Deprecate ADDITIONAL_RETRIEVE_LIST in settings

The `ADDITIONAL_RETRIEVE_LIST` key in the `settings` is deprected and
will be removed in a fetaure release. A warning is introduced,
indicating that one should use the
`CalcJob.metadata.options.additional_retrieve_list` option of
`aiida-core` instead (introduced in
aiidateam/aiida-core@17b7718).

Author: t-reents

docs/source/howto/calculations/pw.md

@@ -280,11 +280,11 @@ All other coordinates are allowed to change.
 ## How to retrieve additional files
 
 The {{ PwCalculation }} plugin will retrieve the most important and common output files by default.
-To retrieve additional output files, specify the list of files in the `ADDITIONAL_RETRIEVE_LIST` key in the `settings` input:
+To retrieve additional output files, specify the list of files in the `CalcJob.metadata.options.additional_retrieve_list` key in the input (**NOTE**: The usage of `ADDITIONAL_RETRIEVE_LIST` in the `settings` input is deprecated and will be removed in a future release):
 
 ```python
 builder = load_code('pw').get_builder()
-builder.settings = Dict({'ADDITIONAL_RETRIEVE_LIST': ['custom-file.txt', 'some-other.xml']})
+builder.metadata.options.additional_retrieve_list = ['custom-file.txt', 'some-other.xml']
 ```
 
 

src/aiida_quantumespresso/calculations/__init__.py

@@ -183,6 +183,13 @@ def validate_inputs(cls, value, port_namespace):
         if 'settings' in value:
             settings = _uppercase_dict(value['settings'].get_dict(), dict_name='settings')
 
+            if 'ADDITIONAL_RETRIEVE_LIST' in settings:
+                warnings.warn(
+                    'The key `ADDITIONAL_RETRIEVE_LIST` in the settings input is deprecated and will be removed in '
+                    'the future. Use the `CalcJob.metadata.options.additional_retrieve_list` input instead.',
+                    FutureWarning
+                )
+
             # Validate the FIXED_COORDS setting
             fixed_coords = settings.get('FIXED_COORDS', None)
 

src/aiida_quantumespresso/calculations/epw.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 """Plugin to create a Quantum Espresso epw.x input file."""
 import os
+import warnings
 
 from aiida import orm
 from aiida.common import datastructures, exceptions
@@ -84,6 +85,12 @@ def test_offset(offset):
 
         if 'settings' in self.inputs:
             settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
+            if 'ADDITIONAL_RETRIEVE_LIST' in settings:
+                warnings.warn(
+                    'The key `ADDITIONAL_RETRIEVE_LIST` in the settings input is deprecated and will be removed in '
+                    'the future. Use the `CalcJob.metadata.options.additional_retrieve_list` input instead.',
+                    FutureWarning
+                )
         else:
             settings = {}
 

src/aiida_quantumespresso/calculations/namelists.py

@@ -4,6 +4,7 @@
 These codes typically only require a few namelists (plus possibly some text afterwards).
 """
 import pathlib
+import warnings
 
 from aiida.common import datastructures, exceptions
 from aiida.orm import Dict, FolderData, RemoteData, SinglefileData
@@ -143,6 +144,12 @@ def prepare_for_submission(self, folder):
         # pylint: disable=too-many-branches,too-many-statements
         if 'settings' in self.inputs:
             settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
+            if 'ADDITIONAL_RETRIEVE_LIST' in settings:
+                warnings.warn(
+                    'The key `ADDITIONAL_RETRIEVE_LIST` in the settings input is deprecated and will be removed in '
+                    'the future. Use the `CalcJob.metadata.options.additional_retrieve_list` input instead.',
+                    FutureWarning
+                )
         else:
             settings = {}
 

src/aiida_quantumespresso/calculations/neb.py

@@ -2,6 +2,7 @@
 """Plugin to create a Quantum Espresso neb.x input file."""
 import copy
 import os
+import warnings
 
 from aiida import orm
 from aiida.common import CalcInfo, CodeInfo, InputValidationError
@@ -178,6 +179,12 @@ def prepare_for_submission(self, folder):
         # Convert settings dictionary to have uppercase keys, or create an empty one if none was given.
         if 'settings' in self.inputs:
             settings_dict = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
+            if 'ADDITIONAL_RETRIEVE_LIST' in settings_dict:
+                warnings.warn(
+                    'The key `ADDITIONAL_RETRIEVE_LIST` in the settings input is deprecated and will be removed in '
+                    'the future. Use the `CalcJob.metadata.options.additional_retrieve_list` input instead.',
+                    FutureWarning
+                )
         else:
             settings_dict = {}
 

src/aiida_quantumespresso/calculations/ph.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 """Plugin to create a Quantum Espresso ph.x input file."""
 import os
+import warnings
 
 from aiida import orm
 from aiida.common import datastructures, exceptions
@@ -105,6 +106,12 @@ def prepare_for_submission(self, folder):
 
         if 'settings' in self.inputs:
             settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
+            if 'ADDITIONAL_RETRIEVE_LIST' in settings:
+                warnings.warn(
+                    'The key `ADDITIONAL_RETRIEVE_LIST` in the settings input is deprecated and will be removed in '
+                    'the future. Use the `CalcJob.metadata.options.additional_retrieve_list` input instead.',
+                    FutureWarning
+                )
         else:
             settings = {}
 

src/aiida_quantumespresso/calculations/pw2wannier90.py

@@ -16,7 +16,7 @@ class Pw2wannier90Calculation(NamelistsCalculation):
     _blocked_keywords = [('INPUTPP', 'outdir', NamelistsCalculation._OUTPUT_SUBFOLDER),
                          ('INPUTPP', 'prefix', NamelistsCalculation._PREFIX), ('INPUTPP', 'seedname', _SEEDNAME)]
     # By default we do not download anything else than aiida.out. One can add the files
-    # _SEEDNAME.amn/.nnm/.eig to inputs.settings['ADDITIONAL_RETRIEVE_LIST'] to retrieve them.
+    # _SEEDNAME.amn/.nnm/.eig to `CalcJob.metadata.options.additional_retrieve_list` to retrieve them.
     _internal_retrieve_list = []
     _default_parser = 'quantumespresso.pw2wannier90'
 

src/aiida_quantumespresso/cli/calculations/pw2wannier90.py

@@ -72,19 +72,17 @@ def launch_calculation(
         parameters['INPUTPP']['scdm_proj'] = True
         parameters['INPUTPP']['scdm_entanglement'] = scdm_mode
 
-    # In this command-line example, we always retrieve .amn, .mmn and .eig,
-    # but we never retrieve the UNK files that are big
-    settings = {'ADDITIONAL_RETRIEVE_LIST': ['*.amn', '*.mmn', '*.eig']}
-
     inputs = {
         'code': code,
         'parent_folder': parent_folder,
         'nnkp_file': nnkp_file,
         'parameters': Dict(parameters),
-        'settings': Dict(settings),
         'metadata': {
             'options': get_default_options(max_num_machines, max_wallclock_seconds, with_mpi),
         }
     }
+    # In this command-line example, we always retrieve .amn, .mmn and .eig,
+    # but we never retrieve the UNK files that are big
+    inputs['metadata'].update({'additional_retrieve_list': ['*.amn', '*.mmn', '*.eig']})
 
     launch.launch_process(CalculationFactory('quantumespresso.pw2wannier90'), daemon, **inputs)

tests/parsers/test_pw2wannier90.py

@@ -21,15 +21,17 @@ def generate_inputs():
         }
     }
 
-    settings = {'ADDITIONAL_RETRIEVE_LIST': ['*.amn', '*.mmn', '*.eig']}
-
     # Since we don't actually run pw2wannier.x, we only pretend to have the output folder
     # of a parent pw.x calculation. The nnkp file, instead, is real.
     inputs = {
         'parent_folder': orm.FolderData().store(),
         'nnkp_file': orm.SinglefileData(file=nnkp_filepath).store(),
         'parameters': orm.Dict(parameters),
-        'settings': orm.Dict(settings),
+        'metadata': {
+            'options': {
+                'additional_retrieve_list': ['*.amn', '*.mmn', '*.eig']
+            }
+        }
     }
 
     return AttributeDict(inputs)