Release 3.1.0

.conan_test_package/conanfile.py

@@ -6,6 +6,7 @@
 
 from conans import ConanFile
 
+
 class TestPackageConan(ConanFile):
     def build(self):
         pass
@@ -16,84 +17,6 @@ def test(self):
             import scine_serenity_wrapper
             self.output.info("Import worked")
 
-            import scine_utilities as utils
-
-            h2 = utils.AtomCollection(
-                [utils.ElementType.H, utils.ElementType.H],
-                [[-0.7, 0.0, 0.0], [0.7, 0.0, 0.0]]
-            )
-
-            # Test R-KS-DFT
-            module_manager = utils.core.ModuleManager.get_instance()
-            calculator = module_manager.get('calculator', 'dft')
-            assert calculator.name() == 'SerenityDFTCalculator'
-            calculator.structure = h2
-            calculator.settings['method'] = 'pbe-d3bj'
-            calculator.settings['basis_set'] = 'def2-tzvp'
-            results = calculator.calculate()
-            assert results.successful_calculation
-            assert abs(results.energy - -1.166043) < 1e-6
-            self.output.info("R-KS-DFT worked")
-
-            # Test U-KS-DFT
-            module_manager = utils.core.ModuleManager.get_instance()
-            calculator = module_manager.get('calculator', 'dft')
-            assert calculator.name() == 'SerenityDFTCalculator'
-            calculator.structure = h2
-            calculator.settings['spin_mode'] = 'unrestricted'
-            calculator.settings['method'] = 'pbe-d3bj'
-            calculator.settings['basis_set'] = 'def2-tzvp'
-            results = calculator.calculate()
-            assert results.successful_calculation
-            assert abs(results.energy - -1.166043) < 1e-6
-            self.output.info("U-KS-DFT worked")
-
-            # Test R-HF
-            module_manager = utils.core.ModuleManager.get_instance()
-            calculator = module_manager.get('calculator', 'hf')
-            assert calculator.name() == 'SerenityHFCalculator'
-            calculator.structure = h2
-            calculator.settings['method'] = 'hf'
-            calculator.settings['basis_set'] = 'def2-tzvp'
-            results = calculator.calculate()
-            assert results.successful_calculation
-            assert abs(results.energy - -1.132535) < 1e-6
-            self.output.info("U-KS-DFT worked")
-
-            # Test U-HF
-            module_manager = utils.core.ModuleManager.get_instance()
-            calculator = module_manager.get('calculator', 'hf')
-            assert calculator.name() == 'SerenityHFCalculator'
-            calculator.structure = h2
-            calculator.settings['spin_mode'] = 'unrestricted'
-            calculator.settings['method'] = 'hf'
-            calculator.settings['basis_set'] = 'def2-tzvp'
-            results = calculator.calculate()
-            assert results.successful_calculation
-            assert abs(results.energy - -1.132535) < 1e-6
-            self.output.info("U-KS-DFT worked")
-
-            # Test R-CCSD(T)
-            module_manager = utils.core.ModuleManager.get_instance()
-            calculator = module_manager.get('calculator', 'cc')
-            assert calculator.name() == 'SerenityCCCalculator'
-            calculator.structure = h2
-            calculator.settings['method'] = 'ccsd(t)'
-            calculator.settings['basis_set'] = 'def2-tzvp'
-            results = calculator.calculate()
-            assert results.successful_calculation
-            assert abs(results.energy - -1.168261) < 1e-6
-            self.output.info("R-CCSD(T) worked")
-
-            # Test R-DLPNO-CCSD(T0)
-            module_manager = utils.core.ModuleManager.get_instance()
-            calculator = module_manager.get('calculator', 'cc')
-            assert calculator.name() == 'SerenityCCCalculator'
-            calculator.structure = h2
-            calculator.settings['method'] = 'dlpno-ccsd(t0)'
-            calculator.settings['basis_set'] = 'def2-tzvp'
-            results = calculator.calculate()
-            assert results.successful_calculation
-            assert abs(results.energy - -1.168311) < 1e-6
-            self.output.info("R-DLPNO-CCSD(T) worked")
+            from scine_serenity_wrapper.Tests.test_calculators import run_all_tests
+            run_all_tests()
 

CHANGELOG.rst

@@ -1,6 +1,11 @@
 Changelog
 =========
 
+Release 3.1.0
+-------------
+
+- Add unit tests for Python package and remove obsolete tests
+
 Release 3.0.0
 -------------
 

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.9)
 
 # Setup the Scine Project
 project(Serenity
-  VERSION 3.0.0
+  VERSION 3.1.0
   DESCRIPTION "SCINE Serenity Wrapper."
 )
 

README.rst

@@ -87,6 +87,13 @@ When publishing results obtained with the SCINE Serenity wrapper, please cite th
 release as archived on `Zenodo <https://doi.org/10.5281/zenodo.6695038>`_ (DOI
 10.5281/zenodo.6695038; please use the DOI of the respective release).
 
+Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:
+
+T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen,
+V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher,
+"SCINE—Software for chemical interaction networks", *J. Chem. Phys.*, **2024**, *160*, 222501
+(DOI `10.1063/5.0206974 <https://doi.org/10.1063/5.0206974>`_).
+
 This wrapper should also not be mistaken for the actual Serenity code it wraps.
 For the latter code and its citations, we refer you to the original
 Serenity repository. There you will find the references of the actual methods

conanfile.py

@@ -3,7 +3,7 @@
 
 class ScineSerenityConan(ScineConan):
     name = "scine_serenity_wrapper"
-    version = "3.0.0"
+    version = "3.1.0"
     url = "https://github.com/qcscine/serenity_wrapper"
     description = """A wrapper around Serenity (https://github.com/qcserenity/serenity),
 it exports DFT, HF and other quantum chemistry capabilities into the SCINE tool
@@ -29,5 +29,5 @@ class ScineSerenityConan(ScineConan):
         "dev/cmake/*", "src/*", "CMakeLists.txt", "README.rst", "LICENSE.txt",
         "dev/conan/hook.cmake", "dev/conan/glue/*"
     ]
-    requires = ["scine_utilities/9.0.0", "serenity/1.5.2"]
+    requires = ["scine_utilities/[=10.0.0]", "serenity/1.5.2"]
     cmake_name = "Serenity"

src/Serenity/CMakeLists.txt

@@ -58,7 +58,7 @@ if(SCINE_BUILD_PYTHON_BINDINGS)
 
   add_custom_command(TARGET Serenity POST_BUILD
     COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:Serenity> ${CMAKE_CURRENT_BINARY_DIR}/scine_serenity_wrapper
-    COMMENT "Copying 'serenity.module.so' to 'scine_serenity'"
+    COMMENT "Copying 'serenity.module.so' to 'scine_serenity_wrapper'"
   )
 
   install(CODE
@@ -68,13 +68,18 @@ if(SCINE_BUILD_PYTHON_BINDINGS)
      message(FATAL_ERROR \"Fatal error when installing Python module using PIP.\")
    endif()"
   )
-  # Copy the setup file and README.rst into the binary dir so you can install
+  # Copy the setup file into the binary dir so you can install
   # using pip or make a distribution with the compiled binary
   file(
     COPY ${CMAKE_CURRENT_SOURCE_DIR}/Python/__init__.py
     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/scine_serenity_wrapper
   )
 
+  file(
+    COPY ${CMAKE_CURRENT_SOURCE_DIR}/Python/Tests
+    DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/scine_serenity_wrapper
+  )
+
   # Figure out the location of serenity's data directory dependending on
   # whether serenity is imported or in-tree
   get_target_property(_serenity_imported serenity IMPORTED)

src/Serenity/Python/Tests/__init__.py

@@ -0,0 +1,4 @@
+__copyright__ = """This code is licensed under the 3-clause BSD license.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
+See LICENSE.txt for details.
+"""

src/Serenity/Python/Tests/test_calculators.py

@@ -0,0 +1,152 @@
+__copyright__ = """This code is licensed under the 3-clause BSD license.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
+See LICENSE.txt for details.
+"""
+
+import pytest
+import scine_utilities as utils
+
+def create_h2() -> utils.AtomCollection:
+    return utils.AtomCollection(
+        [utils.ElementType.H, utils.ElementType.H],
+        [[-0.7, 0.0, 0.0], [0.7, 0.0, 0.0]]
+    )
+
+def test_dft_restricted() -> None:
+    h2 = create_h2()
+    module_manager = utils.core.ModuleManager.get_instance()
+    calculator = module_manager.get('calculator', 'dft')
+    assert calculator.name() == 'SerenityDFTCalculator'
+    calculator.structure = h2
+    calculator.settings['method'] = 'pbe-d3bj'
+    calculator.settings['basis_set'] = 'def2-tzvp'
+    calculator.set_required_properties([utils.Property.Energy])
+    results = calculator.calculate()
+    assert results.successful_calculation
+    assert results.energy
+    assert abs(results.energy - -1.166043) < 1e-6
+
+def test_dft_restricted_other_properties() -> None:
+    h2 = create_h2()
+    module_manager = utils.core.ModuleManager.get_instance()
+    calculator = module_manager.get('calculator', 'dft')
+    assert calculator.name() == 'SerenityDFTCalculator'
+    calculator.structure = h2
+    calculator.settings['method'] = 'pbe-d3bj'
+    calculator.settings['basis_set'] = 'def2-tzvp'
+    calculator.set_required_properties([utils.Property.AOtoAtomMapping,
+                                        utils.Property.AtomicCharges,
+                                        # utils.Property.OneElectronMatrix,
+                                        utils.Property.OverlapMatrix,
+                                        utils.Property.Thermochemistry,
+                                        utils.Property.Gradients])
+    results = calculator.calculate()
+    assert results.successful_calculation
+    assert results.energy is not None
+    assert abs(results.energy - -1.166043) < 1e-6
+    assert results.gradients is not None
+    assert results.ao_to_atom_mapping is not None
+    assert results.atomic_charges is not None
+    assert results.overlap_matrix is not None
+    # assert results.one_electron_matrix is not None
+
+# TODO This should be included again as soon as the serenity wrapper avoids running SCF calculations for everything.
+# def test_dft_restricted_non_scf_properties() -> None:
+#     h2 = create_h2()
+#     module_manager = utils.core.ModuleManager.get_instance()
+#     calculator = module_manager.get('calculator', 'dft')
+#     assert calculator.name() == 'SerenityDFTCalculator'
+#     calculator.structure = h2
+#     calculator.settings['method'] = 'pbe-d3bj'
+#     calculator.settings['basis_set'] = 'def2-tzvp'
+#     calculator.set_required_properties([utils.Property.AOtoAtomMapping,
+#                                         utils.Property.OneElectronMatrix,
+#                                         utils.Property.OverlapMatrix,
+#                                         ])
+#     results = calculator.calculate()
+#     assert results.successful_calculation
+#     assert results.ao_to_atom_mapping is not None
+#     assert results.overlap_matrix is not None
+#     assert results.one_electron_matrix is not None
+#     assert results.energy is None
+
+def test_dft_unrestricted() -> None:
+    h2 = create_h2()
+    module_manager = utils.core.ModuleManager.get_instance()
+    calculator = module_manager.get('calculator', 'dft')
+    assert calculator.name() == 'SerenityDFTCalculator'
+    calculator.structure = h2
+    calculator.settings['spin_mode'] = 'unrestricted'
+    calculator.settings['method'] = 'pbe-d3bj'
+    calculator.settings['basis_set'] = 'def2-tzvp'
+    calculator.set_required_properties([utils.Property.Energy])
+    results = calculator.calculate()
+    assert results.successful_calculation
+    assert results.energy
+    assert abs(results.energy - -1.166043) < 1e-6
+
+def test_hf_restricted() -> None:
+    h2 = create_h2()
+    module_manager = utils.core.ModuleManager.get_instance()
+    calculator = module_manager.get('calculator', 'hf')
+    assert calculator.name() == 'SerenityHFCalculator'
+    calculator.structure = h2
+    calculator.settings['method'] = 'hf'
+    calculator.settings['basis_set'] = 'def2-tzvp'
+    calculator.set_required_properties([utils.Property.Energy])
+    results = calculator.calculate()
+    assert results.successful_calculation
+    assert results.energy
+    assert abs(results.energy - -1.132535) < 1e-6
+
+def test_hf_unrestricted() -> None:
+    h2 = create_h2()
+    module_manager = utils.core.ModuleManager.get_instance()
+    calculator = module_manager.get('calculator', 'hf')
+    assert calculator.name() == 'SerenityHFCalculator'
+    calculator.structure = h2
+    calculator.settings['spin_mode'] = 'unrestricted'
+    calculator.settings['method'] = 'hf'
+    calculator.settings['basis_set'] = 'def2-tzvp'
+    calculator.set_required_properties([utils.Property.Energy])
+    results = calculator.calculate()
+    assert results.successful_calculation
+    assert results.energy
+    assert abs(results.energy - -1.132535) < 1e-6
+
+def test_ccsd_t_restricted() -> None:
+    h2 = create_h2()
+    module_manager = utils.core.ModuleManager.get_instance()
+    calculator = module_manager.get('calculator', 'cc')
+    assert calculator.name() == 'SerenityCCCalculator'
+    calculator.structure = h2
+    calculator.settings['method'] = 'ccsd(t)'
+    calculator.settings['basis_set'] = 'def2-tzvp'
+    calculator.set_required_properties([utils.Property.Energy])
+    results = calculator.calculate()
+    assert results.successful_calculation
+    assert results.energy
+    assert abs(results.energy - -1.168261) < 1e-6
+
+def test_dlpno_ccsd_t0_restricted() -> None:
+    h2 = create_h2()
+    module_manager = utils.core.ModuleManager.get_instance()
+    calculator = module_manager.get('calculator', 'cc')
+    assert calculator.name() == 'SerenityCCCalculator'
+    calculator.structure = h2
+    calculator.settings['method'] = 'dlpno-ccsd(t0)'
+    calculator.settings['basis_set'] = 'def2-tzvp'
+    calculator.set_required_properties([utils.Property.Energy])
+    results = calculator.calculate()
+    assert results.successful_calculation
+    assert results.energy
+    assert abs(results.energy - -1.168311) < 1e-6
+
+def run_all_tests() -> None:
+    test_dft_restricted()
+    test_dft_unrestricted()
+    test_dft_restricted_other_properties()
+    test_hf_restricted()
+    test_hf_unrestricted()
+    test_ccsd_t_restricted()
+    test_dlpno_ccsd_t0_restricted()

src/Serenity/Python/setup.py

@@ -16,7 +16,7 @@ def package_files(directory):
     return paths
 
 # Read README.rst for the long description
-with open("README.rst", "r") as fh:
+with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 
@@ -37,7 +37,8 @@ def __len__(self):
     long_description=long_description,
     url="https://www.scine.ethz.ch",
     packages=["scine_serenity_wrapper"],
-    package_data={"scine_serenity_wrapper": ['*.txt' @serenity_PY_DEPS@]},
+    include_package_data=True,
+    package_data={"scine_serenity_wrapper": ['*.txt' @serenity_PY_DEPS@, "Tests/*"]},
     install_requires=["scine_utilities"],
     classifiers=[
         "Programming Language :: Python",