From 56d58ecb241bcec3b0a55cc1c9748f358b2a02ef Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 24 Feb 2020 19:40:14 +0000 Subject: quantum-espresso: 6.4.1 -> 6.5 --- pkgs/applications/science/chemistry/quantum-espresso/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'pkgs/applications/science') 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 ]; -- cgit 1.4.1 From 95558343993bcae045b955dfc96737ba733e1c69 Mon Sep 17 00:00:00 2001 From: Jan Tojnar Date: Wed, 26 Feb 2020 00:41:09 +0100 Subject: netpbm: split into multiple outputs --- pkgs/applications/editors/texmacs/darwin.nix | 2 +- pkgs/applications/science/electronics/fped/default.nix | 2 +- pkgs/tools/graphics/netpbm/default.nix | 4 ++++ pkgs/tools/graphics/pfstools/default.nix | 6 +++--- pkgs/tools/graphics/sng/default.nix | 2 +- pkgs/tools/misc/yad/default.nix | 2 +- pkgs/tools/text/groff/default.nix | 12 ++++++------ 7 files changed, 17 insertions(+), 13 deletions(-) (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/editors/texmacs/darwin.nix b/pkgs/applications/editors/texmacs/darwin.nix index 5d5843890e14..a5117f3a6786 100644 --- a/pkgs/applications/editors/texmacs/darwin.nix +++ b/pkgs/applications/editors/texmacs/darwin.nix @@ -49,7 +49,7 @@ stdenv.mkDerivation { "${ghostscript}/bin:" + (if aspell == null then "" else "${aspell}/bin:") + (if tex == null then "" else "${tex}/bin:") + - (if netpbm == null then "" else "${netpbm}/bin:") + + (if netpbm == null then "" else "${stdenv.lib.getBin netpbm}/bin:") + (if imagemagick == null then "" else "${imagemagick}/bin:"); enableParallelBuilding = true; 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=${netpbm.out}/share/netpbm/misc/rgb.txt" ]; nativeBuildInputs = [ diff --git a/pkgs/tools/graphics/netpbm/default.nix b/pkgs/tools/graphics/netpbm/default.nix index 2755b6b2a0e5..f50b9d63f002 100644 --- a/pkgs/tools/graphics/netpbm/default.nix +++ b/pkgs/tools/graphics/netpbm/default.nix @@ -19,6 +19,8 @@ stdenv.mkDerivation { # https://sourceforge.net/p/netpbm/code/HEAD/log/?path=/advanced name = "netpbm-10.89.1"; + outputs = [ "bin" "out" "dev" ]; + src = fetchsvn { url = "https://svn.code.sf.net/p/netpbm/code/advanced"; rev = "3735"; @@ -96,6 +98,8 @@ stdenv.mkDerivation { wrapProgram "$out/bin/$prog" --prefix PATH : "$out/bin" done + moveToOutput bin "''${!outputBin}" + runHook postInstall ''; diff --git a/pkgs/tools/graphics/pfstools/default.nix b/pkgs/tools/graphics/pfstools/default.nix index 6a0385614e87..668f73c04f42 100644 --- a/pkgs/tools/graphics/pfstools/default.nix +++ b/pkgs/tools/graphics/pfstools/default.nix @@ -18,9 +18,9 @@ stdenv.mkDerivation rec { preConfigure = '' rm cmake/FindNETPBM.cmake - echo "SET(NETPBM_LIBRARY `find ${netpbm} -name "*.${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake - echo "SET(NETPBM_LIBRARIES `find ${netpbm} -name "*.${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake - echo "SET(NETPBM_INCLUDE_DIR ${netpbm}/include/netpbm)" >> cmake/FindNETPBM.cmake + echo "SET(NETPBM_LIBRARY `find ${stdenv.lib.getLib netpbm} -name "*.${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake + echo "SET(NETPBM_LIBRARIES `find ${stdenv.lib.getLib netpbm} -name "*.${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake + echo "SET(NETPBM_INCLUDE_DIR ${stdenv.lib.getDev netpbm}/include/netpbm)" >> cmake/FindNETPBM.cmake echo "INCLUDE(FindPackageHandleStandardArgs)" >> cmake/FindNETPBM.cmake echo "FIND_PACKAGE_HANDLE_STANDARD_ARGS(NETPBM DEFAULT_MSG NETPBM_LIBRARY NETPBM_INCLUDE_DIR)" >> cmake/FindNETPBM.cmake ''; diff --git a/pkgs/tools/graphics/sng/default.nix b/pkgs/tools/graphics/sng/default.nix index c7d2f49406b7..71bf0160a1e1 100644 --- a/pkgs/tools/graphics/sng/default.nix +++ b/pkgs/tools/graphics/sng/default.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { buildInputs = [ libpng ]; configureFlags = [ - "--with-rgbtxt=${netpbm}/share/netpbm/misc/rgb.txt" + "--with-rgbtxt=${netpbm.out}/share/netpbm/misc/rgb.txt" ]; meta = with stdenv.lib; { diff --git a/pkgs/tools/misc/yad/default.nix b/pkgs/tools/misc/yad/default.nix index 776b41ac1aaf..d6b1b423ae2f 100644 --- a/pkgs/tools/misc/yad/default.nix +++ b/pkgs/tools/misc/yad/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { sed -i src/form.c -e '21i#include ' # there is no point to bring in the whole netpbm package just for this file - install -Dm644 ${netpbm}/share/netpbm/misc/rgb.txt $out/share/yad/rgb.txt + install -Dm644 ${netpbm.out}/share/netpbm/misc/rgb.txt $out/share/yad/rgb.txt ''; postAutoreconf = '' diff --git a/pkgs/tools/text/groff/default.nix b/pkgs/tools/text/groff/default.nix index ec7e724d1fc3..391e7543eca5 100644 --- a/pkgs/tools/text/groff/default.nix +++ b/pkgs/tools/text/groff/default.nix @@ -29,13 +29,13 @@ stdenv.mkDerivation rec { --replace "psselect" "${psutils}/bin/psselect" '' + stdenv.lib.optionalString (netpbm != null) '' substituteInPlace src/preproc/html/pre-html.cpp \ - --replace "pnmcut" "${netpbm}/bin/pnmcut" \ - --replace "pnmcrop" "${netpbm}/bin/pnmcrop" \ - --replace "pnmtopng" "${netpbm}/bin/pnmtopng" + --replace "pnmcut" "${stdenv.lib.getBin netpbm}/bin/pnmcut" \ + --replace "pnmcrop" "${stdenv.lib.getBin netpbm}/bin/pnmcrop" \ + --replace "pnmtopng" "${stdenv.lib.getBin netpbm}/bin/pnmtopng" substituteInPlace tmac/www.tmac \ - --replace "pnmcrop" "${netpbm}/bin/pnmcrop" \ - --replace "pngtopnm" "${netpbm}/bin/pngtopnm" \ - --replace "@PNMTOPS_NOSETPAGE@" "${netpbm}/bin/pnmtops -nosetpage" + --replace "pnmcrop" "${stdenv.lib.getBin netpbm}/bin/pnmcrop" \ + --replace "pngtopnm" "${stdenv.lib.getBin netpbm}/bin/pngtopnm" \ + --replace "@PNMTOPS_NOSETPAGE@" "${stdenv.lib.getBin netpbm}/bin/pnmtops -nosetpage" ''; buildInputs = [ ghostscript psutils netpbm perl ]; -- cgit 1.4.1 From dbb4826457929842e2ae48eb4ad98cba976cd645 Mon Sep 17 00:00:00 2001 From: scalavision Date: Mon, 24 Feb 2020 17:58:21 +0100 Subject: truvari:1.3.2->1.3.4 --- pkgs/applications/science/biology/truvari/default.nix | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'pkgs/applications/science') 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${version}"; - sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1"; + sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v"; }; propagatedBuildInputs = with python3Packages; [ @@ -25,8 +25,9 @@ python3Packages.buildPythonApplication rec { prePatch = '' substituteInPlace ./setup.py \ - --replace '"progressbar2==3.41.0",' "" \ - --replace '"pysam==0.15.2",' "" + --replace '"progressbar2==3.41.0",' '"progressbar2==3.47.0",' \ + --replace '"pysam==0.15.2",' '"pysam==0.15.4",' \ + --replace '"pyfaidx==0.5.5.2",' '"pyfaidx==0.5.8",' ''; meta = with lib; { -- cgit 1.4.1 From b07eb540480ece33e44ddc97d1c072138bac082f Mon Sep 17 00:00:00 2001 From: Brenton Horne Date: Fri, 28 Feb 2020 00:13:58 +1000 Subject: marvin: 20.4.0 -> 20.6.0 --- pkgs/applications/science/chemistry/marvin/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index b27af67c974f..2c155e4e848f 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with stdenv.lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.4.0"; + version = "20.6.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "12kygxq24in7hbp7shkx1baqig8rwmzvv0d3kc3ld9sj9hb0a2n1"; + sha256 = "1vd1hsj36wzghpn6xnppjmva35kdcin7h0xdj3xmi4w5l3qw7fl6"; }; nativeBuildInputs = [ dpkg makeWrapper ]; -- cgit 1.4.1 From 2148a154c627845194217bb9886d24268052d9b4 Mon Sep 17 00:00:00 2001 From: Aiken Cairncross Date: Mon, 2 Mar 2020 22:18:08 +0000 Subject: python3Packages.monosat: Fix Python 3.8 build --- .../applications/science/logic/monosat/default.nix | 24 +++++++++++++++------- 1 file changed, 17 insertions(+), 7 deletions(-) (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/science/logic/monosat/default.nix b/pkgs/applications/science/logic/monosat/default.nix index c0512b744884..d7718f71b727 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 = "0fwsk67798dns7izdry19r7r3nmym4cbgxfpbjbnx4b4mlak65j8"; + }) + ]; + 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/"' ''; -- cgit 1.4.1 From eebd6fe75a2306469ed5554975b11246f3ce3e56 Mon Sep 17 00:00:00 2001 From: Markus Kowalewski Date: Tue, 3 Mar 2020 10:54:23 +0100 Subject: octopus: 9.1 -> 9.2 --- pkgs/applications/science/chemistry/octopus/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science') 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 ]; -- cgit 1.4.1 From 3db82f6fc317516303f93b61ef01138f7c040cbd Mon Sep 17 00:00:00 2001 From: Aiken Cairncross Date: Tue, 3 Mar 2020 17:44:33 +0000 Subject: python3Packages.monosat: Fix hash PR #81562 inadvertently broke these builds --- pkgs/applications/science/logic/monosat/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/science/logic/monosat/default.nix b/pkgs/applications/science/logic/monosat/default.nix index d7718f71b727..ba0e787af721 100644 --- a/pkgs/applications/science/logic/monosat/default.nix +++ b/pkgs/applications/science/logic/monosat/default.nix @@ -24,7 +24,7 @@ let # Python 3.8 compatibility (fetchpatch { url = https://github.com/sambayless/monosat/commit/a5079711d0df0451f9840f3a41248e56dbb03967.patch; - sha256 = "0fwsk67798dns7izdry19r7r3nmym4cbgxfpbjbnx4b4mlak65j8"; + sha256 = "1p2y0jw8hb9c90nbffhn86k1dxd6f6hk5v70dfmpzka3y6g1ksal"; }) ]; -- cgit 1.4.1 From 5b833c08ef127a48cd315dae774d6bbb85ed1bba Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Wed, 4 Mar 2020 06:26:01 +0000 Subject: lean: 3.6.0 -> 3.6.1 --- pkgs/applications/science/logic/lean/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'pkgs/applications/science') 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 ]; -- cgit 1.4.1 From 343ec8071230a84ed7283dad6c726b8e08a96d0e Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Wed, 4 Mar 2020 09:58:40 +0000 Subject: picard-tools: 2.21.8 -> 2.22.0 --- pkgs/applications/science/biology/picard-tools/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 42b13a981d9d..93f66810549b 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.21.8"; + version = "2.22.0"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0wxacfyxqvd39mzmwkwz39g4mf0ig1zcgymwbhsnhmn9j60mdmrf"; + sha256 = "1qgg8r81xn2z965v78kfj05vycrd2cz48gxk5csr6kvwk3ba286c"; }; nativeBuildInputs = [ makeWrapper ]; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF"; license = licenses.mit; - homepage = https://broadinstitute.github.io/picard/; + homepage = "https://broadinstitute.github.io/picard/"; maintainers = with maintainers; [ jbedo ]; platforms = platforms.all; }; -- cgit 1.4.1