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Merge pull request #107845 from danielbarter/openbabel3

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Sandro 2021-01-18 00:37:32 +01:00 committed by GitHub
commit fe2882e5d3
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7 changed files with 106 additions and 22 deletions
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6
maintainers/maintainer-list.nix
View file

@ -2037,6 +2037,12 @@
githubId = 23366017;
name = "Dan Haraj";
};
danielbarter = {
email = "danielbarter@gmail.com";
github = "danielbarter";
githubId = 8081722;
name = "Daniel Barter";
};
danieldk = {
email = "me@danieldk.eu";
github = "danieldk";

6
pkgs/applications/science/chemistry/avogadro/default.nix
View file

@ -21,9 +21,9 @@ stdenv.mkDerivation rec {
})
];
meta = {
meta = with lib; {
description = "Molecule editor and visualizer";
maintainers = [ ];
platforms = lib.platforms.mesaPlatforms;
maintainers = with maintainers; [ danielbarter ];
platforms = platforms.mesaPlatforms;
};
}

31
pkgs/development/libraries/openbabel/2.nix Normal file
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@ -0,0 +1,31 @@
{stdenv, lib, fetchurl, fetchpatch, cmake, zlib, libxml2, eigen, python, cairo, pcre, pkg-config }:
stdenv.mkDerivation rec {
pname = "openbabel";
version = "2.4.1";
src = fetchurl {
url = "https://github.com/openbabel/openbabel/archive/openbabel-${stdenv.lib.replaceStrings ["."] ["-"] version}.tar.gz";
sha256 = "0xm7y859ivq2cp0q08mwshfxm0jq31xkyr4x8s0j6l7khf57yk2r";
};
patches = [
# ARM / AArch64 fixes.
(fetchpatch {
url = "https://github.com/openbabel/openbabel/commit/ee11c98a655296550710db1207b294f00e168216.patch";
sha256 = "0wjqjrkr4pfirzzicdvlyr591vppydk572ix28jd2sagnfnf566g";
})
];
buildInputs = [ zlib libxml2 eigen python cairo pcre ];
nativeBuildInputs = [ cmake pkg-config ];
meta = with lib; {
description = "A toolbox designed to speak the many languages of chemical data";
homepage = "http://openbabel.org";
platforms = platforms.all;
maintainers = with maintainers; [ danielbarter ];
license = licenses.gpl2Plus;
};
}

47
pkgs/development/libraries/openbabel/default.nix
View file

@ -1,34 +1,45 @@
{stdenv, fetchurl, fetchpatch, cmake, zlib, libxml2, eigen, python, cairo, pcre, pkgconfig }:
{stdenv, lib, fetchurl, cmake, zlib, libxml2, eigen, python, cairo, pcre, pkg-config, swig, rapidjson }:
stdenv.mkDerivation rec {
pname = "openbabel";
version = "2.4.1";
version = "3.1.1";
src = fetchurl {
url = "https://github.com/openbabel/openbabel/archive/openbabel-${stdenv.lib.replaceStrings ["."] ["-"] version}.tar.gz";
sha256 = "0xm7y859ivq2cp0q08mwshfxm0jq31xkyr4x8s0j6l7khf57yk2r";
sha256 = "c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02";
};
patches = [
# ARM / AArch64 fixes.
(fetchpatch {
url = "https://github.com/openbabel/openbabel/commit/ee11c98a655296550710db1207b294f00e168216.patch";
sha256 = "0wjqjrkr4pfirzzicdvlyr591vppydk572ix28jd2sagnfnf566g";
})
buildInputs = [ zlib libxml2 eigen python cairo pcre swig rapidjson ];
nativeBuildInputs = [ cmake pkg-config ];
pythonMajorMinor = "${python.sourceVersion.major}.${python.sourceVersion.minor}";
cmakeFlags = [
"-DRUN_SWIG=ON"
"-DPYTHON_BINDINGS=ON"
];
# TODO : perl & python bindings;
# TODO : wxGTK: I have no time to compile
# TODO : separate lib and apps
buildInputs = [ zlib libxml2 eigen python cairo pcre ];
nativeBuildInputs = [ cmake pkgconfig ];
postFixup = ''
cat <<EOF > $out/lib/python$pythonMajorMinor/site-packages/setup.py
from distutils.core import setup
meta = {
setup(
name = 'pyopenbabel',
version = '${version}',
packages = ['openbabel'],
package_data = {'openbabel' : ['_openbabel.so']}
)
EOF
'';
meta = with lib; {
description = "A toolbox designed to speak the many languages of chemical data";
homepage = "http://openbabel.org";
platforms = stdenv.lib.platforms.all;
maintainers = [ ];
license = stdenv.lib.licenses.gpl2Plus;
platforms = platforms.all;
license = licenses.gpl2Plus;
maintainers = with maintainers; [ danielbarter ];
};
}

27
pkgs/development/python-modules/openbabel-bindings/default.nix Normal file
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@ -0,0 +1,27 @@
{ stdenv, lib, openbabel, python, buildPythonPackage }:
buildPythonPackage rec {
pname = "openbabel";
version = "3.1.1";
src = "${openbabel}/lib/python${python.sourceVersion.major}.${python.sourceVersion.minor}/site-packages";
nativeBuildInputs = [ openbabel ];
# these env variables are used by the bindings to find libraries
# they need to be included explicitly in your nix-shell for
# some functionality to work (inparticular, pybel).
# see https://openbabel.org/docs/dev/Installation/install.html
BABEL_LIBDIR = "${openbabel}/lib/openbabel/3.1.0";
LD_LIBRARY_PATH = "$LD_LIBRARY_PATH:${openbabel}/lib";
doCheck = false;
pythonImportsCheck = [ "openbabel" ];
meta = with lib; {
homepage = "http://openbabel.org/wiki/Main_Page";
description = "Python bindings for openbabel";
license = licenses.gpl2Plus;
maintainers = with maintainers; [ danielbarter ];
};
}

7
pkgs/top-level/all-packages.nix
View file

@ -15799,7 +15799,11 @@ in
};
openal = openalSoft;
openbabel = callPackage ../development/libraries/openbabel { };
openbabel = openbabel3;
openbabel2 = callPackage ../development/libraries/openbabel/2.nix { };
openbabel3 = callPackages ../development/libraries/openbabel { };
opencascade = callPackage ../development/libraries/opencascade {
inherit (darwin.apple_sdk.frameworks) OpenCL Cocoa;
@ -27369,6 +27373,7 @@ in
### SCIENCE/CHEMISTY
avogadro = callPackage ../applications/science/chemistry/avogadro {
openbabel = openbabel2;
eigen = eigen2;
};

4
pkgs/top-level/python-packages.nix
View file

@ -4468,6 +4468,10 @@ in {
openapi-spec-validator = callPackage ../development/python-modules/openapi-spec-validator { };
openbabel-bindings = callPackage ../development/python-modules/openbabel-bindings {
openbabel = (callPackage ../development/libraries/openbabel { python = self.python; });
};
opencv3 = toPythonModule (pkgs.opencv3.override {
enablePython = true;
pythonPackages = self;