From 21ca2dec9ffcfb3bf8c1435eea443b999c7e5193 Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@googlemail.com>
Date: Thu, 11 Nov 2021 22:31:47 +0100
Subject: [PATCH] pyscf: 1.7.6.post1 -> 2.0.1

pyscf: hash


pyscf: limit test suite to single core


pyscf: adapting test suite


pyscf: fix pythonpath for tests


pyscf: formatting


pyscf: platforms


remove log


pyscf: enable uadc module


pyscf: platforms


pyscf: formatting


pyscf: disable instable N3 CI test


pyscf: formating


pyscf: increase ulimit


pyscf: ulimit files


pyscf: remove ulimit -n
---
 .../python-modules/pyscf/default.nix          | 90 ++++++++++++++++---
 .../python-modules/pyscf/h5py.patch           | 13 ---
 2 files changed, 77 insertions(+), 26 deletions(-)
 delete mode 100644 pkgs/development/python-modules/pyscf/h5py.patch

diff --git a/pkgs/development/python-modules/pyscf/default.nix b/pkgs/development/python-modules/pyscf/default.nix
index 0be40b5dfe7c..cf6f91e74f7d 100644
--- a/pkgs/development/python-modules/pyscf/default.nix
+++ b/pkgs/development/python-modules/pyscf/default.nix
@@ -1,45 +1,109 @@
-{ buildPythonPackage, lib, fetchFromGitHub, libcint, libxc, xcfun, blas
-, numpy, scipy, h5py
+{ buildPythonPackage
+, python3
+, lib
+, fetchFromGitHub
+, cmake
+, blas
+, libcint
+, libxc
+, xcfun
+, cppe
+, h5py
+, numpy
+, scipy
+, nose
+, nose-exclude
 }:
 
 buildPythonPackage rec {
   pname = "pyscf";
-  version = "1.7.6.post1";
+  version = "2.0.1";
 
   src = fetchFromGitHub {
     owner = "pyscf";
     repo = pname;
-    rev = "f6c9c6654dd9609c5e467a1edd5c2c076f793acc";
-    sha256  = "0xbwkjxxysfpqz72qn6n4a0zr2h6sprbcal8j7kzymh7swjy117w";
+    rev = "v${version}";
+    sha256 = "sha256-nwnhaqSn/9WHBjUPaEabK4x23fJ83WwEYvz6aCcvsDw=";
   };
 
-  # Backport from the 2.0.0 alpha releases of PySCF.
-  # H5Py > 3.3 deprecates the file modes, that PySCF sets.
-  patches = [ ./h5py.patch ];
+  # setup.py calls Cmake and passes the arguments in CMAKE_CONFIGURE_ARGS to cmake.
+  nativeBuildInputs = [ cmake ];
+  dontUseCmakeConfigure = true;
+  preConfigure = ''
+    export CMAKE_CONFIGURE_ARGS="-DBUILD_LIBCINT=0 -DBUILD_LIBXC=0 -DBUILD_XCFUN=0"
+    PYSCF_INC_DIR="${libcint}:${libxc}:${xcfun}";
+  '';
 
   buildInputs = [
+    blas
     libcint
     libxc
     xcfun
-    blas
   ];
 
   propagatedBuildInputs = [
+    cppe
+    h5py
     numpy
     scipy
-    h5py
   ];
 
-  PYSCF_INC_DIR="${libcint}:${libxc}:${xcfun}";
+  checkInputs = [ nose nose-exclude ];
 
-  doCheck = false;
   pythonImportsCheck = [ "pyscf" ];
+  preCheck = ''
+    # Set config used by tests to ensure reproducibility
+    echo 'pbc_tools_pbc_fft_engine = "NUMPY"' > pyscf/pyscf_config.py
+    export OMP_NUM_THREADS=1
+    ulimit -s 20000
+    export PYSCF_CONFIG_FILE=$(pwd)/pyscf/pyscf_config.py
+  '';
+  # As defined for the PySCF CI at https://github.com/pyscf/pyscf/blob/master/.github/workflows/run_tests.sh
+  # minus some additionally numerically instable tests, that are sensitive to BLAS, FFTW, etc.
+  checkPhase = ''
+    runHook preCheck
+
+    nosetests pyscf/ -v \
+      --exclude-dir=examples --exclude-dir=pyscf/pbc/grad \
+      --exclude-dir=pyscf/x2c \
+      --exclude-dir=pyscf/pbc/tdscf \
+      -e test_bz \
+      -e h2o_vdz \
+      -e test_mc2step_4o4e \
+      -e test_ks_noimport \
+      -e test_jk_hermi0 \
+      -e test_j_kpts \
+      -e test_k_kpts \
+      -e high_cost \
+      -e skip \
+      -e call_in_background \
+      -e libxc_cam_beta_bug \
+      -e test_finite_diff_rks_eph \
+      -e test_finite_diff_uks_eph \
+      -e test_pipek \
+      -e test_n3_cis_ewald \
+      -I test_kuccsd_supercell_vs_kpts\.py \
+      -I test_kccsd_ghf\.py \
+      -I test_h_.*\.py \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow_supercell.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow_supercell.DiamondKSTestSupercell3 \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow.DiamondKSTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_krhf_slow_supercell.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_hf.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_ks.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_supercell_hf.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_supercell_ks.DiamondTestSupercell3 \
+      -I .*_slow.*py -I .*_kproxy_.*py -I test_proxy.py tdscf/*_slow.py gw/*_slow.py
+
+    runHook postCheck
+  '';
 
   meta = with lib; {
     description = "Python-based simulations of chemistry framework";
     homepage = "https://github.com/pyscf/pyscf";
     license = licenses.asl20;
-    platforms = platforms.linux;
+    platforms = platforms.unix;
     maintainers = [ maintainers.sheepforce ];
   };
 }
diff --git a/pkgs/development/python-modules/pyscf/h5py.patch b/pkgs/development/python-modules/pyscf/h5py.patch
deleted file mode 100644
index 160128633208..000000000000
--- a/pkgs/development/python-modules/pyscf/h5py.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/pyscf/lib/misc.py b/pyscf/lib/misc.py
-index ed43689ff..a8a0d0e20 100644
---- a/pyscf/lib/misc.py
-+++ b/pyscf/lib/misc.py
-@@ -42,8 +42,6 @@ if h5py.version.version[:4] == '2.2.':
-     sys.stderr.write('h5py-%s is found in your environment. '
-                      'h5py-%s has bug in threading mode.\n'
-                      'Async-IO is disabled.\n' % ((h5py.version.version,)*2))
--if h5py.version.version[:2] == '3.':
--    h5py.get_config().default_file_mode = 'a'
- 
- c_double_p = ctypes.POINTER(ctypes.c_double)
- c_int_p = ctypes.POINTER(ctypes.c_int)