patch | 95 +++++++++++++++++++
.../do-not-test-package-manifests.patch | 26 +++++
.../math/sage/patches/giac-1.5.0.patch | 14 ---
.../sage/patches/ignore-pip-deprecation.patch | 22 -----
.../patches/revert-sphinx-always-fork.patch | 71 --------------
.../science/math/sage/sage-src.nix | 89 ++++++-----------
.../science/math/sage/sagedoc.nix | 3 +
.../science/math/sage/sagelib.nix | 4 +
9 files changed, 158 insertions(+), 167 deletions(-)
create mode 100644 pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
create mode 100644 pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch
delete mode 100644 pkgs/applications/science/math/sage/patches/giac-1.5.0.patch
delete mode 100644 pkgs/applications/science/math/sage/patches/ignore-pip-deprecation.patch
delete mode 100644 pkgs/applications/science/math/sage/patches/revert-sphinx-always-fork.patch
diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix
index 8354629cab5..bda2d23b9e5 100644
--- a/pkgs/applications/science/math/sage/env-locations.nix
+++ b/pkgs/applications/science/math/sage/env-locations.nix
@@ -28,6 +28,7 @@ writeTextFile rec {
export GPDOCDIR="${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="${maxima-ecl}"
diff --git a/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch b/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
new file mode 100644
index 00000000000..3f844e1b1ef
--- /dev/null
+++ b/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
@@ -0,0 +1,95 @@
+diff --git a/src/sage/env.py b/src/sage/env.py
+index 061b94f3f1..67cd091540 100644
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -189,88 +189,13 @@ var('MAXIMA_FAS')
+ var('SAGE_BANNER', '')
+ var('SAGE_IMPORTALL', 'yes')
+
+-
+-def _get_shared_lib_filename(libname, *additional_libnames):
+- """
+- Return the full path to a shared library file installed in the standard
+- location for the system within the ``LIBDIR`` prefix (or
+- ``$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
diff --git a/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch b/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch
new file mode 100644
index 00000000000..9e3f0f5ae88
--- /dev/null
+++ b/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch
@@ -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'
diff --git a/pkgs/applications/science/math/sage/patches/giac-1.5.0.patch b/pkgs/applications/science/math/sage/patches/giac-1.5.0.patch
deleted file mode 100644
index 58090b241d2..00000000000
--- a/pkgs/applications/science/math/sage/patches/giac-1.5.0.patch
+++ /dev/null
@@ -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
- """
diff --git a/pkgs/applications/science/math/sage/patches/ignore-pip-deprecation.patch b/pkgs/applications/science/math/sage/patches/ignore-pip-deprecation.patch
deleted file mode 100644
index 95b377dc955..00000000000
--- a/pkgs/applications/science/math/sage/patches/ignore-pip-deprecation.patch
+++ /dev/null
@@ -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"""
diff --git a/pkgs/applications/science/math/sage/patches/revert-sphinx-always-fork.patch b/pkgs/applications/science/math/sage/patches/revert-sphinx-always-fork.patch
deleted file mode 100644
index 64dd6fd9377..00000000000
--- a/pkgs/applications/science/math/sage/patches/revert-sphinx-always-fork.patch
+++ /dev/null
@@ -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 #
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index e14d24cf70e..f2d65b68a33 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -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', '$out/src')|" \
+ src/sage/env.py
+
# Do not use sage-env-config (generated by ./configure).
# Instead variables are set manually.
echo '# do nothing' > src/bin/sage-env-config
diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix
index cc1a4fc61e0..91c880673a1 100644
--- a/pkgs/applications/science/math/sage/sagedoc.nix
+++ b/pkgs/applications/science/math/sage/sagedoc.nix
@@ -52,6 +52,9 @@ stdenv.mkDerivation rec {
export HOME="$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 \
diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix
index d7f9cb9ee32..d745532d5d7 100644
--- a/pkgs/applications/science/math/sage/sagelib.nix
+++ b/pkgs/applications/science/math/sage/sagelib.nix
@@ -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 = ''