diff options
Diffstat (limited to 'pkgs/applications/science')
7 files changed, 33 insertions, 22 deletions
diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix index bee43da6719d..e64c9d3493e9 100644 --- a/pkgs/applications/science/biology/truvari/default.nix +++ b/pkgs/applications/science/biology/truvari/default.nix @@ -5,13 +5,13 @@ python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "1.3.2"; + version = "1.3.4"; src = fetchFromGitHub { owner = "spiralgenetics"; repo = "truvari"; rev = "v${version}"; - sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1"; + sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v"; }; propagatedBuildInputs = with python3Packages; [ @@ -25,8 +25,9 @@ python3Packages.buildPythonApplication rec { prePatch = '' substituteInPlace ./setup.py \ - --replace '"progressbar2==3.41.0",' "" \ - --replace '"pysam==0.15.2",' "" + --replace '"progressbar2==3.41.0",' '"progressbar2==3.47.0",' \ + --replace '"pysam==0.15.2",' '"pysam==0.15.4",' \ + --replace '"pyfaidx==0.5.5.2",' '"pyfaidx==0.5.8",' ''; meta = with lib; { diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index b27af67c974f..2c155e4e848f 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with stdenv.lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.4.0"; + version = "20.6.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "12kygxq24in7hbp7shkx1baqig8rwmzvv0d3kc3ld9sj9hb0a2n1"; + sha256 = "1vd1hsj36wzghpn6xnppjmva35kdcin7h0xdj3xmi4w5l3qw7fl6"; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix index d37f8d17336e..a5abbe2d1de6 100644 --- a/pkgs/applications/science/chemistry/octopus/default.nix +++ b/pkgs/applications/science/chemistry/octopus/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { pname = "octopus"; - version = "9.1"; + version = "9.2"; src = fetchFromGitLab { owner = "octopus-code"; repo = "octopus"; rev = version; - sha256 = "1l5fqgllk7rij16q7a3la7qq6isy8a5n37vk400qcscw1v32s90h"; + sha256 = "083z51sjv70asr04rv53wb9gf4396nblq1zl22qw7jdr28hji4is"; }; nativeBuildInputs = [ perl procps autoreconfHook ]; diff --git a/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/pkgs/applications/science/chemistry/quantum-espresso/default.nix index ea80e9fd5ca7..bd420519ce01 100644 --- a/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -4,12 +4,12 @@ }: stdenv.mkDerivation rec { - version = "6.4.1"; + version = "6.5"; pname = "quantum-espresso"; src = fetchurl { url = "https://gitlab.com/QEF/q-e/-/archive/qe-${version}/q-e-qe-${version}.tar.gz"; - sha256 = "027skhp2zzx0f4mh6azqjljdimchak5cdn13v4x7aj5q2zvfkmxh"; + sha256 = "00nnsq1vq579xsmkvwrgs6bdqdcbdlsmcp4yfynnvs40ca52m2r5"; }; passthru = { @@ -35,7 +35,7 @@ configureFlags = if (mpi != null) then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${g nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. ''; - homepage = https://www.quantum-espresso.org/; + homepage = "https://www.quantum-espresso.org/"; license = licenses.gpl2; platforms = [ "x86_64-linux" ]; maintainers = [ maintainers.costrouc ]; diff --git a/pkgs/applications/science/electronics/fped/default.nix b/pkgs/applications/science/electronics/fped/default.nix index 4eb666ada7ce..f93fddba8cb5 100644 --- a/pkgs/applications/science/electronics/fped/default.nix +++ b/pkgs/applications/science/electronics/fped/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation { makeFlags = [ "PREFIX=${placeholder "out"}" "LEX=flex" - "RGBDEF=${netpbm}/share/netpbm/misc/rgb.txt" + "RGBDEF=${netpbm.out}/share/netpbm/misc/rgb.txt" ]; nativeBuildInputs = [ diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index d718dd01ed42..ae8b0ada8062 100644 --- a/pkgs/applications/science/logic/lean/default.nix +++ b/pkgs/applications/science/logic/lean/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.6.0"; + version = "3.6.1"; src = fetchFromGitHub { owner = "leanprover-community"; repo = "lean"; rev = "v${version}"; - sha256 = "1filkhyqcjglbavbkjra0nk3y7hw8993wyl7r87ikydb2bjishsc"; + sha256 = "0crcpzbz75mdyi1vi4mygw3mj4lx73vff58fkic1gfxlpwrwgi20"; }; nativeBuildInputs = [ cmake ]; @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Automatic and interactive theorem prover"; - homepage = https://leanprover.github.io/; + homepage = "https://leanprover.github.io/"; license = licenses.asl20; platforms = platforms.unix; maintainers = with maintainers; [ thoughtpolice gebner ]; diff --git a/pkgs/applications/science/logic/monosat/default.nix b/pkgs/applications/science/logic/monosat/default.nix index c0512b744884..ba0e787af721 100644 --- a/pkgs/applications/science/logic/monosat/default.nix +++ b/pkgs/applications/science/logic/monosat/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, zlib, gmp, jdk8, +{ stdenv, fetchpatch, fetchFromGitHub, cmake, zlib, gmp, jdk8, # The JDK we use on Darwin currenly makes extensive use of rpaths which are # annoying and break the python library, so let's not bother for now includeJava ? !stdenv.hostPlatform.isDarwin, includeGplCode ? true }: @@ -20,9 +20,17 @@ let inherit rev sha256; }; + patches = [ + # Python 3.8 compatibility + (fetchpatch { + url = https://github.com/sambayless/monosat/commit/a5079711d0df0451f9840f3a41248e56dbb03967.patch; + sha256 = "1p2y0jw8hb9c90nbffhn86k1dxd6f6hk5v70dfmpzka3y6g1ksal"; + }) + ]; + core = stdenv.mkDerivation { name = "${pname}-${version}"; - inherit src; + inherit src patches; buildInputs = [ cmake zlib gmp jdk8 ]; cmakeFlags = [ @@ -48,20 +56,22 @@ let }; python = { buildPythonPackage, cython }: buildPythonPackage { - inherit pname version src; - - # The top-level "source" is what fetchFromGitHub gives us. The rest is inside the repo - sourceRoot = "source/src/monosat/api/python/"; + inherit pname version src patches; propagatedBuildInputs = [ core cython ]; # This tells setup.py to use cython, which should produce faster bindings MONOSAT_CYTHON = true; + # After patching src, move to where the actually relevant source is. This could just be made + # the sourceRoot if it weren't for the patch. + postPatch = '' + cd src/monosat/api/python + '' + # The relative paths here don't make sense for our Nix build # TODO: do we want to just reference the core monosat library rather than copying the # shared lib? The current setup.py copies the .dylib/.so... - postPatch = '' + '' substituteInPlace setup.py \ --replace 'library_dir = "../../../../"' 'library_dir = "${core}/lib/"' ''; |