diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
20 files changed, 200 insertions, 123 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix index e5a9fca33374..9f65c63f7a6f 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix @@ -7,8 +7,8 @@ let in stdenv.mkDerivation rec { - srcVersion = "jun19b"; - version = "20190601_b"; + srcVersion = "jul19a"; + version = "20190701_a"; name = "gildas-${version}"; src = fetchurl { @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { # source code of the previous release to a different directory urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.xz" "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.xz" ]; - sha256 = "363d191afdb1fda12ec19d6b9c3ab4189e7c3b036e78f7359d17671d846118ce"; + sha256 = "97eaa0d0a0f53f0616462642a9bfaddb0305a8a0948e60531d8a524a13a370b6"; }; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix index fb7963416167..2480b80316eb 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix @@ -6,13 +6,13 @@ mkDerivation rec { name = "stellarium-${version}"; - version = "0.19.0"; + version = "0.19.1"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; rev = "v${version}"; - sha256 = "1x9s9v9ann93nyqd8n8adwhx66xgq5vp0liyzl1h1ji6qk8jla3c"; + sha256 = "0hf1wv2bb5j7ny2xh29mj9m4hjblhn02zylay8gl85w7xlqs7s5r"; }; nativeBuildInputs = [ cmake perl ]; diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix index 781ceb3df59e..0e2b5d8b25fe 100644 --- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix @@ -2,21 +2,22 @@ , fetchFromGitHub , cmake , libyamlcpp +, git }: stdenv.mkDerivation rec { - version = "1.0.20170130"; + version = "1.0.20190410"; name = "dcm2niix-${version}"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; rev = "v${version}"; - sha256 = "1f2nzd8flp1rfn725bi64z7aw3ccxyyygzarxijw6pvgl476i532"; + sha256 = "1prwpvbi76xlpkhc4kadjhyyx0s71cs30hi6anknhfm6hdyd26ms"; }; enableParallelBuilding = true; - nativeBuildInputs = [ cmake ]; + nativeBuildInputs = [ cmake git ]; buildInputs = [ libyamlcpp ]; meta = with stdenv.lib; { diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix index 3cd83a5cdd27..1bdb31616e4d 100644 --- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix @@ -4,26 +4,26 @@ let hts-nim = fetchFromGitHub { owner = "brentp"; repo = "hts-nim"; - rev = "v0.2.5"; - sha256 = "1fma99rjqxgg9dihkd10hm1jjp5amsk5wsxnvq1lk4mcsjix5xqb"; + rev = "v0.2.14"; + sha256 = "0d1z4b6mrppmz3hgkxd4wcy79w68icvhi7q7n3m2k17n8f3xbdx3"; }; docopt = fetchFromGitHub { owner = "docopt"; repo = "docopt.nim"; - rev = "v0.6.5"; - sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr"; + rev = "v0.6.7"; + sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37"; }; in stdenv.mkDerivation rec { name = "mosdepth-${version}"; - version = "0.2.3"; + version = "0.2.6"; src = fetchFromGitHub { owner = "brentp"; repo = "mosdepth"; rev = "v${version}"; - sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7"; + sha256 = "0i9pl9lsli3y84ygxanrr525gfg8fs9h481944cbzsmqmbldwvgk"; }; buildInputs = [ nim ]; diff --git a/nixpkgs/pkgs/applications/science/biology/octopus/default.nix b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix new file mode 100644 index 000000000000..0a2074a06e97 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix @@ -0,0 +1,30 @@ +{stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}: + +stdenv.mkDerivation rec { + pname = "octopus"; + version = "0.6.3-beta"; + name = "${pname}-${version}"; + + src = fetchFromGitHub { + owner = "luntergroup"; + repo = "octopus"; + rev = "v${version}"; + sha256 = "042fycg8ppld7iajpzq2d8h8wr0nw43zbl57y125sfihryvr373n"; + }; + + nativeBuildInputs = [ cmake pkg-config ]; + buildInputs = [ boost gmp htslib zlib lzma ]; + + postInstall = '' + mkdir $out/bin + mv $out/octopus $out/bin + ''; + + meta = with stdenv.lib; { + description = "Bayesian haplotype-based mutation calling"; + license = licenses.mit; + homepage = "https://github.com/luntergroup/octopus"; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.x86_64; + }; +} diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix index 444638db8e9f..90b7db4b545c 100644 --- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix +++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix @@ -13,11 +13,11 @@ let in stdenv.mkDerivation rec { name = "eagle-${version}"; - version = "9.3.2"; + version = "9.4.1"; src = fetchurl { url = "https://eagle-updates.circuits.io/downloads/${builtins.replaceStrings ["."] ["_"] version}/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz"; - sha256 = "0xrrd2d86gxrkbqvssbg8zki40hk05h48w73b0hv7wnc7wg1msir"; + sha256 = "0p3kxryvk853rx24phcadvmqn6f37rnnql8sf6cqn9cqhrrkbvlq"; }; desktopItem = makeDesktopItem { diff --git a/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix b/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix index 36a504e86faf..b531563c5c1c 100644 --- a/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "verilator-${version}"; - version = "4.014"; + version = "4.016"; src = fetchurl { url = "https://www.veripool.org/ftp/${name}.tgz"; - sha256 = "1srk9a03hbq8rdp4mma817aiq61c2hbrs66qv25zj3dfnfqigxgd"; + sha256 = "18fqm6pgscy504ql27i150fdsd2j91hw5qsnpymws3pvqj2qz2ij"; }; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix b/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix new file mode 100644 index 000000000000..21ce6be3e6c1 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix @@ -0,0 +1,55 @@ +{ stdenv, lib, fetchhg, cmake, which, python3, osi, cplex }: + +stdenv.mkDerivation rec { + name = "fast-downward-2019-05-13"; + + src = fetchhg { + url = "http://hg.fast-downward.org/"; + rev = "090f5df5d84a"; + sha256 = "14pcjz0jfzx5269axg66iq8js7lm2w3cnqrrhhwmz833prjp945g"; + }; + + nativeBuildInputs = [ cmake which ]; + buildInputs = [ python3 python3.pkgs.wrapPython osi ]; + + cmakeFlags = + lib.optional osi.withCplex [ "-DDOWNWARD_CPLEX_ROOT=${cplex}/cplex" ]; + + enableParallelBuilding = true; + + postPatch = '' + cd src + # Needed because the package tries to be too smart. + export CC="$(which $CC)" + export CXX="$(which $CXX)" + ''; + + installPhase = '' + install -Dm755 bin/downward $out/libexec/fast-downward/downward + cp -r ../translate $out/libexec/fast-downward/ + install -Dm755 ../../fast-downward.py $out/bin/fast-downward + mkdir -p $out/${python3.sitePackages} + cp -r ../../driver $out/${python3.sitePackages} + + wrapPythonProgramsIn $out/bin "$out $pythonPath" + wrapPythonProgramsIn $out/libexec/fast-downward/translate "$out $pythonPath" + # Because fast-downward calls `python translate.py` we need to return wrapped scripts back. + for i in $out/libexec/fast-downward/translate/.*-wrapped; do + name="$(basename "$i")" + name1="''${name#.}" + name2="''${name1%-wrapped}" + dir="$(dirname "$i")" + dest="$dir/$name2" + echo "Moving $i to $dest" + mv "$i" "$dest" + done + ''; + + meta = with stdenv.lib; { + description = "A domain-independent planning system"; + homepage = "http://www.fast-downward.org/"; + license = licenses.gpl3Plus; + platforms = platforms.linux; + maintainers = with maintainers; [ abbradar ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/logic/gappa/default.nix b/nixpkgs/pkgs/applications/science/logic/gappa/default.nix index 71114d2f9e12..7522eb4790ed 100644 --- a/nixpkgs/pkgs/applications/science/logic/gappa/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/gappa/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, gmp, mpfr, boost }: stdenv.mkDerivation { - name = "gappa-1.2"; + name = "gappa-1.3.5"; src = fetchurl { - url = https://gforge.inria.fr/frs/download.php/file/34787/gappa-1.2.0.tar.gz; - sha256 = "03hfzmaf5jm54sjpbks20q7qixpmagrfbnyyc276vgmiyslk4dkh"; + url = https://gforge.inria.fr/frs/download.php/file/38044/gappa-1.3.5.tar.gz; + sha256 = "0q1wdiwqj6fsbifaayb1zkp20bz8a1my81sqjsail577jmzwi07w"; }; buildInputs = [ gmp mpfr boost.dev ]; diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix index ed107765b467..a791f9a57727 100644 --- a/nixpkgs/pkgs/applications/science/math/R/default.nix +++ b/nixpkgs/pkgs/applications/science/math/R/default.nix @@ -8,11 +8,11 @@ }: stdenv.mkDerivation rec { - name = "R-3.6.0"; + name = "R-3.6.1"; src = fetchurl { url = "https://cran.r-project.org/src/base/R-3/${name}.tar.gz"; - sha256 = "02bmylmzrm9sdidirmwy233lghmd2346z725ca71ari68lzarz1n"; + sha256 = "128kifbq0w25y8aq77w289ddax5i5w2djcfsqgffrb3i7syrxajv"; }; dontUseImakeConfigure = true; @@ -27,10 +27,6 @@ stdenv.mkDerivation rec { patches = [ ./no-usr-local-search-paths.patch - (fetchpatch { - url = "https://github.com/wch/r-source/commit/aeb75e12863019be06fe6c762ab705bf5ed8b38c.patch"; - sha256 = "03xv1g1yw1dbhx4paw6pn6hkawj8sny86km3748l1vnasbham82g"; - }) ]; prePatch = stdenv.lib.optionalString stdenv.isDarwin '' diff --git a/nixpkgs/pkgs/applications/science/math/cplex/default.nix b/nixpkgs/pkgs/applications/science/math/cplex/default.nix index dc0e9ea1aa5d..a14839d3eccc 100644 --- a/nixpkgs/pkgs/applications/science/math/cplex/default.nix +++ b/nixpkgs/pkgs/applications/science/math/cplex/default.nix @@ -71,6 +71,11 @@ stdenv.mkDerivation rec { fi done ''; + + passthru = { + libArch = "x86-64_linux"; + libSuffix = "${version}0"; + }; meta = with stdenv.lib; { description = "Optimization solver for mathematical programming"; diff --git a/nixpkgs/pkgs/applications/science/math/gap/default.nix b/nixpkgs/pkgs/applications/science/math/gap/default.nix index 9b42bcd9f13a..7eb10d1f9525 100644 --- a/nixpkgs/pkgs/applications/science/math/gap/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gap/default.nix @@ -61,11 +61,11 @@ in stdenv.mkDerivation rec { pname = "gap"; # https://www.gap-system.org/Releases/ - version = "4.10.1"; + version = "4.10.2"; src = fetchurl { url = "https://www.gap-system.org/pub/gap/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2"; - sha256 = "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10"; + sha256 = "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"; }; # remove all non-essential packages (which take up a lot of space) diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix index 80b2764cdc0a..1a3ba8096e29 100644 --- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg , zlib, libGLU_combined, libGLU, xorg }: -let version = "4.3.0"; in +let version = "4.4.0"; in stdenv.mkDerivation { name = "gmsh-${version}"; src = fetchurl { url = "http://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "0ab4p2dilk4rfw1qc817rmy56qkhxaajpnqdnvahbhcbf3skd8jl"; + sha256 = "0b0h15cmi6zy31cii7r9jmfm9xksljff255dn6l9frhdjymkmx7l"; }; buildInputs = [ openblasCompat gmm fltk libjpeg zlib libGLU_combined diff --git a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix index be14d1411285..ee9bdcc6f1b0 100644 --- a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix @@ -1,8 +1,10 @@ -{ stdenv, fetchurl, autoPatchelfHook, python }: +{ stdenv, lib, fetchurl, autoPatchelfHook, python }: -stdenv.mkDerivation rec { +let + majorVersion = "8.1"; +in stdenv.mkDerivation rec { name = "gurobi-${version}"; - version = "8.1.0"; + version = "${majorVersion}.0"; src = with stdenv.lib; fetchurl { url = "http://packages.gurobi.com/${versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; @@ -44,6 +46,8 @@ stdenv.mkDerivation rec { ln -s $out/lib/gurobi-javadoc.jar $out/share/java/ ''; + passthru.libSuffix = lib.replaceStrings ["."] [""] majorVersion; + meta = with stdenv.lib; { description = "Optimization solver for mathematical programming"; homepage = https://www.gurobi.com; diff --git a/nixpkgs/pkgs/applications/science/math/sage/default.nix b/nixpkgs/pkgs/applications/science/math/sage/default.nix index 061b3beeb3f2..caf51c3da251 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/default.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/default.nix @@ -130,7 +130,7 @@ let singular = pkgs.singular.override { inherit flint; }; # https://trac.sagemath.org/ticket/26625 - maxima-ecl = pkgs.maxima-ecl-5_41; + maxima-ecl = pkgs.maxima-ecl; # *not* to confuse with the python package "pynac" pynac = pkgs.pynac.override { inherit singular flint; }; diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch deleted file mode 100644 index 9e3f0f5ae880..000000000000 --- a/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch +++ /dev/null @@ -1,26 +0,0 @@ -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/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch new file mode 100644 index 000000000000..933344aa5591 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch @@ -0,0 +1,57 @@ +diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py +index 0f2700168a..60f71357d2 100644 +--- a/src/sage_setup/docbuild/__init__.py ++++ b/src/sage_setup/docbuild/__init__.py +@@ -86,26 +86,6 @@ def builder_helper(type): + """ + Returns a function which builds the documentation for + output type ``type``. +- +- TESTS: +- +- Check that :trac:`25161` has been resolved:: +- +- sage: from sage_setup.docbuild import DocBuilder, setup_parser +- sage: DocBuilder._options = setup_parser().parse_args([])[0] # builder_helper needs _options to be set +- +- sage: import sage_setup.docbuild.sphinxbuild +- sage: def raiseBaseException(): +- ....: raise BaseException("abort pool operation") +- sage: original_runsphinx, sage_setup.docbuild.sphinxbuild.runsphinx = sage_setup.docbuild.sphinxbuild.runsphinx, raiseBaseException +- +- sage: from sage_setup.docbuild import builder_helper, build_many, build_ref_doc +- sage: helper = builder_helper("html") +- sage: try: +- ....: build_many(build_ref_doc, [("docname", "en", "html", {})]) +- ....: except Exception as E: +- ....: "Non-exception during docbuild: abort pool operation" in str(E) +- True + """ + def f(self, *args, **kwds): + output_dir = self._output_dir(type) +@@ -127,10 +107,9 @@ def builder_helper(type): + logger.debug(build_command) + + # 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() + try: +- runsphinx() ++ subprocess.check_call(args) + except Exception: + if ABORT_ON_ERROR: + raise +diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py +index 9a2fba79bc..77c8ed3592 100644 +--- a/src/sage_setup/docbuild/sphinxbuild.py ++++ b/src/sage_setup/docbuild/sphinxbuild.py +@@ -318,3 +318,8 @@ def runsphinx(): + sys.stderr = saved_stderr + sys.stdout.flush() + sys.stderr.flush() ++ ++if __name__ == '__main__': ++ import sys ++ sys.argv[0] = "sphinx-build" ++ runsphinx() diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix index e0050efe6bdd..51460154c5de 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix +++ b/nixpkgs/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 = "8.7"; + version = "8.8"; pname = "sage-src"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "05vvrd6syh0hlmrk6kzjrwd0hpmvxp8vr8p3mkjb0jh5p2kjdd27"; + sha256 = "0jm7zdkz8wfgrmf6620jfr8kgvprrz3qfl8gzx6rl5z5cm734b6x"; }; # Patches needed because of particularities of nix or the way this is packaged. @@ -45,46 +45,23 @@ stdenv.mkDerivation rec { # Fixes a potential race condition which can lead to transient doctest failures. ./patches/fix-ecl-race.patch - # Parallelize docubuild using subprocesses, fixing an isolation issue. See - # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE - (fetchpatch { - name = "sphinx-docbuild-subprocesses.patch"; - url = "https://salsa.debian.org/science-team/sagemath/raw/8a215b17e6f791ddfae6df8ce6d01dfb89acb434/debian/patches/df-subprocess-sphinx.patch"; - 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"; - }) # https://trac.sagemath.org/ticket/28007 ./patches/threejs-offline.patch + + # Parallelize docubuild using subprocesses, fixing an isolation issue. See + # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE + ./patches/sphinx-docbuild-subprocesses.patch ]; # Since sage unfortunately does not release bugfix releases, packagers must # fix those bugs themselves. This is for critical bugfixes, where "critical" # == "causes (transient) doctest failures / somebody complained". - bugfixPatches = [ - # Transient doctest failure in src/sage/modular/abvar/torsion_subgroup.py - # https://trac.sagemath.org/ticket/27477 - (fetchpatch { - name = "sig_on_in_matrix_sparce.patch"; - url = "https://git.sagemath.org/sage.git/patch?id2=10407524b18659e14e184114b61c043fb816f3c2&id=c9b0cc9d0b8748ab85e568f8f57f316c5e8cbe54"; - sha256 = "0wgp7yvn9sm1ynlhcr4l0hzmvr2n28llg4xc01p6k1zz4im64c17"; - }) - ]; + bugfixPatches = [ ]; # Patches needed because of package updates. We could just pin the versions of # dependencies, but that would lead to rebuilds, confusion and the burdons of @@ -116,35 +93,6 @@ stdenv.mkDerivation rec { stripLen = 1; }) - # https://trac.sagemath.org/ticket/26451 - (fetchSageDiff { - name = "sphinx-1.8.patch"; - base = "8.7"; - rev = "737afd8f314bd1e16feaec562bb4b5efa2effa8b"; - sha256 = "0n56ss88ds662bp49j23z5c2i6hsn3jynxw13wv76hyl0h7l1hjh"; - }) - - # https://trac.sagemath.org/ticket/27653 - (fetchpatch { - name = "sympy-1.4.patch"; - url = "https://git.sagemath.org/sage.git/patch/?h=3277ba76d0ba7174608a31a0c6623e9210c63e3d"; - sha256 = "09avaanwmdgqv14mmllbgw9z2scf4lc0y0kzdhlriiq8ss9j8iir"; - }) - - # https://trac.sagemath.org/ticket/27094 - (fetchpatch { - name = "gap-4.10.1.patch"; - url = "https://git.sagemath.org/sage.git/patch?id=d3483110474591ea6cc8e3210cd884f3e0018b3e"; - sha256 = "028i6h8l8npwzx5z0ax0rcywl85gc83qw1jf93zf523msdfcsk0n"; - }) - - # https://trac.sagemath.org/ticket/27738 - (fetchpatch { - name = "R-3.6.0.patch"; - url = "https://git.sagemath.org/sage.git/patch/?h=8b7dbd0805d02d0e8674a272e161ceb24a637966"; - sha256 = "1c81f13z1w62s06yvp43gz6vkp8mxcs289n6l4gj9xj10slimzff"; - }) - # https://trac.sagemath.org/ticket/26932 (fetchSageDiff { name = "givaro-4.1.0_fflas-ffpack-2.4.0_linbox-1.6.0.patch"; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix index 5bb7eda47d5d..e4b1aeae016a 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix @@ -99,6 +99,13 @@ stdenv.mkDerivation rec { for pkg in ${lib.concatStringsSep " " input_names}; do touch "installed/$pkg" done + + # threejs version is in format 0.<version>.minor, but sage currently still + # relies on installed_packages for the online version of threejs to work + # and expects the format r<version>. This is a hotfix for now. + # upstream: https://trac.sagemath.org/ticket/26434 + rm "installed/threejs"* + touch "installed/threejs-r${lib.versions.minor three.version}" ''; installPhase = '' diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index 7583f8c00104..d00b59307c52 100644 --- a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -8,11 +8,11 @@ stdenv.mkDerivation { - name = "gromacs-2019.2"; + name = "gromacs-2019.3"; src = fetchurl { - url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.2.tar.gz"; - sha256 = "0zlzzg27yzfbmmgy2wqmgq82nslqy02gprjvm9xwcswjf705rgxw"; + url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.3.tar.gz"; + sha256 = "0wvm6lj4hbasl2qkjcpicqjh7abxji4196dd2hmwlyivpycaa4a2"; }; buildInputs = [cmake fftw] |