Dependencies: Update requirement aiida-core~=2.1

Author: Sebastiaan Huber

.github/workflows/cd.yml

@@ -35,7 +35,7 @@ jobs:
         -   name: Install Python
             uses: actions/setup-python@v4
             with:
-                python-version: '3.8'
+                python-version: '3.9'
                 cache: 'pip'
                 cache-dependency-path: pyproject.toml
 
@@ -56,7 +56,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.8', '3.9']
+                python-version: ['3.9']
 
         services:
             rabbitmq:
@@ -78,7 +78,7 @@ jobs:
             run: pip install -U pip wheel
 
         -   name: Install Python package and dependencies
-            run: pip install -e .[tests] && reentry scan
+            run: pip install -e .[tests]
 
         -   name: Run pytest
             run: pytest -sv tests

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
         -   name: Install Python
             uses: actions/setup-python@v4
             with:
-                python-version: '3.8'
+                python-version: '3.9'
                 cache: 'pip'
                 cache-dependency-path: pyproject.toml
 
@@ -34,7 +34,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.8', '3.9']
+                python-version: ['3.9']
 
         services:
             rabbitmq:
@@ -56,7 +56,7 @@ jobs:
             run: pip install -U pip wheel
 
         -   name: Install Python package and dependencies
-            run: pip install -e .[tests] && reentry scan
+            run: pip install -e .[tests]
 
         -   name: Run pytest
             env:

aiida_common_workflows/cli/options.py

@@ -105,10 +105,15 @@ def convert(self, value, param, ctx):
                 f'file `{value}` could not be parsed into a `StructureData`: {exception}'
             ) from exception
 
-        duplicate = QueryBuilder().append(StructureData, filters={'extras._aiida_hash': structure._get_hash()}).first()  # pylint: disable=protected-access
+        duplicate = QueryBuilder().append(
+            StructureData,
+            filters={
+                'extras._aiida_hash': structure.base.caching._get_hash()  # pylint: disable=protected-access
+            }
+        ).first()
 
         if duplicate:
-            return duplicate[0]
+            return duplicate[0]  # pylint: disable=unsubscriptable-object
 
         return structure
 

aiida_common_workflows/cli/plot.py

@@ -34,7 +34,7 @@ def cmd_plot_eos(workflow, precisions, print_table, output_file):
         echo.echo_critical(
             f'node {workflow.__class__.__name__}<{workflow.pk}> does not correspond to an EquationOfStateWorkChain.'
         )
-    outputs = workflow.get_outgoing(link_type=LinkType.RETURN).nested()
+    outputs = workflow.base.links.get_outgoing(link_type=LinkType.RETURN).nested()
 
     missing_outputs = tuple(output for output in ('structures', 'total_energies') if output not in outputs)
     if missing_outputs:
@@ -107,7 +107,7 @@ def cmd_plot_dissociation_curve(workflow, precisions, print_table, output_file):
         echo.echo_critical(
             f'node {workflow.__class__.__name__}<{workflow.pk}> does not correspond to a DissociationCurveWorkChain.'
         )
-    outputs = workflow.get_outgoing(link_type=LinkType.RETURN).nested()
+    outputs = workflow.base.links.get_outgoing(link_type=LinkType.RETURN).nested()
 
     missing_outputs = tuple(output for output in ('distances', 'total_energies') if output not in outputs)
     if missing_outputs:

aiida_common_workflows/cli/root.py

@@ -1,10 +1,11 @@
 # -*- coding: utf-8 -*-
 """Command line interface ``acwf``."""
+from aiida.cmdline.groups import VerdiCommandGroup
 from aiida.cmdline.params import options, types
 import click
 
 
-@click.group('acwf', context_settings={'help_option_names': ['-h', '--help']})
-@options.PROFILE(type=types.ProfileParamType(load_profile=True))
-def cmd_root(profile):  # pylint: disable=unused-argument
+@click.group('acwf', cls=VerdiCommandGroup, context_settings={'help_option_names': ['-h', '--help']})
+@options.PROFILE(type=types.ProfileParamType(load_profile=True), expose_value=False)
+def cmd_root():
     """CLI for the ``aiida-common-workflows`` plugin."""

aiida_common_workflows/cli/utils.py

@@ -16,7 +16,7 @@ def echo_process_results(node):
     from aiida.common.links import LinkType
 
     class_name = node.process_class.__name__
-    outputs = node.get_outgoing(link_type=(LinkType.CREATE, LinkType.RETURN)).all()
+    outputs = node.base.links.get_outgoing(link_type=(LinkType.CREATE, LinkType.RETURN)).all()
 
     if node.is_finished and node.exit_message:
         state = f'{node.process_state.value} [{node.exit_status}] `{node.exit_message}`'
@@ -78,13 +78,13 @@ def get_code_from_list_or_database(codes, entry_point: str):
     :param entry_point: calculation job entry point name.
     :return: a ``Code`` instance configured for the given entry point or ``None``.
     """
-    from aiida.orm import Code, QueryBuilder
+    from aiida.orm import InstalledCode, QueryBuilder
 
     for entry in codes:
-        if entry.get_attribute('input_plugin') == entry_point:
+        if entry.default_calc_job_plugin == entry_point:
             return entry
 
-    result = QueryBuilder().append(Code, filters={'attributes.input_plugin': entry_point}).first()
+    result = QueryBuilder().append(InstalledCode, filters={'attributes.input_plugin': entry_point}).first()
 
     if result is not None:
         return result[0]

aiida_common_workflows/generators/ports.py

@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
 """Modules with resources to define specific port types for input generator specifications."""
+from __future__ import annotations
+
 import typing as t
 
 from aiida.engine import InputPort
@@ -30,7 +32,7 @@ def __init__(self, choices: t.Sequence[t.Any]):
         """
         valid_types = tuple({type(choice) for choice in choices})
         self.choices: t.Sequence[t.Any] = choices
-        self.valid_type: t.Tuple[t.Any] = valid_types if len(valid_types) > 1 else valid_types[0]
+        self.valid_type: tuple[t.Any] = valid_types if len(valid_types) > 1 else valid_types[0]
 
 
 class InputGeneratorPort(InputPort):
@@ -45,7 +47,7 @@ def __init__(self, *args, valid_type=None, **kwargs) -> None:
         self.valid_type = valid_type
 
     @Port.valid_type.setter
-    def valid_type(self, valid_type: t.Optional[t.Any]) -> None:
+    def valid_type(self, valid_type: t.Any | None) -> None:
         """Set the valid value type for this port.
 
         :param valid_type: the value valid type.
@@ -60,15 +62,15 @@ def valid_type(self, valid_type: t.Optional[t.Any]) -> None:
 
         self._valid_type = valid_type
 
-    def validate(self, value: t.Any, breadcrumbs: t.Sequence[str] = ()) -> t.Optional[PortValidationError]:
+    def validate(self, value: t.Any, breadcrumbs: t.Sequence[str] = ()) -> PortValidationError | None:
         """Validate the value by calling the super followed by checking it against the choices if defined."""
         result = super().validate(value, breadcrumbs)
 
         if result is not None:
             return result
 
-        if self.code_entry_point is not None and value.get_input_plugin_name() != self.code_entry_point:
-            return f'invalid entry point `{value.get_input_plugin_name()}` for `Code{value}`.'
+        if self.code_entry_point is not None and value.default_calc_job_plugin != self.code_entry_point:
+            return f'invalid entry point `{value.default_calc_job_plugin}` for `Code{value}`.'
 
         if value is not UNSPECIFIED and self.choices is not None and value not in self.choices:
             choices = [str(value) for value in self.choices]

aiida_common_workflows/generators/spec.py

@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
 """Class to define the specification of an input generator."""
+from __future__ import annotations
+
 import typing as t
 
 from aiida.engine import PortNamespace
@@ -24,8 +26,7 @@ def namespace_separator(self) -> str:
         return self.PORT_NAMESPACE_TYPE.NAMESPACE_SEPARATOR
 
     def _create_port(
-        self, port_namespace: PortNamespace, port_class: t.Union[InputGeneratorPort, PortNamespace], name: str,
-        **kwargs: t.Any
+        self, port_namespace: PortNamespace, port_class: InputGeneratorPort | PortNamespace, name: str, **kwargs: t.Any
     ) -> None:
         """Create a new port of a given class and name in a given namespace.
 

aiida_common_workflows/workflows/bands/generator.py

@@ -25,7 +25,7 @@ def define(cls, spec):
         super().define(spec)
         spec.input(
             'bands_kpoints',
-            valid_type=plugins.DataFactory('array.kpoints'),
+            valid_type=plugins.DataFactory('core.array.kpoints'),
             required=True,
             help='The full list of kpoints where to calculate bands, in (direct) coordinates of the reciprocal space.'
         )

aiida_common_workflows/workflows/bands/siesta/__init__.py

@@ -4,4 +4,4 @@
 from .generator import *
 from .workchain import *
 
-__all__ = (generator.__all__ + workchain.__all__)
+__all__ = generator.__all__ + workchain.__all__

aiida_common_workflows/workflows/dissociation.py

@@ -97,8 +97,8 @@ def set_distance(molecule: orm.StructureData, distance: orm.Float) -> orm.Struct
     versor_diff = vector_diff / np.linalg.norm(vector_diff)
     new_molecule = molecule.clone()
     new_position = (distance.value * versor_diff) / 2
-    new_molecule.attributes['sites'][0]['position'] = -new_position
-    new_molecule.attributes['sites'][1]['position'] = new_position
+    new_molecule.base.attributes.get('sites')[0]['position'] = -new_position
+    new_molecule.base.attributes.get('sites')[1]['position'] = new_position
     return new_molecule
 
 

aiida_common_workflows/workflows/relax/abinit/extractors.py

@@ -24,5 +24,5 @@ def get_ts_energy(common_relax_workchain: AbinitCommonRelaxWorkChain) -> float:
     if common_relax_workchain.process_class != AbinitCommonRelaxWorkChain:
         return ValueError('The input workchain is not a `AbinitCommonRelaxWorkChain`')
 
-    abinit_base_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    abinit_base_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     return -abinit_base_wc.outputs.output_parameters['e_entropy']

aiida_common_workflows/workflows/relax/abinit/generator.py

@@ -19,7 +19,7 @@
 
 __all__ = ('AbinitCommonRelaxInputGenerator',)
 
-StructureData = plugins.DataFactory('structure')
+StructureData = plugins.DataFactory('core.structure')
 
 
 class AbinitCommonRelaxInputGenerator(CommonRelaxInputGenerator):
@@ -34,7 +34,7 @@ def __init__(self, *args, **kwargs):
 
     def _initialize_protocols(self):
         """Initialize the protocols class attribute by parsing them from the configuration file."""
-        with open(str(pathlib.Path(__file__).parent / 'protocol.yml')) as handle:
+        with open(str(pathlib.Path(__file__).parent / 'protocol.yml'), encoding='utf-8') as handle:
             self._protocols = yaml.safe_load(handle)
 
     @classmethod
@@ -76,7 +76,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
 
         pseudo_family_label = protocol.pop('pseudo_family')
         try:
-            pseudo_family = orm.Group.objects.get(label=pseudo_family_label)
+            pseudo_family = orm.Group.collection.get(label=pseudo_family_label)
         except exceptions.NotExistent as exception:
             raise ValueError(
                 f'required pseudo family `{pseudo_family_label}` is not installed. '

aiida_common_workflows/workflows/relax/abinit/workchain.py

@@ -18,22 +18,22 @@
 def get_stress(parameters):
     """Return the stress array from the given parameters node."""
     stress = orm.ArrayData()
-    stress.set_array(name='stress', array=np.array(parameters.get_attribute('cart_stress_tensor')) * GPA_TO_EV_A3)
+    stress.set_array(name='stress', array=np.array(parameters.base.attributes.get('cart_stress_tensor')) * GPA_TO_EV_A3)
     return stress
 
 
 @calcfunction
 def get_forces(parameters):
     """Return the forces array from the given parameters node."""
     forces = orm.ArrayData()
-    forces.set_array(name='forces', array=np.array(parameters.get_attribute('forces')))
+    forces.set_array(name='forces', array=np.array(parameters.base.attributes.get('forces')))
     return forces
 
 
 @calcfunction
 def get_total_energy(parameters):
     """Return the total energy from the given parameters node."""
-    return orm.Float(parameters.get_attribute('energy'))
+    return orm.Float(parameters.base.attributes.get('energy'))
 
 
 @calcfunction

aiida_common_workflows/workflows/relax/bigdft/__init__.py

@@ -4,4 +4,4 @@
 from .generator import *
 from .workchain import *
 
-__all__ = (generator.__all__ + workchain.__all__)
+__all__ = generator.__all__ + workchain.__all__

aiida_common_workflows/workflows/relax/bigdft/generator.py

@@ -10,7 +10,7 @@
 __all__ = ('BigDftCommonRelaxInputGenerator',)
 
 BigDFTParameters = plugins.DataFactory('bigdft')
-StructureData = plugins.DataFactory('structure')
+StructureData = plugins.DataFactory('core.structure')
 
 
 class BigDftCommonRelaxInputGenerator(CommonRelaxInputGenerator):

aiida_common_workflows/workflows/relax/castep/__init__.py

@@ -4,4 +4,4 @@
 from .generator import *
 from .workchain import *
 
-__all__ = (generator.__all__ + workchain.__all__)
+__all__ = generator.__all__ + workchain.__all__

aiida_common_workflows/workflows/relax/castep/extractors.py

@@ -28,7 +28,7 @@ def get_ts_energy(common_relax_workchain):
     if common_relax_workchain.process_class != CastepCommonRelaxWorkChain:
         return ValueError('The input workchain is not a `CastepCommonRelaxWorkChain`')
 
-    castep_base_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    castep_base_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     e_ks = castep_base_wc.outputs.output_parameters['total energy']
     free_e = castep_base_wc.outputs.output_parameters['free energy']
 

aiida_common_workflows/workflows/relax/castep/generator.py

@@ -22,7 +22,7 @@
 
 __all__ = ('CastepCommonRelaxInputGenerator',)
 
-StructureData = plugins.DataFactory('structure')  # pylint: disable=invalid-name
+StructureData = plugins.DataFactory('core.structure')  # pylint: disable=invalid-name
 
 
 class CastepCommonRelaxInputGenerator(CommonRelaxInputGenerator):
@@ -37,7 +37,7 @@ def __init__(self, *args, **kwargs):
 
     def _initialize_protocols(self):
         """Initialize the protocols class attribute by parsing them from the configuration file."""
-        with open(str(pathlib.Path(__file__).parent / 'protocol.yml')) as handle:
+        with open(str(pathlib.Path(__file__).parent / 'protocol.yml'), encoding='utf-8') as handle:
             self._protocols = yaml.safe_load(handle)
 
     @classmethod
@@ -170,7 +170,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
         # this is because the small basis set will give rise to errors in EOS / variable volume
         # relaxation even with the "fine" option
         if 'cut_off_energy' not in protocol['relax']['base']['calc']['parameters']:
-            with open(str(pathlib.Path(__file__).parent / 'soft_elements.yml')) as fhandle:
+            with open(str(pathlib.Path(__file__).parent / 'soft_elements.yml'), encoding='utf-8') as fhandle:
                 soft_elements = yaml.safe_load(fhandle)
             symbols = [kind.symbol for kind in structure.kinds]
             if all(sym in soft_elements for sym in symbols):
@@ -256,13 +256,11 @@ def generate_inputs(
     if isinstance(family_name, orm.Str):
         family_name = family_name.value
     try:
-        otfg_family = OTFGGroup.objects.get(label=family_name)
+        otfg_family = OTFGGroup.collection.get(label=family_name)
     except exceptions.NotExistent as exc:
-        raise ValueError(
-            'protocol `{}` requires the `{}` `pseudos family` but could not be found.'.format(
-                protocol['name'], protocol['relax']['base']['pseudos_family']
-            )
-        ) from exc
+        name = protocol['name']
+        family = protocol['relax']['base']['pseudos_family']
+        raise ValueError(f'protocol `{name}` requires the `{family}` `pseudos family` but could not be found.') from exc
 
     CastepCalculation = plugins.CalculationFactory('castep.castep')  # pylint: disable=invalid-name
     CastepBaseWorkChain = plugins.WorkflowFactory('castep.base')  # pylint: disable=invalid-name
@@ -426,7 +424,7 @@ def ensure_otfg_family(family_name, force_update=False):
     if isinstance(family_name, orm.Str):
         family_name = family_name.value
     try:
-        OTFGGroup.objects.get(label=family_name)
+        OTFGGroup.collection.get(label=family_name)
     except NotExistent:
         has_family = False
     else:
@@ -441,7 +439,7 @@ def ensure_otfg_family(family_name, force_update=False):
 
     # Not an known family - check if it in the additional settings list
     # Load configuration from the settings
-    with open(str(pathlib.Path(__file__).parent / 'additional_otfg_families.yml')) as handle:
+    with open(str(pathlib.Path(__file__).parent / 'additional_otfg_families.yml'), encoding='utf-8') as handle:
         additional = yaml.safe_load(handle)
 
     if family_name in additional:

aiida_common_workflows/workflows/relax/castep/workchain.py

@@ -53,7 +53,7 @@ def get_free_energy(parameters):
     Return the free energy from the given parameters node.
     The free energy reported by CASTEP is the one that is consistent with the forces.
     """
-    return orm.Float(parameters.get_attribute('free_energy'))
+    return orm.Float(parameters.base.attributes.get('free_energy'))
 
 
 @calcfunction
@@ -62,7 +62,7 @@ def get_total_magnetization(parameters):
     Return the free energy from the given parameters node.
     The free energy reported by CASTEP is the one that is consistent with the forces.
     """
-    return orm.Float(parameters.get_attribute('spin_density'))
+    return orm.Float(parameters.base.attributes.get('spin_density'))
 
 
 class CastepCommonRelaxWorkChain(CommonRelaxWorkChain):

aiida_common_workflows/workflows/relax/cp2k/__init__.py

@@ -4,4 +4,4 @@
 from .generator import *
 from .workchain import *
 
-__all__ = (generator.__all__ + workchain.__all__)
+__all__ = generator.__all__ + workchain.__all__