Add support for aiida-core==2.X

.gitignore

@@ -271,4 +271,6 @@ tags
 [._]*.un~
 
 # End of https://www.gitignore.io/api/vim,linux,macos,python,pycharm
-submit_test
+submit_test
+
+.vscode

aiida_raspa/calculations/__init__.py

@@ -2,6 +2,7 @@
 """Raspa input plugin."""
 import os
 from shutil import copyfile, copytree
+from pathlib import Path
 
 from aiida.orm import Dict, FolderData, List, RemoteData, SinglefileData
 from aiida.common import CalcInfo, CodeInfo, InputValidationError
@@ -12,7 +13,7 @@
 from aiida_raspa.utils import RaspaInput
 
 # data objects
-CifData = DataFactory('cif')  # pylint: disable=invalid-name
+CifData = DataFactory('core.cif')  # pylint: disable=invalid-name
 
 
 class RaspaCalculation(CalcJob):
@@ -51,7 +52,8 @@ def define(cls, spec):
         spec.input('retrieved_parent_folder',
                    valid_type=FolderData,
                    required=False,
-                   help='To use an old calculation as a starting poing for a new one.')
+                   help='To use an old calculation as a starting poing for a new one.',
+                   validator=cls.validate_retrieved_parent_folder)
         spec.inputs['metadata']['options']['parser_name'].default = cls.DEFAULT_PARSER
         spec.inputs['metadata']['options']['resources'].default = {
             'num_machines': 1,
@@ -77,6 +79,17 @@ def define(cls, spec):
         # Default output node
         spec.default_output_node = 'output_parameters'
 
+    @staticmethod
+    def validate_retrieved_parent_folder(value, _):
+
+        repository = value.base.repository
+
+        if "Restart" not in repository.list_object_names():
+            return "Restart was requested but the restart folder was not found in the previous calculation."
+        for system_path in repository.list_object_names('Restart'):
+            if len(repository.list_object_names(Path('Restart') / system_path)) != 1:
+                return 'There was more than one file in a system directory of the `Restart` directory.'
+
     # --------------------------------------------------------------------------
     # pylint: disable = too-many-locals
     def prepare_for_submission(self, folder):
@@ -168,27 +181,21 @@ def _handle_system_section(self, system_dict, folder):
                         "You specified '{}' framework in the input dictionary, but did not provide the input "
                         "framework with the same name".format(name))
 
-    def _handle_retrieved_parent_folder(self, inp, folder):
-        """Enable restart from the retrieved folder."""
-        if "Restart" not in self.inputs.retrieved_parent_folder._repository.list_object_names():  # pylint: disable=protected-access
-            raise InputValidationError("Restart was requested but the restart "
-                                       "folder was not found in the previos calculation.")
-
-        dest_folder = folder.get_abs_path("RestartInitial")
+    def _handle_retrieved_parent_folder(self, inp):
+        """Construct the local copy list from a the `retrieved_parent_folder` input."""
+        local_copy_list = []
 
-        # we first copy the whole restart folder
-        copytree(
-            os.path.join(self.inputs.retrieved_parent_folder._repository._get_base_folder().abspath, "Restart"),  # pylint: disable=protected-access
-            dest_folder)
+        parent_folder = self.inputs.retrieved_parent_folder
+        base_src_path = Path("Restart")
+        base_dest_path = Path("RestartInitial")
 
-        # once this is done, we rename the files to match temperature, pressure and number of unit cells
         for i_system, system_name in enumerate(inp.system_order):
+
             system = inp.params["System"][system_name]
-            current_folder = folder.get_abs_path("RestartInitial/System_{}".format(i_system))
-            content = os.listdir(current_folder)
-            if len(content) != 1:
-                raise InputValidationError("Restart folder should contain 1 file only, got {}".format(len(content)))
-            old_fname = content[0]
+            system_dir = f'System_{i_system}'
+
+            old_fname = parent_folder.base.repository.list_object_names(base_src_path / system_dir).pop()
+
             if system["type"] == "Box":
                 system_or_box = "Box"
                 (n_x, n_y, n_z) = (1, 1, 1)
@@ -203,6 +210,13 @@ def _handle_retrieved_parent_folder(self, inp, folder):
 
             external_pressure = system['ExternalPressure'] if 'ExternalPressure' in system else 0
 
-            new_fname = "restart_{:s}_{:d}.{:d}.{:d}_{:f}_{:g}".format(system_or_box, n_x, n_y, n_z,
-                                                                       system['ExternalTemperature'], external_pressure)
-            os.rename(os.path.join(current_folder, old_fname), os.path.join(current_folder, new_fname))
+            new_fname = (
+                f"restart_{system_or_box:d}_{n_x:d}.{n_y:d}.{n_z:d}_{system['ExternalTemperature']:f}"
+                f"_{external_pressure:g}"
+            )
+
+            local_copy_list.append(
+                parent_folder.uuid,
+                Path(base_src_path, system_dir, old_fname).as_posix(),
+                Path(base_dest_path, system_dir, new_fname).as_posix(),
+            )

aiida_raspa/parsers/__init__.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 """Raspa output parser."""
 import os
+from pathlib import Path
 
 from aiida.common import NotExistent, OutputParsingError
 from aiida.engine import ExitCode
@@ -24,34 +25,26 @@ def parse(self, **kwargs):  # pylint: disable=too-many-locals
             return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER
         output_folder_name = self.node.process_class.OUTPUT_FOLDER
 
-        if output_folder_name not in out_folder._repository.list_object_names():  # pylint: disable=protected-access
+        if output_folder_name not in out_folder.base.repository.list_object_names():  # pylint: disable=protected-access
             return self.exit_codes.ERROR_NO_OUTPUT_FILE
 
         output_parameters = {}
         warnings = []
         ncomponents = len(self.node.inputs.parameters.get_dict()['Component'])
         for system_id, system_name in enumerate(self.node.get_extra('system_order')):
             # specify the name for the system
-            system = "System_{}".format(system_id)
-            fname = out_folder._repository.list_object_names(os.path.join(output_folder_name, system))[0]  # pylint: disable=protected-access
-
-            # get absolute path of the output file
-            output_abs_path = os.path.join(
-                out_folder._repository._get_base_folder().abspath,  # pylint: disable=protected-access
-                self.node.process_class.OUTPUT_FOLDER,
-                system,
-                fname)
+            output_dir = Path(output_folder_name) / f'System_{system_id}'
+            output_filename = out_folder.base.repository.list_object_names(output_dir).pop()
+            output_contents = out_folder.base.repository.get_object_content(output_dir / output_filename)
 
             # Check for possible errors
-            with open(output_abs_path) as fobj:
-                content = fobj.read()
-                if "Starting simulation" not in content:
-                    return self.exit_codes.ERROR_SIMULATION_DID_NOT_START
-                if "Simulation finished" not in content:
-                    return self.exit_codes.TIMEOUT
+            if "Starting simulation" not in output_contents:
+                return self.exit_codes.ERROR_SIMULATION_DID_NOT_START
+            if "Simulation finished" not in output_contents:
+                return self.exit_codes.TIMEOUT
 
             # parse output parameters and warnings
-            parsed_parameters, parsed_warnings = parse_base_output(output_abs_path, system_name, ncomponents)
+            parsed_parameters, parsed_warnings = parse_base_output(output_contents, system_name, ncomponents)
             output_parameters[system_name] = parsed_parameters
             warnings += parsed_warnings