From 47aa468f70d76bf32c5670b8165219458919c8ae Mon Sep 17 00:00:00 2001 From: Emily Date: Wed, 17 Sep 2025 19:41:54 +0100 Subject: [PATCH] openbabel: unstable-06-12-23 -> 3.1.1-unstable-2024-12-21 Diff: https://github.com/openbabel/openbabel/compare/32cf131444c1555c749b356dab44fb9fe275271f...889c350feb179b43aa43985799910149d4eaa2bc --- pkgs/by-name/op/openbabel/package.nix | 60 +++++++------------ .../chemistry/avogadrolibs/default.nix | 2 +- .../openbabel-bindings/default.nix | 32 ---------- pkgs/top-level/python-aliases.nix | 1 + pkgs/top-level/python-packages.nix | 4 +- 5 files changed, 24 insertions(+), 75 deletions(-) delete mode 100644 pkgs/development/python-modules/openbabel-bindings/default.nix diff --git a/pkgs/by-name/op/openbabel/package.nix b/pkgs/by-name/op/openbabel/package.nix index 8bad13e512a0..0eb3d6771fc5 100644 --- a/pkgs/by-name/op/openbabel/package.nix +++ b/pkgs/by-name/op/openbabel/package.nix @@ -3,6 +3,7 @@ lib, fetchFromGitHub, cmake, + ninja, perl, zlib, libxml2, @@ -17,20 +18,24 @@ coordgenlibs, }: -stdenv.mkDerivation rec { +stdenv.mkDerivation { pname = "openbabel"; - version = "unstable-06-12-23"; + version = "3.1.1-unstable-2024-12-21"; src = fetchFromGitHub { owner = "openbabel"; - repo = pname; - rev = "32cf131444c1555c749b356dab44fb9fe275271f"; - hash = "sha256-V0wrZVrojCZ9Knc5H6cPzPoYWVosRZ6Sn4PX+UFEfHY="; + repo = "openbabel"; + rev = "889c350feb179b43aa43985799910149d4eaa2bc"; + hash = "sha256-pJbvKBjpvXNjTZRxD2AqEarqmq+Pq08uvGvog/k/a7k="; }; - postPatch = '' - sed '1i#include ' -i include/openbabel/obutil.h # gcc12 - ''; + + nativeBuildInputs = [ + cmake + ninja + swig + pkg-config + ]; buildInputs = [ perl @@ -45,40 +50,17 @@ stdenv.mkDerivation rec { coordgenlibs ]; - nativeBuildInputs = [ - cmake - swig - pkg-config + cmakeFlags = [ + (lib.cmakeBool "RUN_SWIG" true) + (lib.cmakeBool "PYTHON_BINDINGS" true) + (lib.cmakeFeature "PYTHON_INSTDIR" "${placeholder "out"}/${python3.sitePackages}") ]; - preConfigure = '' - cmakeFlagsArray+=( - "-DRUN_SWIG=ON" - "-DPYTHON_BINDINGS=ON" - "-DPYTHON_INSTDIR=$out/${python3.sitePackages}" - ) - ''; - - # Setuptools only accepts PEP 440 version strings. The "unstable" identifier - # can not be used. Instead we pretend to be the 3.2 beta release. - postFixup = '' - cat << EOF > $out/${python3.sitePackages}/setup.py - from setuptools import setup - - setup( - name = 'pyopenbabel', - version = '3.2b1', - packages = ['openbabel'], - package_data = {'openbabel' : ['_openbabel.so']} - ) - EOF - ''; - - meta = with lib; { + meta = { description = "Toolbox designed to speak the many languages of chemical data"; homepage = "http://openbabel.org"; - platforms = platforms.all; - license = licenses.gpl2Plus; - maintainers = with maintainers; [ danielbarter ]; + platforms = lib.platforms.all; + license = lib.licenses.gpl2Plus; + maintainers = with lib.maintainers; [ danielbarter ]; }; } diff --git a/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix b/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix index 236f7d5594d4..8dfb4aa0cf09 100644 --- a/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix +++ b/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix @@ -20,7 +20,7 @@ let pythonWP = python3.withPackages ( p: with p; [ - openbabel-bindings + openbabel numpy ] ); diff --git a/pkgs/development/python-modules/openbabel-bindings/default.nix b/pkgs/development/python-modules/openbabel-bindings/default.nix deleted file mode 100644 index ee256647776e..000000000000 --- a/pkgs/development/python-modules/openbabel-bindings/default.nix +++ /dev/null @@ -1,32 +0,0 @@ -{ - lib, - openbabel, - python, - buildPythonPackage, -}: - -buildPythonPackage { - format = "setuptools"; - inherit (openbabel) pname version; - - src = "${openbabel}/${python.sitePackages}"; - - buildInputs = [ 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 = "${openbabel}/lib/openbabel/3.1.0"; - LD_LIBRARY_PATH = "${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 ]; - }; -} diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix index c67d1f74c929..68c0ebc5d27b 100644 --- a/pkgs/top-level/python-aliases.nix +++ b/pkgs/top-level/python-aliases.nix @@ -494,6 +494,7 @@ mapAliases ({ openai-triton-cuda = triton-cuda; # added 2024-07-18 openai-triton-no-cuda = triton-no-cuda; # added 2024-07-18 openapi-schema-pydantic = throw "openapi-schema-pydantic has been removed, since it is no longer maintained"; # added 2023-10-30 + openbabel-bindings = openbabel; # added 2025-09-17 opencv3 = throw "opencv3 has been removed as it is obsolete"; # added 2023-10-12 openllm = throw "openllm has moved to pkgs.openllm"; # added 2021-12-31 openllm-client = throw "openllm-client has been removed, since it is abandoned due to a change in philosophy"; # added 2024-08-24 diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index b5e865fd7bf7..8cd299ecab21 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -10934,9 +10934,7 @@ self: super: with self; { openapi3 = callPackage ../development/python-modules/openapi3 { }; - openbabel-bindings = callPackage ../development/python-modules/openbabel-bindings { - openbabel = pkgs.openbabel.override { python3 = python; }; - }; + openbabel = toPythonModule (pkgs.openbabel.override { python3 = python; }); opencamlib = callPackage ../development/python-modules/opencamlib { };