From e90ec60e33b7ad353749b6e5d415c5211ad48858 Mon Sep 17 00:00:00 2001 From: "Robert T. McGibbon" Date: Tue, 22 Dec 2020 21:55:05 -0500 Subject: [PATCH 1/4] inchi: fix build on darwin --- pkgs/development/libraries/inchi/default.nix | 26 +++++++++++++++++--- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/pkgs/development/libraries/inchi/default.nix b/pkgs/development/libraries/inchi/default.nix index 6acdf340c91..256e0d70243 100644 --- a/pkgs/development/libraries/inchi/default.nix +++ b/pkgs/development/libraries/inchi/default.nix @@ -1,4 +1,11 @@ -{ pkgs, fetchurl, lib, stdenv, unzip }: +{ pkgs +, fetchurl +, lib +, stdenv +, unzip +, fixDarwinDylibNames +}: + stdenv.mkDerivation { pname = "inchi"; version = "1.05"; @@ -7,15 +14,23 @@ stdenv.mkDerivation { sha1 = "e3872a46d58cb321a98f4fd4b93a989fb6920b9c"; }; - nativeBuildInputs = [ pkgs.unzip ]; + nativeBuildInputs = [ unzip ] ++ lib.optional stdenv.isDarwin fixDarwinDylibNames; outputs = [ "out" "doc" ]; enableParallelBuilding = true; - preBuild = '' + preConfigure = '' cd ./INCHI_API/libinchi/gcc + '' + lib.optionalString stdenv.isDarwin '' + substituteInPlace makefile \ + --replace ",--version-script=libinchi.map" "" \ + --replace "LINUX_Z_RELRO = ,-z,relro" "" \ + --replace "-soname" "-install_name" \ + --replace "gcc" $CC ''; installPhase = '' + runHook preInstall + cd ../../.. mkdir -p $out/lib mkdir -p $out/include/inchi @@ -29,6 +44,10 @@ stdenv.mkDerivation { runHook postInstall ''; + preFixup = lib.optionalString stdenv.isDarwin '' + fixDarwinDylibNames $(find "$out" -name "*.so.*") + ''; + postInstall = let src-doc = fetchurl { @@ -45,7 +64,6 @@ stdenv.mkDerivation { homepage = "https://www.inchi-trust.org/"; description = "IUPAC International Chemical Identifier library"; license = licenses.lgpl2Plus; - platforms = platforms.all; maintainers = with maintainers; [ rmcgibbo ]; }; } From 947ccc54ae22014d02883e20b219ce2820fbbffe Mon Sep 17 00:00:00 2001 From: "Robert T. McGibbon" Date: Tue, 22 Dec 2020 21:58:21 -0500 Subject: [PATCH 2/4] maeparser: init at 1.2.4 --- .../libraries/maeparser/default.nix | 28 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 30 insertions(+) create mode 100644 pkgs/development/libraries/maeparser/default.nix diff --git a/pkgs/development/libraries/maeparser/default.nix b/pkgs/development/libraries/maeparser/default.nix new file mode 100644 index 00000000000..cd7cc70907c --- /dev/null +++ b/pkgs/development/libraries/maeparser/default.nix @@ -0,0 +1,28 @@ +{ fetchFromGitHub +, lib +, stdenv +, boost +, zlib +, cmake +}: + +stdenv.mkDerivation rec { + pname = "maeparser"; + version = "1.2.4"; + + src = fetchFromGitHub { + owner = "schrodinger"; + repo = "maeparser"; + rev = "v${version}"; + sha256 = "1qzp8d58ksy88y4fx1b0x65wycslm7zxzbb8ns28gkjh12xpzhwz"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ boost zlib ]; + + meta = with lib; { + description = "maestro file parser"; + maintainers = [ maintainers.rmcgibbo ]; + license = licenses.mit; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 7f69d035573..04c90f4600c 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -6033,6 +6033,8 @@ in madlang = haskell.lib.justStaticExecutables haskellPackages.madlang; + maeparser = callPackage ../development/libraries/maeparser { }; + mailcheck = callPackage ../applications/networking/mailreaders/mailcheck { }; maildrop = callPackage ../tools/networking/maildrop { }; From 4bbdff14c89aa2bdaa0e392b58a016c4398718e9 Mon Sep 17 00:00:00 2001 From: "Robert T. McGibbon" Date: Mon, 1 Feb 2021 12:20:34 -0500 Subject: [PATCH 3/4] coordgenlibs: init at 1.4.2 --- .../libraries/coordgenlibs/default.nix | 29 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 31 insertions(+) create mode 100644 pkgs/development/libraries/coordgenlibs/default.nix diff --git a/pkgs/development/libraries/coordgenlibs/default.nix b/pkgs/development/libraries/coordgenlibs/default.nix new file mode 100644 index 00000000000..f0f0718ab10 --- /dev/null +++ b/pkgs/development/libraries/coordgenlibs/default.nix @@ -0,0 +1,29 @@ +{ fetchFromGitHub +, lib +, stdenv +, boost +, zlib +, cmake +, maeparser +}: + +stdenv.mkDerivation rec { + pname = "coordgenlibs"; + version = "1.4.2"; + + src = fetchFromGitHub { + owner = "schrodinger"; + repo = pname; + rev = "v${version}"; + sha256 = "18s3y9v6x246hapxy0cy4srnll4qqzqfx003j551l5f27b2ng8fn"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ boost zlib maeparser ]; + + meta = with lib; { + description = "Schrodinger-developed 2D Coordinate Generation"; + maintainers = [ maintainers.rmcgibbo ]; + license = licenses.bsd3; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 04c90f4600c..ef336e839c6 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -212,6 +212,8 @@ in containerpilot = callPackage ../applications/networking/cluster/containerpilot { }; + coordgenlibs = callPackage ../development/libraries/coordgenlibs { }; + cp437 = callPackage ../tools/misc/cp437 { }; cpu-x = callPackage ../applications/misc/cpu-x { }; From 8f1b6ae4519a56fe129b523a80b2a26e9c7dd68a Mon Sep 17 00:00:00 2001 From: "Robert T. McGibbon" Date: Tue, 22 Dec 2020 22:00:38 -0500 Subject: [PATCH 4/4] rdkit: init at 2020.09.3 --- .../python-modules/rdkit/default.nix | 157 ++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 159 insertions(+) create mode 100644 pkgs/development/python-modules/rdkit/default.nix diff --git a/pkgs/development/python-modules/rdkit/default.nix b/pkgs/development/python-modules/rdkit/default.nix new file mode 100644 index 00000000000..b747304446b --- /dev/null +++ b/pkgs/development/python-modules/rdkit/default.nix @@ -0,0 +1,157 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, fetchzip +, cmake +, boost +, catch +, inchi +, cairo +, eigen +, python +, rapidjson +, maeparser +, coordgenlibs +, numpy +, pandas +, pillow +, git +}: +let + external = { + avalon = fetchzip { + url = "http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar"; + sha256 = "0nhxfxckb5a5qs0g148f55yarhncqjgjzcvdskkv9rxi2nrs7160"; + stripRoot = false; + }; + yaehmop = fetchFromGitHub { + owner = "greglandrum"; + repo = "yaehmop"; + rev = "1b13b52e2738a77715b1bad876e3b4e93f2b5269"; + sha256 = "1jp7wz8win4mgwxkaz2gnrgsaaqgln04n2lwgfr96isdv1klf62d"; + }; + freesasa = fetchFromGitHub + { + owner = "mittinatten"; + repo = "freesasa"; + rev = "2.0.3"; + sha256 = "0x686zm9fpyg5647fdgxnxgbwav99nc6ymh4bmkr2063yyda4kzc"; + }; + }; +in +buildPythonPackage rec { + version = "2020.09.3"; + pname = "rdkit"; + + src = + let + versionTag = lib.replaceStrings [ "." ] [ "_" ] version; + in + fetchFromGitHub { + owner = pname; + repo = pname; + rev = "Release_${versionTag}"; + sha256 = "1k1wvzcd1yfx4nhz3iq2aaadzdk5w6sfcb4imhvm7pkbzij0nicx"; + }; + + unpackPhase = '' + mkdir -p source/External/AvalonTools/avalon source/External/YAeHMOP/yaehmop source/External/FreeSASA/freesasa + cp -r ${src}/* source + cp -r ${external.avalon}/SourceDistribution/* source/External/AvalonTools/avalon + cp -r ${external.yaehmop}/* source/External/YAeHMOP/yaehmop + cp -r ${external.freesasa}/* source/External/FreeSASA/freesasa + + find source -type d -exec chmod 755 {} + + cp source/External/FreeSASA/freesasa2.c source/External/FreeSASA/freesasa/src + ln -s ${rapidjson} source/External/rapidjson-1.1.0 + ''; + + sourceRoot = "source"; + + nativeBuildInputs = [ + cmake + git # required by freesasa + ]; + + buildInputs = [ + boost + catch + inchi + eigen + cairo + rapidjson + ]; + + propagatedBuildInputs = [ + numpy + pandas + pillow + ]; + + hardeningDisable = [ "format" ]; # required by yaehmop + # doCheck = false; + dontUseSetuptoolsBuild = true; + dontUsePipInstall = true; + dontUseSetuptoolsCheck = true; + + preConfigure = '' + # Don't want this contacting the git remote during the build + substituteInPlace External/YAeHMOP/CMakeLists.txt --replace \ + 'GIT_TAG master' 'DOWNLOAD_COMMAND true' + + # Since we can't expand with bash in cmakeFlags + cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')" + cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa" + cmakeFlags="$cmakeFlags -DFREESASA_SRC_DIR=$PWD/External/FreeSASA/freesasa" + cmakeFlags="$cmakeFlags -DAVALONTOOLS_DIR=$PWD/External/AvalonTools/avalon" + ''; + + cmakeFlags = [ + "-DCATCH_DIR=${catch}/include/catch" + "-DINCHI_LIBRARY=${inchi}/lib/libinchi.so" + "-DINCHI_LIBRARIES=${inchi}/lib/libinchi.so" + "-DINCHI_INCLUDE_DIR=${inchi}/include/inchi" + "-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3" + "-DRDK_INSTALL_INTREE=OFF" + "-DRDK_INSTALL_STATIC_LIBS=OFF" + "-DRDK_BUILD_INCHI_SUPPORT=ON" + "-DRDK_BUILD_AVALON_SUPPORT=ON" + "-DRDK_BUILD_FREESASA_SUPPORT=ON" + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON" + "-DRDK_BUILD_MAEPARSER_SUPPORT=ON" + "-DMAEPARSER_DIR=${maeparser}" + "-DRDK_BUILD_COORDGEN_SUPPORT=ON" + "-DCOORDGEN_DIR=${coordgenlibs}" + "-DRDK_USE_URF=OFF" + "-DRDK_USE_FLEXBISON=OFF" + "-DRDK_BUILD_CAIRO_SUPPORT=ON" + "-DRDK_BUILD_THREADSAFE_SSS=ON" + "-DRDK_TEST_MULTITHREADED=ON" + "-DRDK_BUILD_CPP_TESTS=ON" + "-DRDK_TEST_MULTITHREADED=ON" + "-DPYTHON_EXECUTABLE=${python}/bin/python" + "-DBOOST_ROOT=${boost}" + "-DBoost_NO_SYSTEM_PATHS=ON" + "-DBoost_NO_BOOST_CMAKE=TRUE" + ]; + + checkPhase = '' + export QT_QPA_PLATFORM='offscreen' + export RDBASE=$(realpath ..) + export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH" + (cd $RDBASE/rdkit/Chem && python $RDBASE/rdkit/TestRunner.py test_list.py) + ''; + + pythonImportsCheck = [ + "rdkit" + "rdkit.Chem" + "rdkit.Chem.AllChem" + ]; + + meta = with lib; { + description = "Open source toolkit for cheminformatics"; + maintainers = [ maintainers.rmcgibbo ]; + license = licenses.bsd3; + homepage = "https://www.rdkit.org"; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index c612cb9cde1..f532b282b1a 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -6642,6 +6642,8 @@ in { rdflib-jsonld = callPackage ../development/python-modules/rdflib-jsonld { }; + rdkit = callPackage ../development/python-modules/rdkit { }; + re-assert = callPackage ../development/python-modules/re-assert { }; readchar = callPackage ../development/python-modules/readchar { };