diff options
Diffstat (limited to 'pkgs/applications/science')
33 files changed, 294 insertions, 474 deletions
diff --git a/pkgs/applications/science/logic/cryptoverif/default.nix b/pkgs/applications/science/logic/cryptoverif/default.nix index 28295ea2892..78861786def 100644 --- a/pkgs/applications/science/logic/cryptoverif/default.nix +++ b/pkgs/applications/science/logic/cryptoverif/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "cryptoverif"; - version = "2.03pl1"; + version = "2.04"; src = fetchurl { url = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz"; - sha256 = "0q7qa1qm7mbky3m36445gdmgmkb9mrhrdsk7mmwn8fzw0rfc6z00"; + sha256 = "1mzk6n0g2vdsv38y493zg85lxrpz72b92cmsray3g970xzanqd6s"; }; buildInputs = [ ocaml ]; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { ** from under $out/libexec. By default, it expects to find the files ** in $CWD which doesn't work. */ patchPhase = '' - substituteInPlace ./src/settings.ml \ + substituteInPlace ./src/syntax.ml \ --replace \"default\" \"$out/libexec/default\" ''; diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix index ea9c921f19e..b090274919b 100644 --- a/pkgs/applications/science/math/giac/default.nix +++ b/pkgs/applications/science/math/giac/default.nix @@ -9,11 +9,11 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { pname = "giac${lib.optionalString enableGUI "-with-xcas"}"; - version = "1.5.0-21"; # TODO try to remove preCheck phase on upgrade + version = "1.5.0-87"; # TODO try to remove preCheck phase on upgrade src = fetchurl { url = "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version}.tar.gz"; - sha256 = "1b9khiv0mk2xzw1rblm2jy6qsf8y6f9k7qy15sxpb21d72hzzbl2"; + sha256 = "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"; }; patches = stdenv.lib.optionals (!enableGUI) [ diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix index 1bf7d16f290..cdc81a87646 100644 --- a/pkgs/applications/science/math/maxima/default.nix +++ b/pkgs/applications/science/math/maxima/default.nix @@ -87,6 +87,10 @@ stdenv.mkDerivation ({ enableParallelBuilding = true; + passthru = { + ecl = ecl; + }; + meta = { description = "Computer algebra system"; homepage = "http://maxima.sourceforge.net"; diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix index 76e7c796a13..94b7ad266c4 100644 --- a/pkgs/applications/science/math/nauty/default.nix +++ b/pkgs/applications/science/math/nauty/default.nix @@ -7,7 +7,7 @@ stdenv.mkDerivation rec { version = "27r1"; src = fetchurl { url = "http://pallini.di.uniroma1.it/nauty${version}.tar.gz"; - sha256 = "1nym0p2djws8ylkpr0kgpxfa6fxdlh46cmvz0gn5vd02jzgs0aww"; + sha256 = "0xsfqfcknbd6g6wzpa5l7crmmk3bf3zjh37rhylq6b20dqcmvjkn"; }; outputs = [ "out" "dev" ]; configureFlags = [ diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix index a3e2f99ab27..7ec42d11ab1 100644 --- a/pkgs/applications/science/math/pari/default.nix +++ b/pkgs/applications/science/math/pari/default.nix @@ -15,7 +15,8 @@ stdenv.mkDerivation rec { version = "2.11.4"; src = fetchurl { - url = "https://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz"; + # Versions with current majorMinor values are at http://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz + url = "https://pari.math.u-bordeaux.fr/pub/pari/OLD/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.gz"; sha256 = "sha256-v8iPxPc1L0hA5uNSxy8DacvqikVAOxg0piafNwmXCxw="; }; diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix index 87fb205174b..e3474d865e2 100644 --- a/pkgs/applications/science/math/pynac/default.nix +++ b/pkgs/applications/science/math/pynac/default.nix @@ -1,5 +1,6 @@ { stdenv , fetchFromGitHub +, fetchurl , autoreconfHook , pkgconfig , flint @@ -33,6 +34,14 @@ stdenv.mkDerivation rec { pkgconfig ]; + patches = [ + (fetchurl { + name = "py_ssize_t_clean.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/py_ssize_t_clean.patch?h=9.2"; + sha256 = "0l3gbg9hc4v671zf4w376krnk3wh8hj3649610nlvzzxckcryzab"; + }) + ]; + meta = with stdenv.lib; { description = "Python is Not a CAS -- modified version of Ginac"; longDescription = '' diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index caf51c3da25..416f2b957b7 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -9,31 +9,13 @@ let inherit (pkgs) symlinkJoin callPackage nodePackages; - # https://trac.sagemath.org/ticket/15980 for tracking of python3 support - python = pkgs.python2.override { + python3 = pkgs.python3.override { packageOverrides = self: super: { - # python packages that appear unmaintained and were not accepted into the nixpkgs - # tree because of that. These packages are only dependencies of the more-or-less - # deprecated sagenb. However sagenb is still a default dependency and the doctests - # depend on it. - # See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion. - # The dependency on the sage notebook (and therefore these packages) will be - # removed in the future: - # https://trac.sagemath.org/ticket/25837 - flask-oldsessions = self.callPackage ./flask-oldsessions.nix {}; - flask-openid = self.callPackage ./flask-openid.nix {}; - python-openid = self.callPackage ./python-openid.nix {}; - sagenb = self.callPackage ./sagenb.nix { - mathjax = nodePackages.mathjax; - }; - - # Package with a cyclic dependency with sage - pybrial = self.callPackage ./pybrial.nix {}; - # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies sagelib = self.callPackage ./sagelib.nix { - inherit flint ecl arb; + inherit flint arb; inherit sage-src env-locations pynac singular; + ecl = maxima-ecl.ecl; linbox = pkgs.linbox.override { withSage = true; }; pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig }; @@ -59,9 +41,10 @@ let # A bash script setting various environment variables to tell sage where # the files its looking fore are located. Also see `sage-env`. env-locations = callPackage ./env-locations.nix { - inherit pari_data ecl; + inherit pari_data; inherit singular maxima-ecl; - cysignals = python.pkgs.cysignals; + ecl = maxima-ecl.ecl; + cysignals = python3.pkgs.cysignals; three = nodePackages.three; mathjax = nodePackages.mathjax; }; @@ -69,21 +52,22 @@ let # The shell file that gets sourced on every sage start. Will also source # the env-locations file. sage-env = callPackage ./sage-env.nix { - sagelib = python.pkgs.sagelib; + sagelib = python3.pkgs.sagelib; inherit env-locations; - inherit python ecl singular palp flint pynac pythonEnv maxima-ecl; + inherit python3 singular palp flint pynac pythonEnv maxima-ecl; + ecl = maxima-ecl.ecl; pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig }; # The documentation for sage, building it takes a lot of ram. sagedoc = callPackage ./sagedoc.nix { inherit sage-with-env; - inherit python maxima-ecl; + inherit python3 maxima-ecl; }; # sagelib with added wrappers and a dependency on sage-tests to make sure thet tests were run. sage-with-env = callPackage ./sage-with-env.nix { - inherit pythonEnv; + inherit python3 pythonEnv; inherit sage-env; inherit pynac singular maxima-ecl; pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig @@ -100,10 +84,8 @@ let sage-src = callPackage ./sage-src.nix {}; - pythonRuntimeDeps = with python.pkgs; [ + pythonRuntimeDeps = with python3.pkgs; [ sagelib - pybrial - sagenb cvxopt networkx service-identity @@ -116,11 +98,10 @@ let ipywidgets rpy2 sphinx - typing pillow ]; - pythonEnv = python.buildEnv.override { + pythonEnv = python3.buildEnv.override { extraLibs = pythonRuntimeDeps; ignoreCollisions = true; } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible @@ -129,8 +110,21 @@ let singular = pkgs.singular.override { inherit flint; }; - # https://trac.sagemath.org/ticket/26625 - maxima-ecl = pkgs.maxima-ecl; + maxima-ecl = pkgs.maxima-ecl.override { + ecl = 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 + # only works if threads are disabled. sage 9.2 tests this + # (src/sage/interfaces/tests.py) and ships ecl like so. + # https://gitlab.com/embeddable-common-lisp/ecl/-/merge_requests/1#note_1657275 + threadSupport = false; + + # if we don't use the system boehmgc, sending a SIGINT to ecl + # can segfault if we it happens during memory allocation. + # src/sage/libs/ecl.pyx would intermittently fail in this case. + useBoehmgc = true; + }; + }; # *not* to confuse with the python package "pynac" pynac = pkgs.pynac.override { inherit singular flint; }; @@ -161,9 +155,6 @@ let pari-seadata-small ]; }; - - # https://trac.sagemath.org/ticket/22191 - ecl = pkgs.ecl_16_1_2; in # A wrapper around sage that makes sure sage finds its docs (if they were build). callPackage ./sage.nix { diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix index bda2d23b9e5..b1ad0aad9c7 100644 --- a/pkgs/applications/science/math/sage/env-locations.nix +++ b/pkgs/applications/science/math/sage/env-locations.nix @@ -44,6 +44,6 @@ writeTextFile rec { export JSMOL_DIR="${jmol}/share/jsmol" export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax" export THREEJS_DIR="${three}/lib/node_modules/three" - export SAGE_INCLUDE_DIRECTORIES="${cysignals}/lib/python2.7/site-packages" + export SAGE_INCLUDE_DIRECTORIES="${cysignals}/${cysignals.pythonModule.sitePackages}" ''; } diff --git a/pkgs/applications/science/math/sage/flask-oldsessions.nix b/pkgs/applications/science/math/sage/flask-oldsessions.nix deleted file mode 100644 index 86fe9912c19..00000000000 --- a/pkgs/applications/science/math/sage/flask-oldsessions.nix +++ /dev/null @@ -1,36 +0,0 @@ -{ stdenv -, buildPythonPackage -, fetchFromGitHub -, python -, flask -}: - -buildPythonPackage rec { - pname = "Flask-OldSessions"; - version = "0.10"; - - # no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1 - src = fetchFromGitHub { - owner = "mitsuhiko"; - repo = "flask-oldsessions"; - rev = version; - sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn"; - }; - - propagatedBuildInputs = [ - flask - ]; - - # missing module flask.testsuite, probably assumes an old version of flask - doCheck = false; - checkPhase = '' - ${python.interpreter} run-tests.py - ''; - - meta = with stdenv.lib; { - description = "Provides a session class that works like the one in Flask before 0.10."; - license = licenses.bsd2; - maintainers = teams.sage.members; - homepage = "https://github.com/mitsuhiko/flask-oldsessions"; - }; -} diff --git a/pkgs/applications/science/math/sage/flask-openid.nix b/pkgs/applications/science/math/sage/flask-openid.nix deleted file mode 100644 index 900b033429e..00000000000 --- a/pkgs/applications/science/math/sage/flask-openid.nix +++ /dev/null @@ -1,28 +0,0 @@ -{ stdenv -, buildPythonPackage -, fetchPypi -, flask -, python-openid -}: - -buildPythonPackage rec { - pname = "Flask-OpenID"; - version = "1.2.5"; - - src = fetchPypi { - inherit pname version; - sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss"; - }; - - propagatedBuildInputs = [ - flask - python-openid - ]; - - meta = with stdenv.lib; { - description = "Adds openid support to flask applications"; - license = licenses.bsd2; - maintainers = teams.sage.members; - homepage = "https://pythonhosted.org/Flask-OpenID/"; - }; -} diff --git a/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch b/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch index 8cd80281d0e..d5c19a54fd9 100644 --- a/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch +++ b/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch @@ -1,17 +1,17 @@ -From 8218bd4fdeb4c92de8af0d3aabec55980fc4fb3d Mon Sep 17 00:00:00 2001 +From f5ea42a7aaed7611fb55b65897b9fcf2b7bcf97e Mon Sep 17 00:00:00 2001 From: Timo Kaufmann <timokau@zoho.com> Date: Sun, 21 Oct 2018 17:52:40 +0200 Subject: [PATCH] Only test py2/py3 optional tests when all of sage is tested --- - src/sage/doctest/control.py | 5 +++-- - 1 file changed, 3 insertions(+), 2 deletions(-) + src/sage/doctest/control.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py -index bf18df8b2b..935c67abf7 100644 +index 2d93841e50..6d156e29a1 100644 --- a/src/sage/doctest/control.py +++ b/src/sage/doctest/control.py -@@ -362,7 +362,8 @@ class DocTestController(SageObject): +@@ -375,7 +375,8 @@ class DocTestController(SageObject): if not optionaltag_regex.search(o): raise ValueError('invalid optional tag {!r}'.format(o)) @@ -21,15 +21,6 @@ index bf18df8b2b..935c67abf7 100644 self.options = options -@@ -765,7 +766,7 @@ class DocTestController(SageObject): - sage: DC = DocTestController(DD, [dirname]) - sage: DC.expand_files_into_sources() - sage: sorted(DC.sources[0].options.optional) # abs tol 1 -- ['guava', 'magma', 'py2'] -+ ['guava', 'magma'] - - We check that files are skipped appropriately:: - -- -2.18.1 +2.28.0 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 index 3f844e1b1ef..98175920238 100644 --- 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 @@ -1,17 +1,17 @@ diff --git a/src/sage/env.py b/src/sage/env.py -index 061b94f3f1..67cd091540 100644 +index 1ddfc7cfb9..45033d6328 100644 --- a/src/sage/env.py +++ b/src/sage/env.py -@@ -189,88 +189,13 @@ var('MAXIMA_FAS') +@@ -203,97 +203,13 @@ var('ARB_LIBRARY', 'arb') var('SAGE_BANNER', '') var('SAGE_IMPORTALL', 'yes') - -def _get_shared_lib_filename(libname, *additional_libnames): - """ -- Return the full path to a shared library file installed in the standard -- location for the system within the ``LIBDIR`` prefix (or -- ``$SAGE_LOCAL/lib`` in the case of manual build of Sage). +- Return the full path to a shared library file installed in +- ``$SAGE_LOCAL/lib`` or the directories associated with the +- Python sysconfig. - - This can also be passed more than one library name (e.g. for cases where - some library may have multiple names depending on the platform) in which @@ -25,7 +25,7 @@ index 061b94f3f1..67cd091540 100644 - For distributions like Debian that use a multiarch layout, we also try the - multiarch lib paths (i.e. ``/usr/lib/<arch>/``). - -- Returns ``None`` if the file does not exist. +- This returns ``None`` if the file does not exist. - - EXAMPLES:: - @@ -48,11 +48,17 @@ index 061b94f3f1..67cd091540 100644 - - for libname in (libname,) + additional_libnames: - if sys.platform == 'cygwin': -- bindir = sysconfig.get_config_var('BINDIR') +- # Later down we take the last matching DLL found, so search +- # SAGE_LOCAL second so that it takes precedence +- bindirs = [ +- sysconfig.get_config_var('BINDIR'), +- os.path.join(SAGE_LOCAL, 'bin') +- ] - pats = ['cyg{}.dll'.format(libname), 'cyg{}-*.dll'.format(libname)] - filenames = [] -- for pat in pats: -- filenames += glob.glob(os.path.join(bindir, pat)) +- for bindir in bindirs: +- for pat in pats: +- filenames += glob.glob(os.path.join(bindir, pat)) - - # Note: This is not very robust, since if there are multi DLL - # versions for the same library this just selects one more or less @@ -66,10 +72,13 @@ index 061b94f3f1..67cd091540 100644 - else: - ext = 'so' - -- libdirs = [sysconfig.get_config_var('LIBDIR')] +- libdirs = [ +- os.path.join(SAGE_LOCAL, 'lib'), +- sysconfig.get_config_var('LIBDIR') +- ] - multilib = sysconfig.get_config_var('MULTILIB') - if multilib: -- libdirs.insert(0, os.path.join(libdirs[0], multilib)) +- libdirs.insert(1, os.path.join(libdirs[0], multilib)) - - for libdir in libdirs: - basename = 'lib{}.{}'.format(libname, ext) @@ -89,7 +98,7 @@ index 061b94f3f1..67cd091540 100644 # locate libgap shared object -GAP_SO= _get_shared_lib_filename('gap','') -+GAP_SO= '/default' ++GAP_SO = '/default' var('GAP_SO', GAP_SO) # post process diff --git a/pkgs/applications/science/math/sage/patches/docutils-0.15.patch b/pkgs/applications/science/math/sage/patches/docutils-0.15.patch deleted file mode 100644 index 63f5d2e146d..00000000000 --- a/pkgs/applications/science/math/sage/patches/docutils-0.15.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py -index 4849c2bffa..76b7bc8602 100644 ---- a/src/sage/misc/sphinxify.py -+++ b/src/sage/misc/sphinxify.py -@@ -25,6 +25,7 @@ from __future__ import absolute_import, print_function - import os - import re - import shutil -+import warnings - from tempfile import mkdtemp - from sphinx.application import Sphinx - -@@ -120,7 +121,10 @@ smart_quotes = no""") - # buildername, confoverrides, status, warning, freshenv). - sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format, - confoverrides, None, None, True) -- sphinx_app.build(None, [rst_name]) -+ with warnings.catch_warnings(): -+ # Quick and dirty workaround for https://trac.sagemath.org/ticket/28856#comment:19 -+ warnings.simplefilter("ignore") -+ sphinx_app.build(None, [rst_name]) - sys.path = old_sys_path - - # We need to remove "_" from __builtin__ that the gettext module installs diff --git a/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch b/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch index 11ca7481961..a91ee319b8f 100644 --- a/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch +++ b/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch @@ -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 diff --git a/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch b/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch deleted file mode 100644 index c5f95b498d5..00000000000 --- a/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch +++ /dev/null @@ -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, diff --git a/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch b/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch deleted file mode 100644 index 49cdfd189b9..00000000000 --- a/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch +++ /dev/null @@ -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 diff --git a/pkgs/applications/science/math/sage/patches/pillow-update.patch b/pkgs/applications/science/math/sage/patches/pillow-update.patch new file mode 100644 index 00000000000..19d61552262 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/pillow-update.patch @@ -0,0 +1,39 @@ +diff --git a/src/sage/repl/image.py b/src/sage/repl/image.py +index d7d00b0..cd1607a 100644 +--- a/src/sage/repl/image.py ++++ b/src/sage/repl/image.py +@@ -77,7 +77,7 @@ class Image(SageObject): + + - ``size`` -- 2-tuple, containing (width, height) in pixels. + +- - ``color`` -- string or tuple of numeric. What colour to use ++ - ``color`` -- string, numeric or tuple of numeric. What colour to use + for the image. Default is black. If given, this should be a + a tuple with one value per band. When creating RGB images, + you can also use colour strings as supported by the +@@ -91,9 +91,15 @@ class Image(SageObject): + EXAMPLES:: + + sage: from sage.repl.image import Image +- sage: Image('P', (16, 16), (13,)) ++ sage: Image('P', (16, 16), 13) + 16x16px 8-bit Color image + """ ++ # pillow does not support Sage integers as color ++ from sage.rings.integer import Integer ++ if isinstance(color, Integer): ++ color = int(color) ++ elif isinstance(color, tuple): ++ color = tuple(int(i) if isinstance(i, Integer) else i for i in color) + self._pil = PIL.Image.new(mode, size, color) + + @property +@@ -233,7 +239,7 @@ class Image(SageObject): + EXAMPLES:: + + sage: from sage.repl.image import Image +- sage: img = Image('P', (12, 34), (13,)) ++ sage: img = Image('P', (12, 34), 13) + sage: filename = tmp_filename(ext='.png') + sage: img.save(filename) + sage: with open(filename, 'rb') as f: diff --git a/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch b/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch deleted file mode 100644 index 1b64f39fe60..00000000000 --- a/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch +++ /dev/null @@ -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 diff --git a/pkgs/applications/science/math/sage/patches/register-pretty-printer-earlier.patch b/pkgs/applications/science/math/sage/patches/register-pretty-printer-earlier.patch new file mode 100644 index 00000000000..83bd83a6d33 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/register-pretty-printer-earlier.patch @@ -0,0 +1,36 @@ +diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py +index cb3667659e..867f547d71 100644 +--- a/src/sage/doctest/forker.py ++++ b/src/sage/doctest/forker.py +@@ -200,6 +200,15 @@ def init_sage(controller=None): + from sage.cpython._py2_random import Random + sage.misc.randstate.DEFAULT_PYTHON_RANDOM = Random + ++ # IPython's pretty printer sorts the repr of dicts by their keys by default ++ # (or their keys' str() if they are not otherwise orderable). However, it ++ # disables this for CPython 3.6+ opting to instead display dicts' "natural" ++ # insertion order, which is preserved in those versions). ++ # However, this order is random in some instances. ++ # Also modifications of code may affect the order. ++ # So here we fore sorted dict printing. ++ IPython.lib.pretty.for_type(dict, _sorted_dict_pprinter_factory('{', '}')) ++ + if controller is None: + import sage.repl.ipython_kernel.all_jupyter + else: +@@ -222,15 +231,6 @@ def init_sage(controller=None): + from sage.repl.rich_output.backend_doctest import BackendDoctest + dm.switch_backend(BackendDoctest()) + +- # IPython's pretty printer sorts the repr of dicts by their keys by default +- # (or their keys' str() if they are not otherwise orderable). However, it +- # disables this for CPython 3.6+ opting to instead display dicts' "natural" +- # insertion order, which is preserved in those versions). +- # However, this order is random in some instances. +- # Also modifications of code may affect the order. +- # So here we fore sorted dict printing. +- IPython.lib.pretty.for_type(dict, _sorted_dict_pprinter_factory('{', '}')) +- + # Switch on extra debugging + from sage.structure.debug_options import debug + debug.refine_category_hash_check = True diff --git a/pkgs/applications/science/math/sage/patches/sagenb-cmp-deprecation.patch b/pkgs/applications/science/math/sage/patches/sagenb-cmp-deprecation.patch deleted file mode 100644 index 9f502a66951..00000000000 --- a/pkgs/applications/science/math/sage/patches/sagenb-cmp-deprecation.patch +++ /dev/null @@ -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.*') diff --git a/pkgs/applications/science/math/sage/patches/sagespawn-implicit-casting.patch b/pkgs/applications/science/math/sage/patches/sagespawn-implicit-casting.patch new file mode 100644 index 00000000000..2ee5db3e29c --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/sagespawn-implicit-casting.patch @@ -0,0 +1,13 @@ +diff --git a/src/sage/interfaces/sagespawn.pyx b/src/sage/interfaces/sagespawn.pyx +index 9041238f1d..469befbc66 100644 +--- a/src/sage/interfaces/sagespawn.pyx ++++ b/src/sage/interfaces/sagespawn.pyx +@@ -228,7 +228,7 @@ class SagePtyProcess(PtyProcess): + Check that the process eventually dies after calling + ``terminate_async``:: + +- sage: s.ptyproc.terminate_async(interval=0.2) ++ sage: s.ptyproc.terminate_async(interval=float(0.2)) + sage: while True: + ....: try: + ....: os.kill(s.pid, 0) diff --git a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch index 56f09279622..661077cfa8c 100644 --- a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch +++ b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch @@ -36,7 +36,7 @@ index 73a078e619..059125c59f 100644 # Run Sphinx with Sage's special logger - sys.argv = ["sphinx-build"] + build_command.split() - from .sphinxbuild import runsphinx -+ args = "python -um sage_setup.docbuild.sphinxbuild -N".split() + build_command.split() ++ args = "python3 -um sage_setup.docbuild.sphinxbuild -N".split() + build_command.split() try: - runsphinx() + subprocess.check_call(args) diff --git a/pkgs/applications/science/math/sage/patches/sympow-cache.patch b/pkgs/applications/science/math/sage/patches/sympow-cache.patch index 20020d610f8..d71f3acbc70 100644 --- a/pkgs/applications/science/math/sage/patches/sympow-cache.patch +++ b/pkgs/applications/science/math/sage/patches/sympow-cache.patch @@ -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 diff --git a/pkgs/applications/science/math/sage/pybrial.nix b/pkgs/applications/science/math/sage/pybrial.nix deleted file mode 100644 index 5fc8a4aa6f4..00000000000 --- a/pkgs/applications/science/math/sage/pybrial.nix +++ /dev/null @@ -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; - }; -} diff --git a/pkgs/applications/science/math/sage/python-openid.nix b/pkgs/applications/science/math/sage/python-openid.nix deleted file mode 100644 index 1e8a908ac79..00000000000 --- a/pkgs/applications/science/math/sage/python-openid.nix +++ /dev/null @@ -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/"; - }; -} diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix index ba7f6ccd18b..568a4a39f39 100644 --- a/pkgs/applications/science/math/sage/sage-env.nix +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -1,7 +1,6 @@ { stdenv , lib , writeTextFile -, python , sagelib , env-locations , gfortran @@ -67,11 +66,6 @@ let "@sage-local@" "@sage-local@/build" pythonEnv - # empty python env to add python wrapper that clears PYTHONHOME (see - # wrapper.nix). This is necessary because sage will call the python3 binary - # (from python2 code). The python2 PYTHONHOME (again set in wrapper.nix) - # will then confuse python3, if it is not overwritten. - python3.buildEnv gfortran # for inline fortran stdenv.cc # for cython bash @@ -129,8 +123,21 @@ writeTextFile rec { ] }' export SAGE_ROOT='${sagelib.src}' - export SAGE_LOCAL='@sage-local@' + '' + + # TODO: is using pythonEnv instead of @sage-local@ here a good + # idea? there is a test in src/sage/env.py that checks if the values + # SAGE_ROOT and SAGE_LOCAL set here match the ones set in env.py. + # we fix up env.py's SAGE_ROOT in sage-src.nix (which does not + # have access to sage-with-env), but env.py autodetects + # SAGE_LOCAL to be pythonEnv. + # setting SAGE_LOCAL to pythonEnv also avoids having to create + # python3, ipython, ipython3 and jupyter symlinks in + # sage-with-env.nix. + '' + export SAGE_LOCAL='${pythonEnv}' + export SAGE_SHARE='${sagelib}/share' + export SAGE_ENV_CONFIG_SOURCED=1 # sage-env complains if sage-env-config is not sourced beforehand orig_path="$PATH" export PATH='${runtimepath}' @@ -177,9 +184,9 @@ writeTextFile rec { ]) }' - export SAGE_LIB='${sagelib}/${python.sitePackages}' + export SAGE_LIB='${sagelib}/${python3.sitePackages}' - export SAGE_EXTCODE='${sagelib.src}/src/ext' + export SAGE_EXTCODE='${sagelib.src}/src/sage/ext_data' # for find_library export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH" diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 4791d12450a..8948621a025 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -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. @@ -61,10 +40,17 @@ stdenv.mkDerivation rec { # 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 + # Sage's workaround to pretty print dicts (in + # src/sage/doctest/forker.py:init_sage) runs too late (after + # controller.load_environment(), which imports sage.all.*) to to + # affect sage.sandpiles.Sandpile{Config,Divisor}'s pretty printer. + # Due to the sandpiles module being lazily loaded, this only + # affects the first run (subsequent runs read from an import cache + # at ~/.sage/cache and are not affected), which is probably why + # other distributions don't hit this bug. This breaks two sandpile + # tests, so do the workaround a little bit earlier. + # https://trac.sagemath.org/ticket/31053 + ./patches/register-pretty-printer-earlier.patch ]; # Since sage unfortunately does not release bugfix releases, packagers must @@ -74,6 +60,17 @@ stdenv.mkDerivation rec { # To help debug the transient error in # https://trac.sagemath.org/ticket/23087 when it next occurs. ./patches/configurationpy-error-verbose.patch + + # fix intermittent errors in Sage 9.2's psage.py (this patch is + # already included in Sage 9.3): https://trac.sagemath.org/ticket/30730 + (fetchpatch { + name = "fix-psage-is-locked.patch"; + url = "https://git.sagemath.org/sage.git/patch/?id=75df605f216ddc7b6ca719be942d666b241520e9"; + sha256 = "0g9pl1wbb3sgs26d3bvv70cpa77sfskylv4kd255y1794f1fgk4q"; + }) + + # fix intermittent errors in sagespawn.pyx: https://trac.sagemath.org/ticket/31052 + ./patches/sagespawn-implicit-casting.patch ]; # Patches needed because of package updates. We could just pin the versions of @@ -96,55 +93,16 @@ 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"; - }) + # adapt sage's Image class to pillow 8.0.1 (https://trac.sagemath.org/ticket/30971) + ./patches/pillow-update.patch ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; @@ -152,16 +110,16 @@ stdenv.mkDerivation rec { postPatch = '' # make sure shebangs etc are fixed, but sage-python23 still works find . -type f -exec sed \ - -e 's/sage-python23/python/g' \ + -e 's/sage-python23/python3/g' \ -i {} \; echo '#!${runtimeShell} - python "$@"' > build/bin/sage-python23 + python3 "$@"' > 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', '$out/src')|" \ + "s|var('SAGE_ROOT'.*|var('SAGE_ROOT', '$out')|" \ src/sage/env.py # Do not use sage-env-config (generated by ./configure). @@ -169,7 +127,39 @@ stdenv.mkDerivation rec { echo '# do nothing' > src/bin/sage-env-config ''; - configurePhase = "# do nothing"; + # Test src/doc/en/reference/spkg/conf.py will fail if + # src/doc/en/reference/spkg/index.rst is not generated. It is + # generated by src/doc/bootstrap, so I've copied the relevant part + # here. An alternative would be to create an empty + # src/doc/en/reference/spkg/index.rst file. + configurePhase = '' + OUTPUT_DIR="src/doc/en/reference/spkg" + mkdir -p "$OUTPUT_DIR" + OUTPUT_INDEX="$OUTPUT_DIR"/index.rst + cat > "$OUTPUT_INDEX" <<EOF + + External Packages + ================= + + .. toctree:: + :maxdepth: 1 + + EOF + for PKG_SCRIPTS in build/pkgs/*; do + if [ -d "$PKG_SCRIPTS" ]; then + PKG_BASE=$(basename "$PKG_SCRIPTS") + if [ -f "$PKG_SCRIPTS"/SPKG.rst ]; then + # Instead of just copying, we may want to call + # a version of sage-spkg-info to format extra information. + cp "$PKG_SCRIPTS"/SPKG.rst "$OUTPUT_DIR"/$PKG_BASE.rst + echo >> "$OUTPUT_INDEX" " $PKG_BASE" + fi + fi + done + cat >> "$OUTPUT_INDEX" <<EOF + .. include:: ../footer.txt + EOF + ''; buildPhase = "# do nothing"; diff --git a/pkgs/applications/science/math/sage/sage-with-env.nix b/pkgs/applications/science/math/sage/sage-with-env.nix index 87c1e07f530..f204d97961b 100644 --- a/pkgs/applications/science/math/sage/sage-with-env.nix +++ b/pkgs/applications/science/math/sage/sage-with-env.nix @@ -13,7 +13,7 @@ , pari , gmp , gfan -, python2 +, python3 , flintqs , eclib , ntl @@ -50,11 +50,11 @@ let ]; # remove python prefix, replace "-" in the name by "_", apply patch_names - # python2.7-some-pkg-1.0 -> some_pkg-1.0 + # python3.8-some-pkg-1.0 -> some_pkg-1.0 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; + # remove python3.8- + 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); diff --git a/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix index a21bffea14c..e2acef7b8eb 100644 --- a/pkgs/applications/science/math/sage/sage.nix +++ b/pkgs/applications/science/math/sage/sage.nix @@ -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; diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix index bf618fe64f4..a10672f3a09 100644 --- a/pkgs/applications/science/math/sage/sagedoc.nix +++ b/pkgs/applications/science/math/sage/sagedoc.nix @@ -1,6 +1,6 @@ { stdenv , sage-with-env -, python +, python3 , maxima-ecl , tachyon , jmol @@ -17,16 +17,15 @@ stdenv.mkDerivation rec { # modules are imported and because matplotlib is used to produce plots. buildInputs = [ sage-with-env.env.lib - python + python3 maxima-ecl tachyon jmol cddlib - ] ++ (with python.pkgs; [ + ] ++ (with python3.pkgs; [ psutil future sphinx - sagenb scipy sympy matplotlib @@ -35,8 +34,6 @@ stdenv.mkDerivation rec { ipykernel ipywidgets jupyter_client - typing - pybrial ]); unpackPhase = '' @@ -47,13 +44,26 @@ stdenv.mkDerivation rec { chmod -R 755 "$SAGE_DOC_SRC_OVERRIDE" ''; + postPatch = '' + # src/doc/bootstrap generates installation instructions for + # arch, debian, fedora, cygwin and homebrew. as a hack, disable + # including the generated files. + sed -i "/literalinclude/d" $SAGE_DOC_SRC_OVERRIDE/en/installation/source.rst + ''; + buildPhase = '' export SAGE_NUM_THREADS="$NIX_BUILD_CORES" export HOME="$TMPDIR/sage_home" mkdir -p "$HOME" # needed to link them in the sage docs using intersphinx - export PPLPY_DOCS=${python.pkgs.pplpy.doc}/share/doc/pplpy + export PPLPY_DOCS=${python3.pkgs.pplpy.doc}/share/doc/pplpy + + # adapted from src/doc/bootstrap + OUTPUT_DIR="$SAGE_DOC_SRC_OVERRIDE/en/reference/repl" + mkdir -p "$OUTPUT_DIR" + OUTPUT="$OUTPUT_DIR/options.txt" + ${sage-with-env}/bin/sage -advanced > "$OUTPUT" ${sage-with-env}/bin/sage -python -m sage_setup.docbuild \ --mathjax \ diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index 830d806a8bc..1c2235bf71b 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -15,6 +15,7 @@ , ecm , flint , gd +, giac , givaro , glpk , gsl @@ -51,6 +52,7 @@ , libbraiding , gmpy2 , pplpy +, sqlite }: assert (!blas.isILP64) && (!lapack.isILP64); @@ -94,6 +96,7 @@ buildPythonPackage rec { ecm fflas-ffpack flint + giac givaro glpk gsl @@ -124,6 +127,7 @@ buildPythonPackage rec { libbraiding gmpy2 pplpy + sqlite ]; buildPhase = '' diff --git a/pkgs/applications/science/math/sage/sagenb.nix b/pkgs/applications/science/math/sage/sagenb.nix deleted file mode 100644 index ad5c53b6c11..00000000000 --- a/pkgs/applications/science/math/sage/sagenb.nix +++ /dev/null @@ -1,57 +0,0 @@ -{ stdenv -, python -, buildPythonPackage -, fetchFromGitHub -, mathjax -, twisted -, flask -, flask-oldsessions -, flask-openid -, flask-autoindex -, flask-babel -}: - -# Has a cyclic dependency with sage (not expressed here) and is not useful outside of sage. -# Deprecated, hopefully soon to be removed. See -# https://trac.sagemath.org/ticket/25837 - -buildPythonPackage rec { - pname = "sagenb"; - version = "1.1.2"; - - src = fetchFromGitHub { - owner = "sagemath"; - repo = "sagenb"; - rev = version; - sha256 = "0bxvhr03qh2nsjdfc4pyfiqrn9jhp3vf7irsc9gqx0185jlblbxs"; - }; - - patches = [ - # cmp deprecation in attrs needs to be handled in twisted - ./patches/sagenb-cmp-deprecation.patch - ]; - - propagatedBuildInputs = [ - twisted - flask - flask-oldsessions - flask-openid - flask-autoindex - flask-babel - ]; - - # tests depend on sage - doCheck = false; - - meta = with stdenv.lib; { - description = "Sage Notebook"; - license = licenses.gpl3Plus; - maintainers = teams.sage.members; - }; - - # let sagenb use mathjax - postInstall = '' - mkdir -p "$out/${python.sitePackages}/sagenb/data" - ln -s ${mathjax}/lib/node_modules/mathjax "$out/${python.sitePackages}/sagenb/data/mathjax" - ''; -} diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix index 0ba1cd0d2fa..11d73095834 100644 --- a/pkgs/applications/science/misc/simgrid/default.nix +++ b/pkgs/applications/science/misc/simgrid/default.nix @@ -18,14 +18,14 @@ in stdenv.mkDerivation rec { pname = "simgrid"; - version = "3.25"; + version = "3.26"; src = fetchFromGitLab { domain = "framagit.org"; owner = pname; repo = pname; rev = "v${version}"; - sha256 = "019fgryfwpcrkv1f3271v7qxk0mfw2w990vgnk1cqhmr9i1f17gs"; + sha256 = "0kwiggdjqjhjvmwb1m7hb9clvm3xz948fy5ia67dif2pakwad754"; }; nativeBuildInputs = [ cmake perl python3 boost valgrind ] |