mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-11-24 06:31:02 +00:00
sage: 8.9 -> 9.2
This commit is contained in:
Masanori Ogino
Mauricio Collares
parent
dd95aa337e
commit
5c4136daf7
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@ -9,30 +9,11 @@
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let
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inherit (pkgs) symlinkJoin callPackage nodePackages;
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# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
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python = pkgs.python2.override {
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python = pkgs.python3.override {
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packageOverrides = self: super: {
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# python packages that appear unmaintained and were not accepted into the nixpkgs
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# tree because of that. These packages are only dependencies of the more-or-less
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# deprecated sagenb. However sagenb is still a default dependency and the doctests
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# depend on it.
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# See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
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# The dependency on the sage notebook (and therefore these packages) will be
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# removed in the future:
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# https://trac.sagemath.org/ticket/25837
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flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
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flask-openid = self.callPackage ./flask-openid.nix {};
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python-openid = self.callPackage ./python-openid.nix {};
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sagenb = self.callPackage ./sagenb.nix {
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mathjax = nodePackages.mathjax;
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};
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# Package with a cyclic dependency with sage
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pybrial = self.callPackage ./pybrial.nix {};
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# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
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sagelib = self.callPackage ./sagelib.nix {
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inherit flint ecl arb;
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inherit flint arb;
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inherit sage-src env-locations pynac singular;
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linbox = pkgs.linbox.override { withSage = true; };
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pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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@ -59,7 +40,7 @@ let
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# A bash script setting various environment variables to tell sage where
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# the files its looking fore are located. Also see `sage-env`.
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env-locations = callPackage ./env-locations.nix {
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inherit pari_data ecl;
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inherit pari_data;
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inherit singular maxima-ecl;
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cysignals = python.pkgs.cysignals;
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three = nodePackages.three;
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@ -71,7 +52,7 @@ let
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sage-env = callPackage ./sage-env.nix {
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sagelib = python.pkgs.sagelib;
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inherit env-locations;
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inherit python ecl singular palp flint pynac pythonEnv maxima-ecl;
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inherit python singular palp flint pynac pythonEnv maxima-ecl;
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pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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};
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@ -102,8 +83,6 @@ let
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pythonRuntimeDeps = with python.pkgs; [
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sagelib
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pybrial
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sagenb
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cvxopt
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networkx
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service-identity
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@ -129,7 +108,6 @@ let
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singular = pkgs.singular.override { inherit flint; };
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# https://trac.sagemath.org/ticket/26625
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maxima-ecl = pkgs.maxima-ecl;
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# *not* to confuse with the python package "pynac"
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@ -161,9 +139,6 @@ let
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pari-seadata-small
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];
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};
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# https://trac.sagemath.org/ticket/22191
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ecl = pkgs.ecl_16_1_2;
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in
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# A wrapper around sage that makes sure sage finds its docs (if they were build).
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callPackage ./sage.nix {
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|
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@ -1,36 +0,0 @@
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{ stdenv
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, buildPythonPackage
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, fetchFromGitHub
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, python
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, flask
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}:
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buildPythonPackage rec {
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pname = "Flask-OldSessions";
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version = "0.10";
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# no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1
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src = fetchFromGitHub {
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owner = "mitsuhiko";
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repo = "flask-oldsessions";
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rev = version;
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sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn";
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};
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propagatedBuildInputs = [
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flask
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];
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# missing module flask.testsuite, probably assumes an old version of flask
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doCheck = false;
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checkPhase = ''
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${python.interpreter} run-tests.py
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'';
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meta = with stdenv.lib; {
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description = "Provides a session class that works like the one in Flask before 0.10.";
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license = licenses.bsd2;
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maintainers = teams.sage.members;
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homepage = "https://github.com/mitsuhiko/flask-oldsessions";
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};
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}
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@ -1,28 +0,0 @@
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{ stdenv
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, buildPythonPackage
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, fetchPypi
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, flask
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, python-openid
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}:
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buildPythonPackage rec {
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pname = "Flask-OpenID";
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version = "1.2.5";
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src = fetchPypi {
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inherit pname version;
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sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss";
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};
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propagatedBuildInputs = [
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flask
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python-openid
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];
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meta = with stdenv.lib; {
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description = "Adds openid support to flask applications";
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license = licenses.bsd2;
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maintainers = teams.sage.members;
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homepage = "https://pythonhosted.org/Flask-OpenID/";
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};
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}
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@ -1,17 +1,17 @@
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From 8218bd4fdeb4c92de8af0d3aabec55980fc4fb3d Mon Sep 17 00:00:00 2001
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From f5ea42a7aaed7611fb55b65897b9fcf2b7bcf97e Mon Sep 17 00:00:00 2001
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From: Timo Kaufmann <timokau@zoho.com>
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Date: Sun, 21 Oct 2018 17:52:40 +0200
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Subject: [PATCH] Only test py2/py3 optional tests when all of sage is tested
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---
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src/sage/doctest/control.py | 5 +++--
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1 file changed, 3 insertions(+), 2 deletions(-)
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src/sage/doctest/control.py | 3 ++-
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1 file changed, 2 insertions(+), 1 deletion(-)
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diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
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index bf18df8b2b..935c67abf7 100644
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index 2d93841e50..6d156e29a1 100644
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--- a/src/sage/doctest/control.py
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+++ b/src/sage/doctest/control.py
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@@ -362,7 +362,8 @@ class DocTestController(SageObject):
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@@ -375,7 +375,8 @@ class DocTestController(SageObject):
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if not optionaltag_regex.search(o):
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raise ValueError('invalid optional tag {!r}'.format(o))
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@ -21,15 +21,6 @@ index bf18df8b2b..935c67abf7 100644
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self.options = options
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@@ -765,7 +766,7 @@ class DocTestController(SageObject):
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sage: DC = DocTestController(DD, [dirname])
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sage: DC.expand_files_into_sources()
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sage: sorted(DC.sources[0].options.optional) # abs tol 1
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- ['guava', 'magma', 'py2']
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+ ['guava', 'magma']
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We check that files are skipped appropriately::
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--
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2.18.1
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2.28.0
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|
|
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@ -1,17 +1,17 @@
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diff --git a/src/sage/env.py b/src/sage/env.py
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index 061b94f3f1..67cd091540 100644
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index 1ddfc7cfb9..45033d6328 100644
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--- a/src/sage/env.py
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+++ b/src/sage/env.py
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@@ -189,88 +189,13 @@ var('MAXIMA_FAS')
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@@ -203,97 +203,13 @@ var('ARB_LIBRARY', 'arb')
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var('SAGE_BANNER', '')
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var('SAGE_IMPORTALL', 'yes')
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-
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-def _get_shared_lib_filename(libname, *additional_libnames):
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- """
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- Return the full path to a shared library file installed in the standard
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- location for the system within the ``LIBDIR`` prefix (or
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- ``$SAGE_LOCAL/lib`` in the case of manual build of Sage).
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- Return the full path to a shared library file installed in
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- ``$SAGE_LOCAL/lib`` or the directories associated with the
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- Python sysconfig.
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-
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- This can also be passed more than one library name (e.g. for cases where
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- some library may have multiple names depending on the platform) in which
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@ -25,7 +25,7 @@ index 061b94f3f1..67cd091540 100644
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- For distributions like Debian that use a multiarch layout, we also try the
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- multiarch lib paths (i.e. ``/usr/lib/<arch>/``).
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-
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- Returns ``None`` if the file does not exist.
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- This returns ``None`` if the file does not exist.
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-
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- EXAMPLES::
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-
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@ -48,11 +48,17 @@ index 061b94f3f1..67cd091540 100644
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-
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- for libname in (libname,) + additional_libnames:
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- if sys.platform == 'cygwin':
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- bindir = sysconfig.get_config_var('BINDIR')
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- # Later down we take the last matching DLL found, so search
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- # SAGE_LOCAL second so that it takes precedence
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- bindirs = [
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- sysconfig.get_config_var('BINDIR'),
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- os.path.join(SAGE_LOCAL, 'bin')
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- ]
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- pats = ['cyg{}.dll'.format(libname), 'cyg{}-*.dll'.format(libname)]
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- filenames = []
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- for pat in pats:
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- filenames += glob.glob(os.path.join(bindir, pat))
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- for bindir in bindirs:
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- for pat in pats:
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- filenames += glob.glob(os.path.join(bindir, pat))
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-
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- # Note: This is not very robust, since if there are multi DLL
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- # versions for the same library this just selects one more or less
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@ -66,10 +72,13 @@ index 061b94f3f1..67cd091540 100644
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- else:
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- ext = 'so'
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-
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- libdirs = [sysconfig.get_config_var('LIBDIR')]
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- libdirs = [
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- os.path.join(SAGE_LOCAL, 'lib'),
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- sysconfig.get_config_var('LIBDIR')
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- ]
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- multilib = sysconfig.get_config_var('MULTILIB')
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- if multilib:
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- libdirs.insert(0, os.path.join(libdirs[0], multilib))
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- libdirs.insert(1, os.path.join(libdirs[0], multilib))
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-
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- for libdir in libdirs:
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- basename = 'lib{}.{}'.format(libname, ext)
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|
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@ -89,7 +98,7 @@ index 061b94f3f1..67cd091540 100644
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# locate libgap shared object
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-GAP_SO= _get_shared_lib_filename('gap','')
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+GAP_SO= '/default'
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+GAP_SO = '/default'
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var('GAP_SO', GAP_SO)
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|
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# post process
|
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|
|
|
|||
|
|
@ -1,24 +0,0 @@
|
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diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py
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index 4849c2bffa..76b7bc8602 100644
|
||||
--- a/src/sage/misc/sphinxify.py
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+++ b/src/sage/misc/sphinxify.py
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@@ -25,6 +25,7 @@ from __future__ import absolute_import, print_function
|
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import os
|
||||
import re
|
||||
import shutil
|
||||
+import warnings
|
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from tempfile import mkdtemp
|
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from sphinx.application import Sphinx
|
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|
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@@ -120,7 +121,10 @@ smart_quotes = no""")
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# buildername, confoverrides, status, warning, freshenv).
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sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format,
|
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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
|
||||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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,
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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.*')
|
||||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
};
|
||||
}
|
||||
|
|
@ -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/";
|
||||
};
|
||||
}
|
||||
|
|
@ -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;
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
|
|
|
|||
|
|
@ -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 = ''
|
||||
|
|
|
|||
|
|
@ -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 = ''
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
'';
|
||||
}
|
||||
Loading…
Reference in a new issue