pythonPackages.pyscf: init at 1.7.1

pkgs/development/libraries/libcint/default.nix

@@ -1,10 +1,11 @@
 { stdenv
 , lib
 , fetchFromGitHub
+, fetchpatch
 , cmake
 , openblas
   # Check Inputs
-, python2
+, python
 }:
 
 stdenv.mkDerivation rec {
@@ -24,11 +25,22 @@ stdenv.mkDerivation rec {
     "-DENABLE_TEST=1"
     "-DQUICK_TEST=1"
     "-DCMAKE_INSTALL_PREFIX=" # ends up double-adding /nix/store/... prefix, this avoids issue
+    "-DWITH_F12=1"
+    "-DWITH_RANGE_COULOMB=1"
+    "-DWITH_COULOMB_ERF=1"
+  ];
+
+  patches = [
+    (fetchpatch {
+      name = "libcint-python3-test-syntax-patch";
+      url = "http://patch-diff.githubusercontent.com/raw/sunqm/libcint/pull/33.patch";
+      sha256 = "1pg9rz8vffijl3kkk6f4frsivd7m2gp2k44llzkaajav4m5q8q4a";
+    })
   ];
 
   doCheck = true;
-  # Test syntax (like print statements) is written in python2. Fixed when #33 merged: https://github.com/sunqm/libcint/pull/33
-  checkInputs = [ python2.pkgs.numpy ];
+
+  checkInputs = [ python.pkgs.numpy ];
 
   meta = with lib; {
     description = "General GTO integrals for quantum chemistry";

pkgs/development/libraries/xcfun/default.nix

@@ -0,0 +1,51 @@
+{ stdenv
+, fetchFromGitHub
+, cmake
+, gfortran
+, perl
+, bzip2
+}:
+
+stdenv.mkDerivation rec {
+  pname = "xcfun";
+  version = "1.0.X";
+
+  src = fetchFromGitHub {
+    owner = "dftlibs";
+    repo = pname;
+    rev = "355f42497a9cd17d16ae91da1f1aaaf93756ae8b"; # rev recommended by pythonPackages.pyscf: https://sunqm.github.io/pyscf/install.html#installation-without-network
+    sha256 = "09hs8lxks2d98a5q2xky9dz5sfsrxaww3kyryksi9b6l1f1m3hxp";
+  };
+
+  nativeBuildInputs = [
+    cmake
+  ];
+
+  buildInputs = [
+    bzip2
+    gfortran
+    perl
+  ];
+
+  cmakeFlags = [
+    "-DBUILD_TESTING=1"
+    "-DBUILD_SHARED_LIBS=1"
+    "-DXC_MAX_ORDER=3"
+  ];
+
+  # TODO: tests are very quick. check it actually does something.
+  doCheck = true;
+  checkPhase = ''
+    # set path for finding libxc.so for tests
+    export LD_LIBRARY_PATH=/build/source/build
+    ctest --progress
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Exchange-correlation functionals with arbitrary order derivatives";
+    homepage = "https://xcfun.readthedocs.io/en/latest/";
+    downloadPage = "https://github.com/dftlibs/xcfun/releases";
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ drewrisinger ];
+  };
+}

pkgs/development/python-modules/pyscf/default.nix

@@ -0,0 +1,164 @@
+{ lib
+, buildPythonPackage
+, isPy27
+, fetchFromGitHub
+# C/build dependencies
+, cmake
+, openblas
+, libcint
+, libxc
+, xcfun
+# Python dependencies
+, h5py
+, numpy
+, scipy
+  # Check Inputs
+, nose
+, nose-exclude
+}:
+
+buildPythonPackage rec {
+  pname = "pyscf";
+  version = "1.7.1";
+
+  # must download from GitHub to get the Cmake & C source files
+  src = fetchFromGitHub {
+    owner = "pyscf";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0fciw9id8fr9396sz52ap5gys0i9hmrmrwm0i1k1k7aciqab3kls";
+  };
+
+  disabled = isPy27;
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [
+    libcint
+    libxc
+    openblas
+    xcfun
+  ];
+
+  postPatch = ''
+    mkdir -p ./pyscf/lib/deps/include ./pyscf/lib/deps/lib
+    ln -s ${lib.getDev xcfun}/include/xc.h ./pyscf/lib/deps/include/xcfun.h
+    ln -s ${lib.getLib xcfun}/lib/libxc.so ./pyscf/lib/deps/lib/libxcfun.so
+    substituteInPlace pyscf/rt/__init__.py --replace "from tdscf import *" "from pyscf.tdscf import *"
+  '';
+
+
+  cmakeFlags = [
+    # disable rebuilding/downloading the required libraries
+    "-DBUILD_LIBCINT=0"
+    "-DBUILD_LIBXC=0"
+    "-DBUILD_XCFUN=0"
+    "-DENABLE_XCFUN=1"
+  ];
+  # Configure CMake to build C files in pyscf/lib. Python build expects files in ./pyscf/lib/build
+  preConfigure = ''
+    pushd pyscf/lib
+  '';
+  postConfigure = ''
+    popd
+  '';
+
+  # Build C dependencies, then build python package.
+  preBuild = ''
+    pushd pyscf/lib/build
+    make
+    popd
+  '';
+
+  propagatedBuildInputs = [
+    h5py
+    numpy
+    scipy
+  ];
+
+  # add libcint, libxc, xcfun headers to include path.
+  PYSCF_INC_DIR = lib.makeSearchPath "include" (map lib.getDev [
+    libcint
+    libxc
+    xcfun
+  ]);
+
+  pythonImportsCheck = [ "pyscf" ];
+
+  checkInputs = [ nose nose-exclude ];
+  # from source/.travis.yml, mostly
+  # Tests take about 30 mins to run
+  preCheck = ''
+    # HACK: Move compiled libraries to test dir so pyscf import mechanism can find them
+    cp ./dist/tmpbuild/pyscf/pyscf/lib/*.so ./pyscf/lib/
+
+    # Set config used by tests to ensure reproducibility
+    echo 'pbc_tools_pbc_fft_engine = "NUMPY"' > pyscf/pyscf_config.py
+    export OMP_NUM_THREADS=1
+    export PYSCF_CONFIG_FILE=$(pwd)/pyscf/pyscf_config.py
+  '';
+  checkPhase = ''
+    runHook preCheck
+
+    nosetests -v \
+      --where=pyscf \
+      --detailed-errors \
+      --exclude-dir=geomopt \
+      --exclude-dir=dmrgscf \
+      --exclude-dir=fciqmcscf \
+      --exclude-dir=icmpspt \
+      --exclude-dir=shciscf \
+      --exclude-dir=nao \
+      --exclude-dir=cornell_shci \
+      --exclude-dir=xianci \
+      --exclude=test_bz \
+      --exclude=h2o_vdz \
+      --exclude=test_mc2step_4o4e \
+      --exclude=test_ks_noimport \
+      --exclude=test_jk_single_kpt \
+      --exclude=test_jk_hermi0 \
+      --exclude=test_j_kpts \
+      --exclude=test_k_kpts \
+      --exclude=high_cost \
+      --exclude=skip \
+      --exclude=call_in_background \
+      --exclude=libxc_cam_beta_bug \
+      --ignore-files=test_kuccsd_supercell_vs_kpts\.py \
+      --ignore-files=test_kccsd_ghf\.py \
+      --ignore-files=test_h_.*\.py \
+      --ignore-files=test_P_uadc_ip\.py \
+      --ignore-files=test_P_uadc_ea\.py \
+      --exclude-test=pbc/tdscf/test/test_kproxy_hf.DiamondTestSupercell3 \
+      --exclude-test=pbc/tdscf/test/test_kproxy_ks.DiamondTestSupercell3 \
+      --exclude-test=pbc/tdscf/test/test_kproxy_supercell_hf.DiamondTestSupercell3 \
+      --exclude-test=pbc/tdscf/test/test_kproxy_supercell_ks.DiamondTestSupercell3 \
+      --ignore-files=.*_slow.*\.py \
+      --ignore-files=.*_kproxy_.*\.py \
+      --ignore-files=test_proxy\.py \
+      --ignore-files=test_krhf_slow_gamma\.py \
+      --ignore-files=test_krhf_slow\.py \
+      --ignore-files=test_krhf_slow_supercell\.py \
+      --ignore-files=test_ddcosmo_grad\.py \
+      --exclude=test_range_separated \
+      --ignore-files=test_ksproxy_ks\.py \
+      --ignore-files=test_kproxy_hf\.py \
+      --ignore-files=test_kgw_slow\.py
+
+    # NOTE: disables below test_proxy.py are manually added to get it to pass in Nix, and are NOT in the upstream Travis config
+
+    runHook postCheck
+  '';
+
+  meta = with lib; {
+    description = "Python-based Simulations of Chemistry Framework";
+    longDescription = ''
+      PySCF is an open-source collection of electronic structure modules powered by Python.
+      The package aims to provide a simple, lightweight, and efficient platform
+      for quantum chemistry calculations and methodology development.
+    '';
+    homepage = "http://www.pyscf.org/";
+    downloadPage = "https://github.com/pyscf/pyscf/releases";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ drewrisinger ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -14717,6 +14717,8 @@ in
 
   xcbutilxrm = callPackage ../servers/x11/xorg/xcb-util-xrm.nix { };
 
+  xcfun = callPackage ../development/libraries/xcfun { };
+
   xdo = callPackage ../tools/misc/xdo { };
 
   xineLib = callPackage ../development/libraries/xine-lib { };

pkgs/top-level/python-packages.nix

@@ -5019,6 +5019,8 @@ in {
 
   pyqtgraph = callPackage ../development/python-modules/pyqtgraph { };
 
+  pyscf = callPackage ../development/python-modules/pyscf { };
+
   PyStemmer = callPackage ../development/python-modules/pystemmer {};
 
   # Missing expression?