Add a test for a full silicon SCF workchain (#9)

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.8', '3.9', '3.10', '3.11']
+                python-version: ['3.9', '3.10', '3.11', '3.12']
 
         services:
             postgres:

pyproject.toml

@@ -14,22 +14,22 @@ classifiers = [
     'Framework :: AiiDA',
     'License :: OSI Approved :: MIT License',
     'Programming Language :: Python',
-    'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
-    'Programming Language :: Python :: 3.11'
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
 ]
 keywords = ['aiida', 'workflows']
 requires-python = '>=3.8'
 dependencies = [
-    'aiida_core[atomic_tools]>=2.0',
+    'aiida_core[atomic_tools]>=2.5',
     'aiida-pseudo',
     'click~=8.0',
     'h5py',
     'importlib_resources',
     'jsonschema',
     'numpy',
-    'packaging'
+    'packaging',
     'pymatgen',
 ]
 

tests/conftest.py

@@ -1,132 +1,36 @@
-# -*- coding: utf-8 -*-
-# pylint: disable=redefined-outer-name,too-many-statements
-"""Initialise a text database and profile for pytest."""
+import logging
 import os
-
 import pytest
 
-pytest_plugins = ['aiida.manage.tests.pytest_fixtures']  # pylint: disable=invalid-name
-
-
-@pytest.fixture(scope='session')
-def filepath_tests():
-    """Return the absolute filepath of the `tests` folder.
-    .. warning:: if this file moves with respect to the `tests` folder, the implementation should change.
-    :return: absolute filepath of `tests` folder which is the basepath for all test resources.
-    """
-    return os.path.dirname(os.path.abspath(__file__))
-
-
-@pytest.fixture
-def filepath_fixtures(filepath_tests):
-    """Return the absolute filepath to the directory containing the file `fixtures`."""
-    return os.path.join(filepath_tests, 'fixtures')
-
-
-@pytest.fixture(scope='function')
-def fixture_sandbox():
-    """Return a `SandboxFolder`."""
-    from aiida.common.folders import SandboxFolder
-    with SandboxFolder() as folder:
-        yield folder
-
-
-@pytest.fixture
-def fixture_localhost(aiida_localhost):
-    """Return a localhost `Computer`."""
-    localhost = aiida_localhost
-    localhost.set_default_mpiprocs_per_machine(1)
-    return localhost
-
-
-@pytest.fixture
-def fixture_code(fixture_localhost):
-    """Return a ``Code`` instance configured to run calculations of given entry point on localhost ``Computer``."""
-
-    def _fixture_code(entry_point_name):
-        from aiida.common import exceptions
-        from aiida.orm import Code
-
-        label = f'test.{entry_point_name}'
-
-        try:
-            return Code.objects.get(label=label)  # pylint: disable=no-member
-        except exceptions.NotExistent:
-            return Code(
-                label=label,
-                input_plugin_name=entry_point_name,
-                remote_computer_exec=[fixture_localhost, '/bin/true'],
-            )
-
-    return _fixture_code
-
-
-@pytest.fixture
-def serialize_builder():
-    """Serialize the given process builder into a dictionary with nodes turned into their value representation.
-    :param builder: the process builder to serialize
-    :return: dictionary
-    """
-
-    def serialize_data(data):
-        # pylint: disable=too-many-return-statements
-        from aiida.orm import BaseType, Code, Dict
-        from aiida.plugins import DataFactory
-
-        StructureData = DataFactory('core.structure')
-        UpfData = DataFactory('pseudo.upf')
-
-        if isinstance(data, dict):
-            return {key: serialize_data(value) for key, value in data.items()}
-
-        if isinstance(data, BaseType):
-            return data.value
-
-        if isinstance(data, Code):
-            return data.full_label
+pytest_plugins = 'aiida.manage.tests.pytest_fixtures'
 
-        if isinstance(data, Dict):
-            return data.get_dict()
+_LOGGER = logging.getLogger(__name__)
+_julia_project_path = os.path.join(__file__, "..", "julia_environment")
 
-        if isinstance(data, StructureData):
-            return data.get_formula()
 
-        if isinstance(data, UpfData):
-            return f'{data.element}<md5={data.md5}>'
+def pytest_sessionstart():
+    """Instantiates the test Julia environment before any test runs."""
+    import subprocess
 
-        return data
-
-    def _serialize_builder(builder):
-        return serialize_data(builder._inputs(prune=True))  # pylint: disable=protected-access
-
-    return _serialize_builder
+    # Pkg.Registry.add() seems necessary for GitHub Actions
+    subprocess.run(['julia', f'--project={_julia_project_path}', '-e', 'using Pkg; Pkg.Registry.add(); Pkg.resolve(); Pkg.precompile();'], check=True)
 
 
 @pytest.fixture
-def generate_calc_job():
-    """Fixture to construct a new `CalcJob` instance and call `prepare_for_submission` for testing `CalcJob` classes.
-    The fixture will return the `CalcInfo` returned by `prepare_for_submission` and the temporary folder that was passed
-    to it, into which the raw input files will have been written.
-    """
-
-    def _generate_calc_job(folder, entry_point_name, inputs=None):
-        """Fixture to generate a mock `CalcInfo` for testing calculation jobs."""
-        from aiida.engine.utils import instantiate_process
-        from aiida.manage.manager import get_manager
-        from aiida.plugins import CalculationFactory
-
-        manager = get_manager()
-        runner = manager.get_runner()
-
-        process_class = CalculationFactory(entry_point_name)
-        process = instantiate_process(runner, process_class, **inputs)
-
-        calc_info = process.prepare_for_submission(folder)
-
-        return calc_info
-
-    return _generate_calc_job
+def get_dftk_code(aiida_local_code_factory):
+    """Return an ``InstalledCode`` instance configured to run DFTK calculations on localhost."""
+
+    def _get_code():
+        return aiida_local_code_factory(
+            'dftk',
+            'julia',
+            label='dftk',
+            prepend_text=f"""\
+                export JULIA_PROJECT="{_julia_project_path}"
+            """,
+        )
 
+    return _get_code
 
 @pytest.fixture
 def generate_structure():
@@ -144,6 +48,12 @@ def _generate_structure(structure_id='silicon'):
             structure = StructureData(cell=cell)
             structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si')
             structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
+        elif structure_id == 'silicon_perturbed':
+            param = 5.43
+            cell = [[param / 2., param / 2., 0], [param / 2., 0, param / 2.], [0, param / 2., param / 2.]]
+            structure = StructureData(cell=cell)
+            structure.append_atom(position=(0.05, 0., 0.), symbols='Si', name='Si')
+            structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
         elif structure_id == 'water':
             structure = StructureData(cell=[[5.29177209, 0., 0.], [0., 5.29177209, 0.], [0., 0., 5.29177209]])
             structure.append_atom(position=[12.73464656, 16.7741411, 24.35076238], symbols='H', name='H')
@@ -177,90 +87,55 @@ def _generate_kpoints_mesh(npoints):
 
     return _generate_kpoints_mesh
 
-
-@pytest.fixture(scope='session')
-def generate_parser():
-    """Fixture to load a parser class for testing parsers."""
-
-    def _generate_parser(entry_point_name):
-        """Fixture to load a parser class for testing parsers.
-        :param entry_point_name: entry point name of the parser class
-        :return: the `Parser` sub class
-        """
-        from aiida.plugins import ParserFactory
-        return ParserFactory(entry_point_name)
-
-    return _generate_parser
-
-
+# TODO: It would be nicer to automatically download the psp through aiida-pseudo
 @pytest.fixture
-def generate_remote_data():
-    """Return a `RemoteData` node."""
-
-    def _generate_remote_data(computer, remote_path, entry_point_name=None):
-        """Return a `KpointsData` with a mesh of npoints in each direction."""
-        from aiida.common.links import LinkType
-        from aiida.orm import CalcJobNode, RemoteData
-        from aiida.plugins.entry_point import format_entry_point_string
-
-        entry_point = format_entry_point_string('aiida.calculations', entry_point_name)
+def load_psp():
+    """Return the pd_nc_sr_pbe_standard_0.4.1_upf pseudopotential for an element"""
 
-        remote = RemoteData(remote_path=remote_path)
-        remote.computer = computer
+    def _load_psp(element: str):
+        from aiida import plugins
+        from pathlib import Path
 
-        if entry_point_name is not None:
-            creator = CalcJobNode(computer=computer, process_type=entry_point)
-            creator.set_option('resources', {'num_machines': 1, 'num_mpiprocs_per_machine': 1})
-            remote.base.links.add_incoming(creator, link_type=LinkType.CREATE, link_label='remote_folder')
-            creator.store()
+        if element != "Si":
+            raise ValueError("Only the Si psp is available for the moment.")
 
-        return remote
+        UpfData = plugins.DataFactory('pseudo.upf')
+        with open((Path(__file__) / ".." / "pseudos" / (element + ".upf")).resolve(), "rb") as stream:
+            return UpfData(stream)
 
-    return _generate_remote_data
+    return _load_psp
 
 
+# TODO: Something like this should exist in aiida! We shouldn't have to do it ourselves just to capture why the test failed.
 @pytest.fixture
-def generate_bands_data():
-    """Return a `BandsData` node."""
-
-    def _generate_bands_data():
-        """Return a `BandsData` instance with some basic `kpoints` and `bands` arrays."""
-        from aiida.plugins import DataFactory
-        import numpy
-        BandsData = DataFactory('core.array.bands')  #pylint: disable=invalid-name
-        bands_data = BandsData()
-
-        bands_data.set_kpoints(numpy.array([[0., 0., 0.], [0.625, 0.25, 0.625]]))
-
-        bands_data.set_bands(
-            numpy.array([[-5.64024889, 6.66929678, 6.66929678, 6.66929678, 8.91047649],
-                         [-1.71354964, -0.74425095, 1.82242466, 3.98697455, 7.37979746]]),
-            units='eV'
-        )
+def submit_and_await_success(submit_and_await):
+    """
+    Submits a process or process builder to the engine.
+    Validates that the process succeeds, or logs a report if it doesn't.
+    """
 
-        return bands_data
+    def _submit_and_await_success(*args, **kwargs):
+        from aiida.cmdline.utils.common import get_calcjob_report, get_workchain_report
+        from aiida.orm.nodes.process import CalcJobNode, WorkChainNode
 
-    return _generate_bands_data
+        result = submit_and_await(*args, **kwargs)
 
+        if result.exit_status != 0:
+            if isinstance(result, CalcJobNode):
+                _LOGGER.warning("Report of CalcJobNode:")
+                _LOGGER.warning(get_calcjob_report(result))
+            elif isinstance(result, WorkChainNode):
+                _LOGGER.warning("Report of WorkChainNode:")
+                _LOGGER.warning(get_workchain_report(result, "REPORT"))
 
-@pytest.fixture
-def generate_workchain():
-    """Generate an instance of a `WorkChain`."""
-
-    def _generate_workchain(entry_point, inputs):
-        """Generate an instance of a `WorkChain` with the given entry point and inputs.
-        :param entry_point: entry point name of the work chain subclass.
-        :param inputs: inputs to be passed to process construction.
-        :return: a `WorkChain` instance.
-        """
-        from aiida.engine.utils import instantiate_process
-        from aiida.manage.manager import get_manager
-        from aiida.plugins import WorkflowFactory
+                # Also log reports of all child calcjobs:
+                for link in result.base.links.get_outgoing(CalcJobNode):
+                    if isinstance(link.node, CalcJobNode):
+                        _LOGGER.warning("Report of child CalcJobNode:")
+                        _LOGGER.warning(get_calcjob_report(link.node))
 
-        process_class = WorkflowFactory(entry_point)
-        runner = get_manager().get_runner()
-        process = instantiate_process(runner, process_class, **inputs)
+            assert result.exit_status == 0
 
-        return process
+        return result
 
-    return _generate_workchain
+    return _submit_and_await_success

tests/julia_environment/.gitignore

@@ -0,0 +1,2 @@
+LocalPreferences.toml
+Manifest.toml

tests/julia_environment/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+AiidaDFTK = "26386dbc-b74b-4d9a-b75a-41d28ada84fc"
+
+[compat]
+AiidaDFTK = "0.1"