diff options
Diffstat (limited to 'infra/libkookie/nixpkgs/pkgs/applications/science/chemistry')
4 files changed, 24 insertions, 17 deletions
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index 6545472a5295..e09abccad121 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -17,14 +17,14 @@ let }; in stdenv.mkDerivation rec { - version = "14.31.3"; + version = "14.31.18"; 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-${version}-binary.tar.gz"; - sha256 = "067051wp9kgkgcy3mvqwxhim0h1qfcf4jk8vrbzd3y9pwmjismzy"; + sha256 = "0hkc7c08azbw3k91ygwz6r5y4yw6k8l7h4gcq5p71knd5k1fa5jd"; }; patchPhase = '' @@ -48,6 +48,6 @@ stdenv.mkDerivation rec { homepage = "https://sourceforge.net/projects/jmol"; license = licenses.lgpl2; platforms = platforms.all; - maintainers = with maintainers; [ timokau mounium ]; + maintainers = with maintainers; [ mounium ] ++ teams.sage.members; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix index e8cd077afd20..ddab526ebe79 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with stdenv.lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.17.0"; + version = "20.20.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "0ip6ma9ivk5b74s9najn2rrkiha7hya1rjhgyrc71kwsj5gqgli0"; + sha256 = "1a8b0drb0c95c8arm3aa0z0sbdm9ilj4h1g90i0qyn4g2wk2xsal"; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix index 0d74e784d772..d432e66a19f1 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -7,7 +7,7 @@ assert blas.implementation == "openblas" && lapack.implementation == "openblas"; let - version = "19.11"; + version = "20.10"; gitLabRev = "v${version}"; python = python3.withPackages (ps : with ps; [ six pyparsing ]); @@ -20,18 +20,13 @@ in stdenv.mkDerivation { owner = "Molcas"; repo = "OpenMolcas"; rev = gitLabRev; - sha256 = "1wwqhkyyi7pw5x1ghnp83ir17zl5jsj7phhqxapybyi3bmg0i00q"; + sha256 = "0xr9plgb0cfmxxqmd3wrhvl0hv2jqqfqzxwzs1jysq2m9cxl314v"; }; - patches = [ (fetchpatch { - name = "Fix-MPI-INT-size"; # upstream patch, fixes a Fortran compiler error - url = "https://gitlab.com/Molcas/OpenMolcas/commit/860e3350523f05ab18e49a428febac8a4297b6e4.patch"; - sha256 = "0h96h5ikbi5l6ky41nkxmxfhjiykkiifq7vc2s3fdy1r1siv09sb"; - }) (fetchpatch { - name = "fix-cisandbox"; # upstream patch, fixes a Fortran compiler error - url = "https://gitlab.com/Molcas/OpenMolcas/commit/d871590c8ce4689cd94cdbbc618954c65589393d.patch"; - sha256 = "0dgz1w2rkglnis76spai3m51qa72j4bz6ppnk5zmzrr6ql7gwpgg"; - })]; + patches = [ + # Required to handle openblas multiple outputs + ./openblasPath.patch +]; nativeBuildInputs = [ perl cmake texlive.combined.scheme-minimal makeWrapper ]; buildInputs = [ @@ -55,7 +50,7 @@ in stdenv.mkDerivation { "-DTOOLS=ON" "-DHDF5=ON" "-DFDE=ON" - "-DOPENBLASROOT=${openblas}" + "-DOPENBLASROOT=${openblas.dev}" ]; GAROOT=globalarrays; diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/openblasPath.patch b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/openblasPath.patch new file mode 100644 index 000000000000..e47adcc3e9a3 --- /dev/null +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/openblasPath.patch @@ -0,0 +1,12 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 276ae4e2..db13e6e3 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -1507,7 +1507,6 @@ if (LINALG STREQUAL "OpenBLAS") + NAMES openblas + PATHS ${OPENBLASROOT} + PATH_SUFFIXES lib +- NO_DEFAULT_PATH + ) + + if (NOT LIBOPENBLAS) |