commit 036a9242f1d8459e6fb9dc2d56dbcd4f74e8c4c3 · pyrox.dev/nixpkgs

+21 -3

pkgs/by-name/co/coordgenlibs/package.nix

···

       1
       1
        
       {

     

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       2
        
         fetchFromGitHub,

     

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       +
         fetchpatch,

     

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         lib,

     

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         stdenv,

     

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         boost,

     
···

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           hash = "sha256-casFPNbPv9mkKpzfBENW7INClypuCO1L7clLGBXvSvI=";

     

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         };

     

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       +
         patches = [

     

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       +
           (fetchpatch {

     

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       +
             name = "coordgenlibs-fix-unused-but-set-variable.patch";

     

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       +
             url = "https://github.com/schrodinger/coordgenlibs/commit/6a1485643feb71c6d609d263f28751004c733cf7.patch";

     

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       +
             hash = "sha256-x34v+XumVip43LYb4bEkdqPFcTRTeC/zsRuQjnrh2zw=";

     

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           })

     

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         ];

     

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       +
       

     

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         nativeBuildInputs = [ cmake ];

     

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         buildInputs = [

     

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           boost

     
···

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           maeparser

     

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         ];

     

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       -
         env = lib.optionalAttrs stdenv.cc.isClang {

     

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       -
           NIX_CFLAGS_COMPILE = "-Wno-unused-but-set-variable";

     

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       -
         };

     

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       +
         # Fix the build with CMake 4.

     

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         #

     

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         # See: <https://github.com/schrodinger/coordgenlibs/pull/130>

     

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       +
         postPatch = ''

     

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       +
           substituteInPlace CMakeLists.txt \

     

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       +
             --replace-fail \

     

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       +
               'cmake_minimum_required(VERSION 3.2)' \

     

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       +
               'cmake_minimum_required(VERSION 3.5)'

     

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       +
         '';

     

       32
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         doCheck = true;

     

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       +
       

     

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       +
         # Fix the build with Clang 20.

     

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       +
         env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-error=deprecated-literal-operator";

     

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         meta = with lib; {

     

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           description = "Schrodinger-developed 2D Coordinate Generation";

+77

pkgs/by-name/op/openbabel/fix-cmake-4.patch

···

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       +
       From fda825d390af8b5eaf79d7b7c39c19ab5ce317ac Mon Sep 17 00:00:00 2001

     

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       From: Nicolas PARLANT <nicolas.parlant@parhuet.fr>

     

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       +
       Date: Wed, 26 Mar 2025 10:24:42 +0000

     

       4
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       +
       Subject: [PATCH] cmake4 compat :

     

       5
       5
       +
       

     

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       +
       * up cmake_minimum_required to 3.10

     

       7
       7
       +
       * delete CMP0042 because OLD behavior is removed in cmake-4 and

     

       8
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       +
       is no longer used.

     

       9
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       +
       * set ENABLE_EXPORTS for test_runner (OLD behavior for CMP0065 is removed

     

       10
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       +
       in cmake4)

     

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       +
       

     

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       Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr>

     

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       ---

     

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        CMakeLists.txt                                | 7 ++-----

     

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       +
        doc/examples/static_executable/CMakeLists.txt | 2 +-

     

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       +
        scripts/CMakeLists.txt                        | 2 +-

     

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       +
        test/CMakeLists.txt                           | 1 +

     

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        4 files changed, 5 insertions(+), 7 deletions(-)

     

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       +
       

     

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       diff --git a/CMakeLists.txt b/CMakeLists.txt

     

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       +
       index 9d2a9f143e..f8440e412e 100644

     

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       --- a/CMakeLists.txt

     

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       +
       +++ b/CMakeLists.txt

     

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       @@ -1,6 +1,6 @@

     

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       +
       -# Please ensure that any changes remain compliant with 3.1.

     

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       +
       +# Please ensure that any changes remain compliant with 3.10.

     

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       +
        if(NOT EMBED_OPENBABEL)

     

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       -  cmake_minimum_required(VERSION 3.1)

     

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       +  cmake_minimum_required(VERSION 3.10)

     

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        endif()

     

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       +
        

     

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        project(openbabel)

     

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       @@ -10,9 +10,6 @@ set (CMAKE_CXX_STANDARD 11)

     

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       +
        if(COMMAND cmake_policy)

     

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          cmake_policy(SET CMP0003 NEW)

     

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       +
       -  if(POLICY CMP0042)

     

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       -    cmake_policy(SET CMP0042 OLD)

     

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       -  endif()

     

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        endif()

     

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       +
        

     

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        include (CheckCXXCompilerFlag)

     

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       +
       diff --git a/doc/examples/static_executable/CMakeLists.txt b/doc/examples/static_executable/CMakeLists.txt

     

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       +
       index 0ed21beaaf..63dae2a468 100644

     

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       +
       --- a/doc/examples/static_executable/CMakeLists.txt

     

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       +
       +++ b/doc/examples/static_executable/CMakeLists.txt

     

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       +
       @@ -25,7 +25,7 @@

     

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        #

     

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       +
        

     

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        # This line is required for cmake backwards compatibility.

     

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       +
       -cmake_minimum_required(VERSION 2.6)

     

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       +
       +cmake_minimum_required(VERSION 3.10)

     

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       +
        

     

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       +
        # Name of your project

     

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       +
        project(myproject)

     

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       +
       diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt

     

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       +
       index 792e4592d0..eafda66c5a 100644

     

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       +
       --- a/scripts/CMakeLists.txt

     

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       +
       +++ b/scripts/CMakeLists.txt

     

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       +
       @@ -1,4 +1,4 @@

     

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       +
       -cmake_minimum_required(VERSION 2.6.0)

     

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       +cmake_minimum_required(VERSION 3.10.0)

     

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       +
        # Library versioning (used in Mac Python bindings)x

     

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       +
        set(SOVERSION 4)

     

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       +
        

     

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       +
       diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt

     

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       +
       index 2ecf0dbe22..280eac471f 100644

     

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       +
       --- a/test/CMakeLists.txt

     

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       +
       +++ b/test/CMakeLists.txt

     

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       +
       @@ -152,6 +152,7 @@ endif()

     

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       +
        

     

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        add_executable(test_runner ${srclist} obtest.cpp)

     

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        target_link_libraries(test_runner ${libs})

     

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       +
       +set_target_properties(test_runner PROPERTIES ENABLE_EXPORTS TRUE)

     

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       +
        

     

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       +
        if(NOT BUILD_SHARED AND NOT BUILD_MIXED)

     

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       +
          set_target_properties(test_runner PROPERTIES LINK_SEARCH_END_STATIC TRUE)

+84

pkgs/by-name/op/openbabel/package.nix

···

       1
       1
       +
       {

     

       2
       2
       +
         stdenv,

     

       3
       3
       +
         lib,

     

       4
       4
       +
         fetchFromGitHub,

     

       5
       5
       +
         cmake,

     

       6
       6
       +
         ninja,

     

       7
       7
       +
         perl,

     

       8
       8
       +
         zlib,

     

       9
       9
       +
         libxml2,

     

       10
       10
       +
         eigen,

     

       11
       11
       +
         python3,

     

       12
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       +
         cairo,

     

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       +
         pkg-config,

     

       14
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       +
         swig,

     

       15
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       +
         rapidjson,

     

       16
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       +
         boost,

     

       17
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       +
         maeparser,

     

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       +
         coordgenlibs,

     

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       +
         ctestCheckHook,

     

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       +
       }:

     

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       +
       

     

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       +
       stdenv.mkDerivation {

     

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       +
         pname = "openbabel";

     

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       +
         version = "3.1.1-unstable-2024-12-21";

     

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       +
       

     

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       +
         src = fetchFromGitHub {

     

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       +
           owner = "openbabel";

     

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       +
           repo = "openbabel";

     

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       +
           rev = "889c350feb179b43aa43985799910149d4eaa2bc";

     

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       +
           hash = "sha256-pJbvKBjpvXNjTZRxD2AqEarqmq+Pq08uvGvog/k/a7k=";

     

       31
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       +
         };

     

       32
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       +
       

     

       33
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       +
         patches = [

     

       34
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       +
           # <https://github.com/openbabel/openbabel/pull/2784>

     

       35
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       +
           ./fix-cmake-4.patch

     

       36
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       +
         ];

     

       37
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       +
       

     

       38
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       +
         nativeBuildInputs = [

     

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       +
           cmake

     

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       +
           ninja

     

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       +
           swig

     

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       +
           pkg-config

     

       43
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       +
         ];

     

       44
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       +
       

     

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       +
         buildInputs = [

     

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       +
           perl

     

       47
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       +
           zlib

     

       48
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       +
           libxml2

     

       49
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       +
           eigen

     

       50
       50
       +
           python3

     

       51
       51
       +
           cairo

     

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       52
       +
           rapidjson

     

       53
       53
       +
           boost

     

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       +
           maeparser

     

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       +
           coordgenlibs

     

       56
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       +
         ];

     

       57
       57
       +
       

     

       58
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       +
         nativeCheckInputs = [

     

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       +
           ctestCheckHook

     

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       +
         ];

     

       61
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       +
       

     

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       +
         cmakeFlags = [

     

       63
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       +
           (lib.cmakeBool "RUN_SWIG" true)

     

       64
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       +
           (lib.cmakeBool "PYTHON_BINDINGS" true)

     

       65
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       +
           (lib.cmakeFeature "PYTHON_INSTDIR" "${placeholder "out"}/${python3.sitePackages}")

     

       66
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       +
         ];

     

       67
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       +
       

     

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       +
         disabledTests = [

     

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       +
           "test_cifspacegroup_11"

     

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       +
           "pybindtest_obconv_writers"

     

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       +
         ];

     

       72
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       +
       

     

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       +
         doCheck = true;

     

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       +
       

     

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       +
         dontUseNinjaCheck = true;

     

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       +
       

     

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       +
         meta = {

     

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       +
           description = "Toolbox designed to speak the many languages of chemical data";

     

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       79
       +
           homepage = "http://openbabel.org";

     

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       +
           platforms = lib.platforms.all;

     

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       81
       +
           license = lib.licenses.gpl2Plus;

     

       82
       82
       +
           maintainers = with lib.maintainers; [ danielbarter ];

     

       83
       83
       +
         };

     

       84
       84
       +
       }

-62

pkgs/development/libraries/openbabel/2.nix

···

       1
       1
       -
       {

     

       2
       2
       -
         stdenv,

     

       3
       3
       -
         lib,

     

       4
       4
       -
         fetchFromGitHub,

     

       5
       5
       -
         fetchpatch,

     

       6
       6
       -
         cmake,

     

       7
       7
       -
         zlib,

     

       8
       8
       -
         libxml2,

     

       9
       9
       -
         eigen,

     

       10
       10
       -
         python3,

     

       11
       11
       -
         cairo,

     

       12
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       -
         pcre,

     

       13
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       -
         pkg-config,

     

       14
       14
       -
       }:

     

       15
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       -
       

     

       16
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       -
       stdenv.mkDerivation rec {

     

       17
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       -
         pname = "openbabel";

     

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       -
         version = "2.4.1";

     

       19
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       -
       

     

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       -
         src = fetchFromGitHub {

     

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       -
           owner = "openbabel";

     

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       -
           repo = "openbabel";

     

       23
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       -
           rev = "openbabel-${lib.replaceStrings [ "." ] [ "-" ] version}";

     

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       -
           sha256 = "sha256-+pXsWMzex7rB1mm6dnTHzAcyw9jImgx1OZuLeCvbeJ0=";

     

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       -
         };

     

       26
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       -
       

     

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         patches = [

     

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           # ARM / AArch64 fixes.

     

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       -
           (fetchpatch {

     

       30
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       -
             url = "https://github.com/openbabel/openbabel/commit/ee11c98a655296550710db1207b294f00e168216.patch";

     

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       -
             sha256 = "0wjqjrkr4pfirzzicdvlyr591vppydk572ix28jd2sagnfnf566g";

     

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       -
           })

     

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       -
         ];

     

       34
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       -
       

     

       35
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       -
         postPatch = ''

     

       36
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       -
           sed '1i#include <ctime>' -i include/openbabel/obutil.h # gcc12

     

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       -
         '';

     

       38
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       -
       

     

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       -
         buildInputs = [

     

       40
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       -
           zlib

     

       41
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       -
           libxml2

     

       42
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       -
           eigen

     

       43
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       -
           python3

     

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       -
           cairo

     

       45
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       -
           pcre

     

       46
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       -
         ];

     

       47
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       -
       

     

       48
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       -
         cmakeFlags = [ "-DCMAKE_CXX_STANDARD=14" ];

     

       49
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       -
       

     

       50
       50
       -
         nativeBuildInputs = [

     

       51
       51
       -
           cmake

     

       52
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       -
           pkg-config

     

       53
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       -
         ];

     

       54
       54
       -
       

     

       55
       55
       -
         meta = with lib; {

     

       56
       56
       -
           description = "Toolbox designed to speak the many languages of chemical data";

     

       57
       57
       -
           homepage = "http://openbabel.org";

     

       58
       58
       -
           platforms = platforms.all;

     

       59
       59
       -
           maintainers = with maintainers; [ danielbarter ];

     

       60
       60
       -
           license = licenses.gpl2Plus;

     

       61
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       -
         };

     

       62
       62
       -
       }

-84

pkgs/development/libraries/openbabel/default.nix

···

       1
       1
       -
       {

     

       2
       2
       -
         stdenv,

     

       3
       3
       -
         lib,

     

       4
       4
       -
         fetchFromGitHub,

     

       5
       5
       -
         cmake,

     

       6
       6
       -
         perl,

     

       7
       7
       -
         zlib,

     

       8
       8
       -
         libxml2,

     

       9
       9
       -
         eigen,

     

       10
       10
       -
         python3,

     

       11
       11
       -
         cairo,

     

       12
       12
       -
         pkg-config,

     

       13
       13
       -
         swig,

     

       14
       14
       -
         rapidjson,

     

       15
       15
       -
         boost,

     

       16
       16
       -
         maeparser,

     

       17
       17
       -
         coordgenlibs,

     

       18
       18
       -
       }:

     

       19
       19
       -
       

     

       20
       20
       -
       stdenv.mkDerivation rec {

     

       21
       21
       -
         pname = "openbabel";

     

       22
       22
       -
         version = "unstable-06-12-23";

     

       23
       23
       -
       

     

       24
       24
       -
         src = fetchFromGitHub {

     

       25
       25
       -
           owner = "openbabel";

     

       26
       26
       -
           repo = pname;

     

       27
       27
       -
           rev = "32cf131444c1555c749b356dab44fb9fe275271f";

     

       28
       28
       -
           hash = "sha256-V0wrZVrojCZ9Knc5H6cPzPoYWVosRZ6Sn4PX+UFEfHY=";

     

       29
       29
       -
         };

     

       30
       30
       -
       

     

       31
       31
       -
         postPatch = ''

     

       32
       32
       -
           sed '1i#include <ctime>' -i include/openbabel/obutil.h # gcc12

     

       33
       33
       -
         '';

     

       34
       34
       -
       

     

       35
       35
       -
         buildInputs = [

     

       36
       36
       -
           perl

     

       37
       37
       -
           zlib

     

       38
       38
       -
           libxml2

     

       39
       39
       -
           eigen

     

       40
       40
       -
           python3

     

       41
       41
       -
           cairo

     

       42
       42
       -
           rapidjson

     

       43
       43
       -
           boost

     

       44
       44
       -
           maeparser

     

       45
       45
       -
           coordgenlibs

     

       46
       46
       -
         ];

     

       47
       47
       -
       

     

       48
       48
       -
         nativeBuildInputs = [

     

       49
       49
       -
           cmake

     

       50
       50
       -
           swig

     

       51
       51
       -
           pkg-config

     

       52
       52
       -
         ];

     

       53
       53
       -
       

     

       54
       54
       -
         preConfigure = ''

     

       55
       55
       -
           cmakeFlagsArray+=(

     

       56
       56
       -
             "-DRUN_SWIG=ON"

     

       57
       57
       -
             "-DPYTHON_BINDINGS=ON"

     

       58
       58
       -
             "-DPYTHON_INSTDIR=$out/${python3.sitePackages}"

     

       59
       59
       -
           )

     

       60
       60
       -
         '';

     

       61
       61
       -
       

     

       62
       62
       -
         # Setuptools only accepts PEP 440 version strings. The "unstable" identifier

     

       63
       63
       -
         # can not be used. Instead we pretend to be the 3.2 beta release.

     

       64
       64
       -
         postFixup = ''

     

       65
       65
       -
           cat << EOF > $out/${python3.sitePackages}/setup.py

     

       66
       66
       -
           from setuptools import setup

     

       67
       67
       -
       

     

       68
       68
       -
           setup(

     

       69
       69
       -
               name = 'pyopenbabel',

     

       70
       70
       -
               version = '3.2b1',

     

       71
       71
       -
               packages = ['openbabel'],

     

       72
       72
       -
               package_data = {'openbabel' : ['_openbabel.so']}

     

       73
       73
       -
           )

     

       74
       74
       -
           EOF

     

       75
       75
       -
         '';

     

       76
       76
       -
       

     

       77
       77
       -
         meta = with lib; {

     

       78
       78
       -
           description = "Toolbox designed to speak the many languages of chemical data";

     

       79
       79
       -
           homepage = "http://openbabel.org";

     

       80
       80
       -
           platforms = platforms.all;

     

       81
       81
       -
           license = licenses.gpl2Plus;

     

       82
       82
       -
           maintainers = with maintainers; [ danielbarter ];

     

       83
       83
       -
         };

     

       84
       84
       -
       }

+1 -1

pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix

···

       20
       20
        
       let

     

       21
       21
        
         pythonWP = python3.withPackages (

     

       22
       22
        
           p: with p; [

     

       23
       23
       -
             openbabel-bindings

     

       23
       23
       +
             openbabel

     

       24
       24
        
             numpy

     

       25
       25
        
           ]

     

       26
       26
        
         );

-32

pkgs/development/python-modules/openbabel-bindings/default.nix

···

       1
       1
       -
       {

     

       2
       2
       -
         lib,

     

       3
       3
       -
         openbabel,

     

       4
       4
       -
         python,

     

       5
       5
       -
         buildPythonPackage,

     

       6
       6
       -
       }:

     

       7
       7
       -
       

     

       8
       8
       -
       buildPythonPackage {

     

       9
       9
       -
         format = "setuptools";

     

       10
       10
       -
         inherit (openbabel) pname version;

     

       11
       11
       -
       

     

       12
       12
       -
         src = "${openbabel}/${python.sitePackages}";

     

       13
       13
       -
       

     

       14
       14
       -
         buildInputs = [ openbabel ];

     

       15
       15
       -
       

     

       16
       16
       -
         # these env variables are used by the bindings to find libraries

     

       17
       17
       -
         # they need to be included explicitly in your nix-shell for

     

       18
       18
       -
         # some functionality to work (inparticular, pybel).

     

       19
       19
       -
         # see https://openbabel.org/docs/dev/Installation/install.html

     

       20
       20
       -
         BABEL_LIBDIR = "${openbabel}/lib/openbabel/3.1.0";

     

       21
       21
       -
         LD_LIBRARY_PATH = "${openbabel}/lib";

     

       22
       22
       -
       

     

       23
       23
       -
         doCheck = false;

     

       24
       24
       -
         pythonImportsCheck = [ "openbabel" ];

     

       25
       25
       -
       

     

       26
       26
       -
         meta = with lib; {

     

       27
       27
       -
           homepage = "http://openbabel.org/wiki/Main_Page";

     

       28
       28
       -
           description = "Python bindings for openbabel";

     

       29
       29
       -
           license = licenses.gpl2Plus;

     

       30
       30
       -
           maintainers = with maintainers; [ danielbarter ];

     

       31
       31
       -
         };

     

       32
       32
       -
       }

pkgs/top-level/aliases.nix

···

       1860
       1860
        
         onevpl-intel-gpu = lib.warnOnInstantiate "onevpl-intel-gpu has been renamed to vpl-gpu-rt" vpl-gpu-rt; # Added 2024-06-04

     

       1861
       1861
        
         openai-triton-llvm = triton-llvm; # added 2024-07-18

     

       1862
       1862
        
         openai-whisper-cpp = whisper-cpp; # Added 2024-12-13

     

       1863
       1863
       +
         openbabel2 = throw "openbabel2 has been removed, as it was unused and unmaintained upstream; please use openbabel"; # Added 2025-09-17

     

       1864
       1864
       +
         openbabel3 = openbabel; # Added 2025-09-17

     

       1863
       1865
        
         opencv2 = throw "opencv2 has been removed as it is obsolete and was not used by any other package; please migrate to OpenCV 4"; # Added 2024-08-20

     

       1864
       1866
        
         opencv3 = throw "opencv3 has been removed as it is obsolete and was not used by any other package; please migrate to OpenCV 4"; # Added 2024-08-20

     

       1865
       1867
        
         openafs_1_8 = openafs; # Added 2022-08-22

-6

pkgs/top-level/all-packages.nix

···

       8499
       8499
        
       

     

       8500
       8500
        
         openal = openalSoft;

     

       8501
       8501
        
       

     

       8502
       8502
       -
         openbabel = openbabel3;

     

       8503
       8503
       -
       

     

       8504
       8504
       -
         openbabel2 = callPackage ../development/libraries/openbabel/2.nix { };

     

       8505
       8505
       -
       

     

       8506
       8506
       -
         openbabel3 = callPackage ../development/libraries/openbabel { };

     

       8507
       8507
       -
       

     

       8508
       8502
        
         opencascade-occt_7_6 = opencascade-occt.overrideAttrs rec {

     

       8509
       8503
        
           pname = "opencascade-occt";

     

       8510
       8504
        
           version = "7.6.2";

pkgs/top-level/python-aliases.nix

···

       494
       494
        
         openai-triton-cuda = triton-cuda; # added 2024-07-18

     

       495
       495
        
         openai-triton-no-cuda = triton-no-cuda; # added 2024-07-18

     

       496
       496
        
         openapi-schema-pydantic = throw "openapi-schema-pydantic has been removed, since it is no longer maintained"; # added 2023-10-30

     

       497
       497
       +
         openbabel-bindings = openbabel; # added 2025-09-17

     

       497
       498
        
         opencv3 = throw "opencv3 has been removed as it is obsolete"; # added 2023-10-12

     

       498
       499
        
         openllm = throw "openllm has moved to pkgs.openllm"; # added 2021-12-31

     

       499
       500
        
         openllm-client = throw "openllm-client has been removed, since it is abandoned due to a change in philosophy"; # added 2024-08-24

+1 -3

pkgs/top-level/python-packages.nix

···

       10934
       10934
        
       

     

       10935
       10935
        
         openapi3 = callPackage ../development/python-modules/openapi3 { };

     

       10936
       10936
        
       

     

       10937
       10937
       -
         openbabel-bindings = callPackage ../development/python-modules/openbabel-bindings {

     

       10938
       10938
       -
           openbabel = pkgs.openbabel.override { python3 = python; };

     

       10939
       10939
       -
         };

     

       10937
       10937
       +
         openbabel = toPythonModule (pkgs.openbabel.override { python3 = python; });

     

       10940
       10938
        
       

     

       10941
       10939
        
         opencamlib = callPackage ../development/python-modules/opencamlib { };

     

       10942
       10940