diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
7 files changed, 29 insertions, 16 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix index eaf0b5932726..a199e41d50aa 100644 --- a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix @@ -2,15 +2,17 @@ with python.pkgs; buildPythonApplication rec { pname = "deepTools"; - version = "3.5.1"; + version = "3.5.4"; src = fetchFromGitHub { owner = "deeptools"; repo = "deepTools"; rev = version; - sha256 = "07v8vb2x4b0mgw0mvcj91vj1fqbcwizwsniysl2cvmv93gad8gbp"; + sha256 = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI="; }; + format = "pyproject"; + propagatedBuildInputs = [ numpy numpydoc @@ -21,9 +23,10 @@ buildPythonApplication rec { matplotlib plotly deeptoolsintervals + importlib-metadata ]; - nativeCheckInputs = [ nose ]; + nativeCheckInputs = [ pytest ]; meta = with lib; { homepage = "https://deeptools.readthedocs.io/en/develop"; @@ -36,7 +39,7 @@ buildPythonApplication rec { publication-ready visualizations to identify enrichments and for functional annotations of the genome. ''; - license = licenses.gpl3; + license = with licenses; [ mit bsd3 ]; maintainers = with maintainers; [ scalavision ]; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix index 78f226350f60..febfde548fd7 100644 --- a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix @@ -3,6 +3,7 @@ , cmake , eigen , fetchFromGitHub +, fetchpatch , libcifpp , libmcfp , zlib @@ -15,18 +16,26 @@ let inherit (oldAttrs.src) owner repo rev; hash = "sha256-Sj10j6HxUoUvQ66cd2B8CO7CVBRd7w9CTovxkwPDOvs="; }; + patches = [ + (fetchpatch { + # https://github.com/PDB-REDO/libcifpp/issues/51 + name = "fix-build-on-darwin.patch"; + url = "https://github.com/PDB-REDO/libcifpp/commit/641f06a7e7c0dc54af242b373820f2398f59e7ac.patch"; + hash = "sha256-eWNfp9nA/+2J6xjZR6Tj+5OM3L5MxdfRi0nBzyaqvS0="; + }) + ]; }); in stdenv.mkDerivation (finalAttrs: { pname = "dssp"; - version = "4.4.3"; + version = "4.4.4.1"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = "dssp"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-zPmRR7sxVNErwabLqA5CNMO4K1qHdmC9FBPjcx91KuM="; + hash = "sha256-sy6GBCnTGRD1YP00dKIolkr1RMboLGcd0f4kU8gCOnA="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/raxml/default.nix b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix index d02d47266297..0cc20b063503 100644 --- a/nixpkgs/pkgs/applications/science/biology/raxml/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { pname = "RAxML${lib.optionalString useMpi "-mpi"}"; - version = "8.2.12"; + version = "8.2.13"; src = fetchFromGitHub { owner = "stamatak"; repo = "standard-RAxML"; rev = "v${version}"; - sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"; + sha256 = "sha256-w+Eqi0GhVira1H6ZnMNeZGBMzDjiGT7JSFpQEVXONyk="; }; buildInputs = lib.optionals useMpi [ mpi ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix index bb306fa322fe..5bc0dddd79b6 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix @@ -146,7 +146,8 @@ stdenv.mkDerivation rec { -fopenmp -ftree-vectorize -funroll-loops \ -I${lib.getDev libint}/include ${lib.optionalString enableElpa "$(pkg-config --variable=fcflags elpa)"} \ -I${lib.getDev sirius}/include/sirius \ - -I${lib.getDev libxc}/include -I${lib.getDev libxsmm}/include + -I${lib.getDev libxc}/include -I${lib.getDev libxsmm}/include \ + -fallow-argument-mismatch LIBS = -lfftw3 -lfftw3_threads \ -lscalapack -lblas -llapack \ -lxcf03 -lxc -lxsmmf -lxsmm -lsymspg \ diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index f80085278e0a..0b99c9a849d0 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.41"; + version = "16.1.43"; pname = "jmol"; src = let baseVersion = "${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 = "sha256-91vPipS5FTqCl7BUSu47aApIfq2e8dD1SW/LEGQWWio="; + hash = "sha256-lqHlnAeJKbj2Xs9AeAKqdWMWkmD8xWR7f3+nJsBx2YE="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix b/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix index 0ce67ec4dbb1..593e9d9187b7 100644 --- a/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix @@ -18,13 +18,13 @@ stdenv.mkDerivation rec { pname = "qucs-s"; - version = "2.0.0"; + version = "2.1.0"; src = fetchFromGitHub { owner = "ra3xdh"; repo = "qucs_s"; rev = version; - sha256 = "sha256-9/1sgxFqn9d9zlwrzjQosFO3m+2lC83qVcCtzfqY5XY="; + sha256 = "sha256-C7TLOuC0CHredDiWFIAFmOlV8ivX0j4bs3b8IB8FsqE="; }; nativeBuildInputs = [ flex bison wrapQtAppsHook cmake ]; diff --git a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix index 8abcd96f08d2..603a3c4f60bf 100644 --- a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix +++ b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2023-08-03"; + version = "unstable-2023-10-26"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "f202cf0c342e54e994c4d416daecc1b1dc8b9c98"; - hash = "sha256-kp4zWTPYt2DiuPgTK+ib8NbKg2BJVxJDDCvIlWNuwgs="; + rev = "043895fbaed27a4baace7c7c0c1f69ea5a9f3d1a"; + hash = "sha256-roPyRaT89I3HbyvBK/owiigMus1EeKEhhKHFsgfzp10="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' |