Dependencies: Add support for aiida-core~=2.0

.github/workflows/cd.yml

@@ -86,7 +86,7 @@ jobs:
             run: sudo apt update && sudo apt install postgresql
 
         -   name: Install Python dependencies
-            run: pip install -e .[tests] && reentry scan
+            run: pip install -e .[tests]
 
         -   name: Run pytest
             run: pytest -sv tests

.github/workflows/ci.yml

@@ -67,7 +67,9 @@ jobs:
             run: sudo apt update && sudo apt install postgresql
 
         -   name: Install Python package and dependencies
-            run: pip install -e .[tests] && reentry scan
+            run: pip install -e .[tests]
 
         -   name: Run pytest
+            env:
+                AIIDA_WARN_v3: True
             run: pytest -sv tests

README.md

@@ -95,7 +95,7 @@ Some addition utility functions are:
 1. If using GPAW it is possible to run parallel calculations using `/path/to/execut/gpaw python run_gpaw.py`. Set up the code through AiiDA by adding in the `gpaw` executable. The add the `python` tag using the command line option
 ```
 settings = {'CMDLINE': ['python']}
-builder.settings = orm.Dict(dict=settings)
+builder.settings = orm.Dict(settings)
 ```
 
 2. If the code you are interested in is present in this plugin registry it might make more sense to use that https://aiidateam.github.io/aiida-registry/

examples/calculations/example_grid_gpaw_relax.py

@@ -32,7 +32,7 @@ def runner():
     ]
 
     # BaTiO3 cubic structure
-    StructureData = DataFactory('structure')
+    StructureData = DataFactory('core.structure')
     structure = StructureData(cell=cell)
     structure.append_atom(position=(0., 0., 0.), symbols=['Ba'])
     structure.append_atom(position=(alat / 2., alat / 2., alat / 2.), symbols=['Ti'])
@@ -43,7 +43,7 @@ def runner():
     builder.structure = structure
 
     # k-point information
-    KpointsData = DataFactory('array.kpoints')
+    KpointsData = DataFactory('core.array.kpoints')
     kpoints = KpointsData()
     kpoints.set_kpoints_mesh([2,2,2])
     builder.kpoints = kpoints
@@ -69,11 +69,11 @@ def runner():
     }
 
 
-    builder.parameters = orm.Dict(dict=parameters)
+    builder.parameters = orm.Dict(parameters)
 
     # Running the calculation using gpaw python
     settings = {'CMDLINE': ['python']}
-    builder.settings = orm.Dict(dict=settings)
+    builder.settings = orm.Dict(settings)
 
     builder.metadata.options.resources = {'num_machines': 1}
     builder.metadata.options.max_wallclock_seconds = 1 * 30 * 60

examples/calculations/example_pw_gpaw_relax.py

@@ -6,9 +6,9 @@
 # Change the following value to the ``Code`` that you have configured
 CODE_NAME = 'gpaw-21.6.0@localhost'
 
-Dict = plugins.DataFactory('dict')
-StructureData = plugins.DataFactory('structure')
-KpointsData = plugins.DataFactory('array.kpoints')
+Dict = plugins.DataFactory('core.dict')
+StructureData = plugins.DataFactory('core.structure')
+KpointsData = plugins.DataFactory('core.array.kpoints')
 AseCalculation = plugins.CalculationFactory('ase.ase')
 
 
@@ -33,7 +33,7 @@ def main():
     ]
 
     # BaTiO3 cubic structure
-    StructureData = DataFactory('structure')
+    StructureData = DataFactory('core.structure')
     structure = StructureData(cell=cell)
     structure.append_atom(position=(0., 0., 0.), symbols=['Ba'])
     structure.append_atom(position=(alat / 2., alat / 2., alat / 2.), symbols=['Ti'])
@@ -44,7 +44,7 @@ def main():
     builder.structure = structure
 
     # k-point information
-    KpointsData = DataFactory('array.kpoints')
+    KpointsData = DataFactory('core.array.kpoints')
     kpoints = KpointsData()
     kpoints.set_kpoints_mesh([2,2,2])
     builder.kpoints = kpoints
@@ -79,8 +79,8 @@ def main():
     builder.code = load_code(CODE_NAME)
     builder.structure = structure
     builder.kpoints = kpoints
-    builder.parameters = orm.Dict(dict=parameters)
-    builder.settings = orm.Dict(dict=settings)
+    builder.parameters = orm.Dict(parameters)
+    builder.settings = orm.Dict(settings)
     builder.metadata.options.resources = {'num_machines': 1}
     builder.metadata.options.max_wallclock_seconds = 30 * 60  # 30 minutes
     builder.metadata.options.withmpi = False

examples/calculations/example_pw_gpaw_scf.py

@@ -6,20 +6,20 @@
 # Change the following value to the ``Code`` that you have configured
 CODE_NAME = 'gpaw-21.6.0@localhost'
 
-Dict = plugins.DataFactory('dict')
-StructureData = plugins.DataFactory('structure')
-KpointsData = plugins.DataFactory('array.kpoints')
+Dict = plugins.DataFactory('core.dict')
+StructureData = plugins.DataFactory('core.structure')
+KpointsData = plugins.DataFactory('core.array.kpoints')
 AseCalculation = plugins.CalculationFactory('ase.ase')
 
 
 def main():
     # generate an example structure
     atoms = bulk('Si', 'diamond', a=5.4)
-    StructureData = DataFactory('structure')
+    StructureData = DataFactory('core.structure')
     structure = StructureData(ase=atoms)
 
     # k-point information
-    KpointsData = DataFactory('array.kpoints')
+    KpointsData = DataFactory('core.array.kpoints')
     kpoints = KpointsData()
     kpoints.set_kpoints_mesh([1,1,1])
 
@@ -49,8 +49,8 @@ def main():
     builder.code = load_code(CODE_NAME)
     builder.structure = structure
     builder.kpoints = kpoints
-    builder.parameters = orm.Dict(dict=parameters)
-    builder.settings = orm.Dict(dict=settings)
+    builder.parameters = orm.Dict(parameters)
+    builder.settings = orm.Dict(settings)
     builder.metadata.options.resources = {'num_machines': 1}
     builder.metadata.options.max_wallclock_seconds = 30 * 60  # 30 minutes
     builder.metadata.options.withmpi = False

examples/workflows/example_base_gpaw.py

@@ -31,7 +31,7 @@ def runner():
     ]
 
     # BaTiO3 cubic structure
-    StructureData = DataFactory('structure')
+    StructureData = DataFactory('core.structure')
     structure = StructureData(cell=cell)
     structure.append_atom(position=(0., 0., 0.), symbols=['Ba'])
     structure.append_atom(position=(alat / 2., alat / 2., alat / 2.), symbols=['Ti'])
@@ -44,7 +44,7 @@ def runner():
     builder.gpaw.code = code
 
     # k-point information
-    KpointsData = DataFactory('array.kpoints')
+    KpointsData = DataFactory('core.array.kpoints')
     kpoints = KpointsData()
     kpoints.set_kpoints_mesh([2,2,2])
     builder.gpaw.kpoints = kpoints
@@ -68,11 +68,11 @@ def runner():
         },
     }
 
-    builder.gpaw.parameters = orm.Dict(dict=parameters)
+    builder.gpaw.parameters = orm.Dict(parameters)
 
     # Running the calculation using gpaw python
     settings = {'CMDLINE': ['python']}
-    builder.gpaw.settings = orm.Dict(dict=settings)
+    builder.gpaw.settings = orm.Dict(settings)
 
     builder.gpaw.metadata.options.resources = {'num_machines': 1}
     builder.gpaw.metadata.options.max_wallclock_seconds = 1 * 30 * 60

pyproject.toml

@@ -25,7 +25,7 @@ classifiers = [
 keywords = ['aiida', 'workflows', 'ase']
 requires-python = '>=3.8'
 dependencies = [
-    'aiida-core~=1.6',
+    'aiida-core~=2.0',
     'ase',
 ]
 

src/aiida_ase/calculations/ase.py

@@ -2,9 +2,9 @@
 """`CalcJob` implementation that can be used to wrap around the ASE calculators."""
 from aiida import common, engine, orm, plugins
 
-Dict = plugins.DataFactory('dict')
-StructureData = plugins.DataFactory('structure')
-KpointsData = plugins.DataFactory('array.kpoints')
+Dict = plugins.DataFactory('core.dict')
+StructureData = plugins.DataFactory('core.structure')
+KpointsData = plugins.DataFactory('core.array.kpoints')
 
 
 class AseCalculation(engine.CalcJob):
@@ -218,7 +218,7 @@ def return_a_function(v):
             else:
                 raise ValueError('format for extra imports not recognized')
 
-        if self.options.withmpi:
+        if self.options.get('withmpi', False):
             all_imports.append('from ase.parallel import paropen')
 
         all_imports_string = '\n'.join(all_imports) + '\n'
@@ -291,7 +291,7 @@ def return_a_function(v):
 
         input_txt += '\n'
         # Dump results to file
-        right_open = 'paropen' if self.options.withmpi else 'open'
+        right_open = 'paropen' if self.options.get('withmpi', False) else 'open'
         input_txt += f"with {right_open}('{self._OUTPUT_FILE_NAME}', 'w') as f:\n"
         input_txt += '    json.dump(results,f)'
         input_txt += '\n'
@@ -307,7 +307,7 @@ def return_a_function(v):
             input_txt += '\n'
 
         # write all the input script to a file
-        with folder.open(self._INPUT_FILE_NAME, 'w') as handle:
+        with folder.base.repository.open(self._INPUT_FILE_NAME, 'w') as handle:
             handle.write(input_txt)
 
         # ============================ calcinfo ================================

src/aiida_ase/parsers/ase.py

@@ -6,9 +6,9 @@
 from ase.io import read
 import numpy
 
-Dict = plugins.DataFactory('dict')
-ArrayData = plugins.DataFactory('array')
-StructureData = plugins.DataFactory('structure')
+Dict = plugins.DataFactory('core.dict')
+ArrayData = plugins.DataFactory('core.array')
+StructureData = plugins.DataFactory('core.structure')
 AseCalculation = plugins.CalculationFactory('ase.ase')
 
 
@@ -20,7 +20,7 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements
         retrieved = self.retrieved
 
         # check what is inside the folder
-        list_of_files = retrieved.list_object_names()
+        list_of_files = retrieved.base.repository.list_object_names()
 
         # at least the stdout should exist
         if AseCalculation._OUTPUT_FILE_NAME not in list_of_files:  # pylint: disable=protected-access
@@ -29,15 +29,15 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements
 
         # output structure
         if AseCalculation._output_aseatoms in list_of_files:  # pylint: disable=protected-access
-            with retrieved.open(AseCalculation._output_aseatoms, 'r') as handle:  # pylint: disable=protected-access
+            with retrieved.base.repository.open(AseCalculation._output_aseatoms, 'r') as handle:  # pylint: disable=protected-access
                 atoms = read(handle, format='json')
                 structure = StructureData(ase=atoms)
                 self.out('structure', structure)
 
-        filename_stdout = self.node.get_attribute('output_filename')
+        filename_stdout = self.node.base.base.attributes.all.get('output_filename')
 
         # load the results dictionary
-        with retrieved.open(filename_stdout, 'r') as handle:
+        with retrieved.base.repository.open(filename_stdout, 'r') as handle:
             json_params = json.load(handle)
 
         # extract arrays from json_params
@@ -48,7 +48,7 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements
 
         # look at warnings
         warnings = []
-        with retrieved.open('_scheduler-stderr.txt', 'r') as handle:
+        with retrieved.base.repository.open('_scheduler-stderr.txt', 'r') as handle:
             errors = handle.read()
         if errors:
             warnings = [errors]
@@ -61,6 +61,6 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements
             self.out('array', array_data)
 
         if json_params:
-            self.out('parameters', Dict(dict=json_params))
+            self.out('parameters', Dict(json_params))
 
         return

src/aiida_ase/parsers/gpaw.py

@@ -7,10 +7,10 @@
 from ase.io import read
 import numpy
 
-Dict = plugins.DataFactory('dict')
-ArrayData = plugins.DataFactory('array')
-StructureData = plugins.DataFactory('structure')
-TrajectoryData = plugins.DataFactory('array.trajectory')
+Dict = plugins.DataFactory('core.dict')
+ArrayData = plugins.DataFactory('core.array')
+StructureData = plugins.DataFactory('core.structure')
+TrajectoryData = plugins.DataFactory('core.array.trajectory')
 AseCalculation = plugins.CalculationFactory('ase.ase')
 
 
@@ -60,7 +60,7 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements,too
         """Parse the retrieved files from a ``AseCalculation``."""
 
         # check what is inside the folder
-        list_of_files = self.retrieved.list_object_names()
+        list_of_files = self.retrieved.base.repository.list_object_names()
 
         # check if it was a relaxation
         optimizer = self.node.inputs.parameters.get_dict().pop('optimizer', None)
@@ -74,7 +74,7 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements,too
             # Probably helpful for restarts
             self.logger.error('Output results was not found, inspecting log file')
             # Checking for possible errors common to all calculations
-            with self.retrieved.open('_scheduler-stderr.txt', 'r') as handle:
+            with self.retrieved.base.repository.open('_scheduler-stderr.txt', 'r') as handle:
                 lines = handle.readlines()
                 if check_paw_missing(lines):
                     self.logger.error('Could not find paw potentials')
@@ -87,7 +87,9 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements,too
                 # This is a relaxation calculation that did not complete
                 # try to get all the structures that are available
                 try:
-                    with self.retrieved.open(self.node.get_attribute('log_filename'), 'r') as handle:
+                    with self.retrieved.base.repository.open(
+                        self.node.base.attributes.get('log_filename'), 'r'
+                    ) as handle:
                         all_ase_traj = read(handle, index=':', format='gpaw-out')
                     trajectory = store_to_trajectory_data(all_ase_traj)
                     self.outputs.trajectory = trajectory
@@ -108,19 +110,19 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements,too
         # Check if output structure is needed
         if optimizer is not None:
             # If we are here the calculation did complete sucessfully
-            with self.retrieved.open(AseCalculation._output_aseatoms, 'r') as handle:  # pylint: disable=protected-access
+            with self.retrieved.base.repository.open(AseCalculation._output_aseatoms, 'r') as handle:  # pylint: disable=protected-access
                 atoms = read(handle, format='json')
                 self.out('structure', StructureData(ase=atoms))
             # Store the trajectory as well
-            with self.retrieved.open(self.node.get_attribute('log_filename'), 'r') as handle:
+            with self.retrieved.base.repository.open(self.node.base.attributes.get('log_filename'), 'r') as handle:
                 all_ase_traj = read(handle, index=':', format='gpaw-out')
             self.outputs.trajectory = store_to_trajectory_data(all_ase_traj)
         # load the results dictionary
-        with self.retrieved.open(AseCalculation._OUTPUT_FILE_NAME, 'r') as handle:  # pylint: disable=protected-access
+        with self.retrieved.base.repository.open(AseCalculation._OUTPUT_FILE_NAME, 'r') as handle:  # pylint: disable=protected-access
             json_params = json.load(handle)
 
         # get the relavent data from the log file for the final structure
-        with self.retrieved.open(self.node.get_attribute('log_filename'), 'r') as handle:
+        with self.retrieved.base.repository.open(self.node.base.attributes.get('log_filename'), 'r') as handle:
             atoms_log = read(handle, format='gpaw-out')
         create_output_parameters(atoms_log, json_params)
 
@@ -130,7 +132,7 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements,too
             return self.exit_codes.ERROR_FERMI_LEVEL_INF
 
         # look at warnings
-        with self.retrieved.open('_scheduler-stderr.txt', 'r') as handle:
+        with self.retrieved.base.repository.open('_scheduler-stderr.txt', 'r') as handle:
             errors = handle.read()
         if errors:
             json_params['warnings'] = [errors]
@@ -148,6 +150,6 @@ def parse(self, **kwargs):  # pylint: disable=inconsistent-return-statements,too
             self.out('array', array_data)
 
         if json_params:
-            self.out('parameters', Dict(dict=json_params))
+            self.out('parameters', Dict(json_params))
 
         return