diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
28 files changed, 170 insertions, 130 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix index 2eef054d5ff5..8fed2a51877f 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix @@ -3,13 +3,13 @@ stdenv.mkDerivation rec { pname = "phd2"; - version = "2.6.11"; + version = "2.6.12"; src = fetchFromGitHub { owner = "OpenPHDGuiding"; repo = "phd2"; rev = "v${version}"; - sha256 = "sha256-iautgHOVzdLWYGOVu3wHBDt30uCbaP58mDz/l7buB1k="; + sha256 = "sha256-vq6qhwL8mB5ET/9qFWDZHxqL+RDXRly+CwbRz/wuyZg="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/astronomy/xearth/default.nix b/nixpkgs/pkgs/applications/science/astronomy/xearth/default.nix index bd92ae01ebb1..7fcc588658ae 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/xearth/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/xearth/default.nix @@ -17,14 +17,18 @@ stdenv.mkDerivation rec { meta = with lib; { description = "sets the X root window to an image of the Earth"; - homepage = "http://xplanet.org"; + homepage = "https://xearth.org"; longDescription = '' Xearth sets the X root window to an image of the Earth, as seen from your favorite vantage point in space, correctly shaded for the current position of the Sun. By default, xearth updates the displayed image every five minutes. ''; maintainers = [ maintainers.mafo ]; - license = "xearth"; + license = { + fullName = "xearth license"; + url = "https://xearth.org/copyright.html"; + free = true; + }; platforms=platforms.unix; }; diff --git a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix index febfde548fd7..006b46db9974 100644 --- a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix @@ -29,13 +29,13 @@ in stdenv.mkDerivation (finalAttrs: { pname = "dssp"; - version = "4.4.4.1"; + version = "4.4.5"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = "dssp"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-sy6GBCnTGRD1YP00dKIolkr1RMboLGcd0f4kU8gCOnA="; + hash = "sha256-X0aMWqoMhmQVRHWKVm2S6JAOYiBuBBMzMoivMdpNx0M="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix index 52d388ab023d..a74208c706a1 100644 --- a/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchzip, jdk11 }: +{ lib, stdenv, fetchzip, jdk11, wrapGAppsHook }: stdenv.mkDerivation rec { pname = "igv"; @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { chmod +x $out/bin/igv chmod +x $out/bin/igvtools ''; + nativeBuildInputs = [ wrapGAppsHook ]; meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; diff --git a/nixpkgs/pkgs/applications/science/biology/kent/default.nix b/nixpkgs/pkgs/applications/science/biology/kent/default.nix index f1e891bb85aa..b6e4661ccfd6 100644 --- a/nixpkgs/pkgs/applications/science/biology/kent/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/kent/default.nix @@ -24,16 +24,12 @@ stdenv.mkDerivation rec { buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; - patchPhase = '' - runHook prePatch - + postPatch = '' substituteInPlace ./src/checkUmask.sh \ --replace "/bin/bash" "${bash}/bin/bash" substituteInPlace ./src/hg/sqlEnvTest.sh \ --replace "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config" - - runHook postPatch ''; buildPhase = '' diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix deleted file mode 100644 index f2825eeb97be..000000000000 --- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ /dev/null @@ -1,25 +0,0 @@ -{ lib, nimPackages, fetchFromGitHub, docopt, hts, pcre }: - -nimPackages.buildNimPackage rec { - pname = "mosdepth"; - version = "0.3.5"; - nimBinOnly = true; - - src = fetchFromGitHub { - owner = "brentp"; - repo = "mosdepth"; - rev = "v${version}"; - sha256 = "sha256-tG3J51PS6A0WBCZ+j/Nf7aaukFV+DZJsxpbTbvwu0zc="; - }; - - buildInputs = [ docopt hts pcre ]; - nimFlags = hts.nimFlags ++ [ "--threads:off" ]; - - meta = with lib; { - description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing"; - license = licenses.mit; - homepage = "https://github.com/brentp/mosdepth"; - maintainers = with maintainers; [ jbedo ]; - platforms = platforms.linux; - }; -} diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index 0b99c9a849d0..f006df2ae5c0 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.43"; + version = "16.1.45"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - hash = "sha256-lqHlnAeJKbj2Xs9AeAKqdWMWkmD8xWR7f3+nJsBx2YE="; + hash = "sha256-rLq0QrY1M0OptmRZ/dKUVssREnH1im9Ti89AbpsiFtg="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix index 9c98d7302f2b..b938d1659553 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,23 +3,23 @@ { "kicad" = { kicadVersion = { - version = "7.0.7"; + version = "7.0.9"; src = { - rev = "dc7665e950aa0d42de36e928af48be3b060ba5d1"; - sha256 = "1xbzf29rhqh6kl0vggdn2dblgp927096fc1lr3y4yw63b8n0qq50"; + rev = "1c81053cc40579ecd5febef1aeb1164008039deb"; + sha256 = "1hq9rba1gcks14zwbr8nbicpsil4imslgfch6ll33fhizbks3fq4"; }; }; libVersion = { - version = "7.0.7"; + version = "7.0.9"; libSources = { - symbols.rev = "c7df225d1c79b3ea842c77d928ce1f9bc1a63c5b"; - symbols.sha256 = "1wr754m4ykidds3i14gqhvyrj3mbkchp2hkfnr0rjsdaqf4zmqdf"; - templates.rev = "1561dd81d116a661a17147c3b941a3e96335eecc"; - templates.sha256 = "1qi20mrsfn4fxmr1fyphmil2i9p2nzmwk5rlfchc5aq2194nj3lq"; - footprints.rev = "ecb85886616b7a6bb957699037f6fb680ce01d30"; - footprints.sha256 = "0xnnivlqgcyaz9qay73p43jnvmvshp2b3fbh3569j7rmgi5pn8x0"; - packages3d.rev = "4fb0672db1d405b661d0cde8edb5d54ac0a95fc7"; - packages3d.sha256 = "141r5wd8s1bgyf77kvb9q14cpsiwwv4zmfzwbgcd42rflsk2lcbc"; + symbols.rev = "1ed4ed6c0696e50165b8e3d7978136a05db2d7c3"; + symbols.sha256 = "0ynsnjq3z126cjkgm1fjbjvdvpc0walnr42ya9dv46l27kxy2j77"; + templates.rev = "856bacc6782ea8c9bcb5a49a2d438a4689e0579b"; + templates.sha256 = "11582ldnv7hkljmhaym83962kixq1hjbfmdrn5laq7l4jk3l19vh"; + footprints.rev = "fe7b9aec7635caabbaa85fa8a15b85038394099b"; + footprints.sha256 = "16a4c2xs4i8wbm01a901yxabxk0qdsjkzlccfawddv82bkh4b87h"; + packages3d.rev = "5bc66f3c0f6dabf09df6c5188b8d955968500eab"; + packages3d.sha256 = "1cly28vc07i54v487zbb8d1h70nrd3naxvq146b0xnbrjwnd2q28"; }; }; }; diff --git a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix index c816b3562671..8d28e4da0f14 100644 --- a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.447"; + version = "8.3.449"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-t/gJ43VIdBIiozLfqaTy7tJsXK674gWBbW1aPHKEj3U="; + sha256 = "sha256-y0+HS1LkIFwcgDbHEvs5SXJY2b340RDT7KVupp+ZX9Y="; }; nativeBuildInputs = [ python3 ]; diff --git a/nixpkgs/pkgs/applications/science/geometry/gama/default.nix b/nixpkgs/pkgs/applications/science/geometry/gama/default.nix index 790a9b2d216e..f66770721b0e 100644 --- a/nixpkgs/pkgs/applications/science/geometry/gama/default.nix +++ b/nixpkgs/pkgs/applications/science/geometry/gama/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, lib, expat, octave, libxml2, texinfo, zip }: stdenv.mkDerivation rec { pname = "gama"; - version = "2.26"; + version = "2.27"; src = fetchurl { url = "mirror://gnu/${pname}/${pname}-${version}.tar.gz"; - sha256 = "sha256-8zKPPpbp66tD2zMmcv2H5xeCSdDhUk0uYPhqwpGqx9Y="; + sha256 = "sha256-k4s7TK/ym68v40KDzZoMMxDWFMRnsMuk6V/G9P/jM0E="; }; buildInputs = [ expat ]; diff --git a/nixpkgs/pkgs/applications/science/logic/acgtk/default.nix b/nixpkgs/pkgs/applications/science/logic/acgtk/default.nix index c876f77e12f4..3fa4111668eb 100644 --- a/nixpkgs/pkgs/applications/science/logic/acgtk/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/acgtk/default.nix @@ -3,14 +3,14 @@ stdenv.mkDerivation { pname = "acgtk"; - version = "1.5.4"; + version = "2.0.0"; src = fetchFromGitLab { domain = "gitlab.inria.fr"; owner = "acg"; repo = "dev/acgtk"; - rev = "8e630b6d91bad022bd1d1a075e7768034065c428"; - sha256 = "sha256-W/BDhbng5iYuiB7desMKvRtDFdhoaxiJNvNvtbLlA6E="; + rev = "release-2.0.0-20231009"; + hash = "sha256-ZymSQkBMBePPw7pJkfLkmqbIkQyIqB+7Pyrih2WAO50="; }; strictDeps = true; @@ -18,7 +18,7 @@ stdenv.mkDerivation { nativeBuildInputs = with ocamlPackages; [ menhir ocaml findlib dune_3 ]; buildInputs = with ocamlPackages; [ - ansiterminal cairo2 cmdliner fmt logs menhirLib mtime_1 sedlex yojson + ansiterminal cairo2 cmdliner fmt logs menhirLib mtime ocamlgraph readline sedlex yojson ]; buildPhase = '' diff --git a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix index a9b27877ab1e..ddad93b1e18a 100644 --- a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cadical"; - version = "1.8.0"; + version = "1.9.0"; src = fetchFromGitHub { owner = "arminbiere"; repo = "cadical"; rev = "rel-${version}"; - sha256 = "sha256-hY7+gTwBqQegbm5RjLKhM2vfBOjIRz797Z6wd6usj9s="; + sha256 = "sha256-2cMaBo4u7uqrsp11dc9PHOI9ZBnir51BftPE4C6/U7Q="; }; outputs = [ "out" "dev" "lib" ]; diff --git a/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix b/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix index 32243455ae5f..2ea2dea70718 100644 --- a/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, ocamlPackages, why3 }: +{ lib, stdenv, fetchFromGitHub, ocamlPackages, why3, python3 }: stdenv.mkDerivation rec { pname = "easycrypt"; @@ -16,6 +16,7 @@ stdenv.mkDerivation rec { findlib menhir ocaml + python3.pkgs.wrapPython ]; buildInputs = with ocamlPackages; [ batteries @@ -33,10 +34,13 @@ stdenv.mkDerivation rec { substituteInPlace dune-project --replace '(name easycrypt)' '(name easycrypt)(version ${version})' ''; + pythonPath = with python3.pkgs; [ pyyaml ]; + installPhase = '' runHook preInstall dune install --prefix $out ${pname} rm $out/bin/ec-runtest + wrapPythonProgramsIn "$out/lib/easycrypt/commands" "$pythonPath" runHook postInstall ''; diff --git a/nixpkgs/pkgs/applications/science/logic/lean4/default.nix b/nixpkgs/pkgs/applications/science/logic/lean4/default.nix index ecc929cb5f0e..0f3d9c99ba88 100644 --- a/nixpkgs/pkgs/applications/science/logic/lean4/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/lean4/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "lean4"; - version = "4.2.0"; + version = "4.3.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; rev = "v${version}"; - hash = "sha256-56YtHCiNMP5fJoddSokEl0ws06IwetYLer4aLCnujZA="; + hash = "sha256-2F6sibGMG1U5By/aKGluLgkXIlMpZ7m06gVEG2Uz4RQ="; }; postPatch = '' @@ -48,6 +48,11 @@ stdenv.mkDerivation rec { "-DUSE_GITHASH=OFF" ]; + # Work around https://github.com/NixOS/nixpkgs/issues/166205. + env = lib.optionalAttrs stdenv.cc.isClang { + NIX_LDFLAGS = "-l${stdenv.cc.libcxx.cxxabi.libName}"; + }; + meta = with lib; { description = "Automatic and interactive theorem prover"; homepage = "https://leanprover.github.io/"; diff --git a/nixpkgs/pkgs/applications/science/logic/surelog/default.nix b/nixpkgs/pkgs/applications/science/logic/surelog/default.nix index 5c7be408bf4a..3b58331562a2 100644 --- a/nixpkgs/pkgs/applications/science/logic/surelog/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/surelog/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "surelog"; - version = "1.76"; + version = "1.80"; src = fetchFromGitHub { owner = "chipsalliance"; repo = finalAttrs.pname; rev = "v${finalAttrs.version}"; - hash = "sha256-Vg9NZrgzFRVIsEbZQe8DItDhFOVG1XZoQWBrLzVNwLU="; + hash = "sha256-jpt/5h0HnkiJowyVDoMSyiuL6/dokB4xg1sdyctHrDs="; fetchSubmodules = false; # we use all dependencies from nix }; diff --git a/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix b/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix index ec25d58efcbf..6698e47844a2 100644 --- a/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "UHDM"; # When updating this package, also consider updating science/logic/surelog - version = "1.77"; + version = "1.80"; src = fetchFromGitHub { owner = "chipsalliance"; repo = finalAttrs.pname; rev = "v${finalAttrs.version}"; - hash = "sha256-JKhpcPG4hWlcn2C+Wlx7yNIMXXurAMxLSK4xWN2akMQ="; + hash = "sha256-/aWiN+DPlIjI89u5kx6QoyrGD4DOJTHXxIZ0qHJNDls="; fetchSubmodules = false; # we use all dependencies from nix }; diff --git a/nixpkgs/pkgs/applications/science/math/bcal/default.nix b/nixpkgs/pkgs/applications/science/math/bcal/default.nix index fedb219a0c19..fdf07a2a3299 100644 --- a/nixpkgs/pkgs/applications/science/math/bcal/default.nix +++ b/nixpkgs/pkgs/applications/science/math/bcal/default.nix @@ -32,6 +32,6 @@ stdenv.mkDerivation rec { homepage = "https://github.com/jarun/bcal"; license = licenses.gpl3Only; platforms = platforms.unix; - maintainers = with maintainers; [ jfrankenau ]; + maintainers = with maintainers; [ ]; }; } diff --git a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix index 536d520058a2..35b9e9d7a8d4 100644 --- a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix @@ -52,6 +52,6 @@ stdenv.mkDerivation rec { ]; license = licenses.unfree; platforms = [ "x86_64-linux" ]; - maintainers = with maintainers; [ jfrankenau ]; + maintainers = with maintainers; [ ]; }; } diff --git a/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix b/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix index 6a1bc86abced..ee54def6eb97 100644 --- a/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix +++ b/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix @@ -22,6 +22,12 @@ stdenv.mkDerivation rec { autoSignDarwinBinariesHook ]; + env = { + NIX_CFLAGS_COMPILE = "-Wno-error=implicit-int"; + } // lib.optionalAttrs (stdenv.isDarwin && stdenv.isx86_64) { + NIX_LDFLAGS = "-headerpad_max_install_names"; + }; + dontConfigure = true; buildPhase = diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix index 289c9b7b6580..c4cebcd8e29a 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix @@ -77,7 +77,7 @@ callPackage real-drv { homepage = "http://www.wolfram.com/mathematica/"; license = licenses.unfree; sourceProvenance = with sourceTypes; [ binaryNativeCode ]; - maintainers = with maintainers; [ herberteuler ]; + maintainers = with maintainers; [ herberteuler rafaelrc ]; platforms = [ "x86_64-linux" ]; }; } diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/generic.nix b/nixpkgs/pkgs/applications/science/math/mathematica/generic.nix index 7cd699e58e3c..5064a3ddbdf4 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/generic.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/generic.nix @@ -158,9 +158,10 @@ in stdenv.mkDerivation { # Remove PATH restriction, root and avahi daemon checks, and hostname call sed -i ' - s/^PATH=/# &/ + s/^\s*PATH=/# &/ s/isRoot="false"/# &/ - s/^checkAvahiDaemon$/# &/ + s/^\s*checkAvahiDaemon$/:/ + s/^\s*installBundledInstall$/:/ s/`hostname`/""/ ' MathInstaller diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/versions.nix b/nixpkgs/pkgs/applications/science/math/mathematica/versions.nix index 2bcce6c58c3d..74422621c7b4 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/versions.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/versions.nix @@ -8,6 +8,20 @@ let versions = [ { + version = "13.3.1"; + lang = "en"; + language = "English"; + sha256 = "sha256-0+mYVGiF4Qn3eiLIoINSHVIqT8GtlBPFRYIOF+nHyQo="; + installer = "Mathematica_13.3.1_LINUX.sh"; + } + { + version = "13.3.1"; + lang = "en"; + language = "English"; + sha256 = "sha256-03R4s05fmTcZnlZIMSI6xlLER58MIoccoCr27F8BXOk="; + installer = "Mathematica_13.3.1_BNDL_LINUX.sh"; + } + { version = "13.3.0"; lang = "en"; language = "English"; diff --git a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix index d30d560f47fd..23e4ffc8b5a5 100644 --- a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix +++ b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix @@ -12,13 +12,13 @@ stdenv.mkDerivation (finalAttrs:{ pname = "wxmaxima"; - version = "23.10.0"; + version = "23.11.0"; src = fetchFromGitHub { owner = "wxMaxima-developers"; repo = "wxmaxima"; rev = "Version-${finalAttrs.version}"; - sha256 = "sha256-3zQzpw0KWNAAvML55O2FMlid9j0GtP8OWy1eqifzVwI="; + sha256 = "sha256-QOXRtWFY76aIvRPSN+i8jkvMZvuPO3Yr3yqFOh0PSXY="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix b/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix index c927df9a5491..cdc083a467d8 100644 --- a/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix +++ b/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix @@ -1,59 +1,70 @@ -{ lib, stdenv -, autoPatchelfHook -, buildFHSEnv -, dpkg -, fetchurl -, gcc-unwrapped -, ocl-icd -, zlib -, extraPkgs ? [] +{ lib +, stdenv +, fetchFromGitHub +, scons +, openssl }: let - majMin = lib.versions.majorMinor version; - version = "7.6.21"; - - fahclient = stdenv.mkDerivation rec { - inherit version; - pname = "fahclient"; - - src = fetchurl { - url = "https://download.foldingathome.org/releases/public/release/fahclient/debian-stable-64bit/v${majMin}/fahclient_${version}_amd64.deb"; - sha256 = "2827f05f1c311ee6c7eca294e4ffb856c81957e8f5bfc3113a0ed27bb463b094"; - }; - - nativeBuildInputs = [ - autoPatchelfHook - dpkg - ]; - - buildInputs = [ - gcc-unwrapped.lib - zlib - ]; - - unpackPhase = "dpkg-deb -x ${src} ./"; - installPhase = "cp -ar usr $out"; + version = "8.1.18"; + + cbangSrc = fetchFromGitHub { + owner = "cauldrondevelopmentllc"; + repo = "cbang"; + rev = "bastet-v${version}"; + hash = "sha256-G0rknVmZiyC4sRTOowFjf7EQ5peGf+HLPPcLWXXFlX4="; + }; + + fah-web-client-bastetSrc = fetchFromGitHub { + owner = "foldingathome"; + repo = "fah-web-client-bastet"; + rev = "v${version}"; + hash = lib.fakeHash; }; in -buildFHSEnv { - name = fahclient.name; +stdenv.mkDerivation { + pname = "fah-client"; + inherit version; + + src = fetchFromGitHub { + owner = "FoldingAtHome"; + repo = "fah-client-bastet"; + rev = "v${version}"; + hash = "sha256-IgT/5NqCwN8N8OObjtASuT4IRb2EN4bdixxUdjiyddI="; + }; + + nativeBuildInputs = [ scons ]; + + buildInputs = [ openssl ]; + + postUnpack = '' + export CBANG_HOME=$NIX_BUILD_TOP/cbang + + cp -r --no-preserve=mode ${cbangSrc} $CBANG_HOME + ''; + + preBuild = '' + scons -C $CBANG_HOME + ''; + + installPhase = '' + runHook preInstall + + mkdir -p $out/{bin,share/applications,share/feh-client} + + cp fah-client $out/bin/fah-client - targetPkgs = pkgs': [ - fahclient - ocl-icd - ] ++ extraPkgs; + cp install/lin/fah-client.desktop $out/share/applications/ + cp -r images $out/share/feh-client/ - runScript = "/bin/FAHClient"; + sed -e "s|Icon=.*|Icon=$out/share/feh-client/images/fahlogo.png|g" -i $out/share/applications/fah-client.desktop - extraInstallCommands = '' - mv $out/bin/$name $out/bin/FAHClient + runHook postInstall ''; meta = { description = "Folding@home client"; homepage = "https://foldingathome.org/"; - sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; - license = lib.licenses.unfree; + license = lib.licenses.gpl3; maintainers = [ lib.maintainers.zimbatm ]; platforms = [ "x86_64-linux" ]; }; diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix index d2172f614f64..3f3b64069bb1 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix @@ -195,6 +195,9 @@ stdenv.mkDerivation rec { "-Druntime_cxxmodules=OFF" ]; + # suppress warnings from compilation of the vendored clang to avoid running into log limits on the Hydra + NIX_CFLAGS_COMPILE = lib.optionals stdenv.cc.isGNU [ "-Wno-shadow" "-Wno-maybe-uninitialized" ]; + # Workaround the xrootd runpath bug #169677 by prefixing [DY]LD_LIBRARY_PATH with ${lib.makeLibraryPath xrootd}. # TODO: Remove the [DY]LDLIBRARY_PATH prefix for xrootd when #200830 get merged. postInstall = '' diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index 2ca47d812bbf..e669562c9cc7 100644 --- a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -1,8 +1,10 @@ { lib, stdenv, fetchurl, cmake, hwloc, fftw, perl, blas, lapack, mpi, cudatoolkit +, plumed , singlePrec ? true , config -, enableMpi ? false , enableCuda ? config.cudaSupport +, enableMpi ? false +, enablePlumed ? false , cpuAcceleration ? null }: @@ -18,20 +20,39 @@ let if stdenv.hostPlatform.system == "aarch64-linux" then "ARM_NEON_ASIMD" else "None"; + source = + if enablePlumed then + { + version = "2023"; + hash = "sha256-rJLG2nL7vMpBT9io2Xnlbs8XxMHNq+0tpc+05yd7e6g="; + } + else + { + version = "2023.3"; + hash = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs="; + }; + in stdenv.mkDerivation rec { pname = "gromacs"; - version = "2023.3"; + version = source.version; src = fetchurl { url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz"; - sha256 = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs="; + inherit (source) hash; }; patches = [ ./pkgconfig.patch ]; + postPatch = lib.optionalString enablePlumed '' + plumed patch -p -e gromacs-2023 + ''; + outputs = [ "out" "dev" "man" ]; - nativeBuildInputs = [ cmake ]; + nativeBuildInputs = + [ cmake ] + ++ lib.optional enablePlumed plumed + ; buildInputs = [ fftw diff --git a/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix index dd3fef5bf26c..3d9615cf5329 100644 --- a/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix @@ -1,12 +1,11 @@ -{ mkDerivation, lib, fetchurl, qmake }: +{ mkDerivation, lib, fetchzip, qmake }: mkDerivation rec { pname = "xflr5"; - version = "6.47"; - - src = fetchurl { - url = "mirror://sourceforge/xflr5/${pname}_v${version}_src.tar.gz"; - sha256 = "02x3r9iv3ndwxa65mxn9m5dlhcrnjiq7cffi6rmb456gs3v3dnav"; + version = "6.61"; + src = fetchzip { + url = "https://sourceforge.net/code-snapshots/svn/x/xf/xflr5/code/xflr5-code-r1481-tags-v6.61-xflr5.zip"; + sha256 = "sha256-voWnXiBo7+kBPiZLVpSiXyBsYJv/Phd3noA81SQ5Vtw="; }; nativeBuildInputs = [ qmake ]; diff --git a/nixpkgs/pkgs/applications/science/programming/groove/default.nix b/nixpkgs/pkgs/applications/science/programming/groove/default.nix index e42aa253dbfe..fb314cdff30c 100644 --- a/nixpkgs/pkgs/applications/science/programming/groove/default.nix +++ b/nixpkgs/pkgs/applications/science/programming/groove/default.nix @@ -50,6 +50,6 @@ in stdenv.mkDerivation rec { license = licenses.asl20; sourceProvenance = with sourceTypes; [ binaryBytecode ]; platforms = platforms.all; - maintainers = with maintainers; [ jfrankenau ]; + maintainers = with maintainers; [ ]; }; } |