Implement mechanism to override defaults using a custom config file (#…

…1007)

This PR implement a merging mechanism for custom app defaults configurations. Users can now drop a custom config.yml in the /home/jovyan/.aiidalab/quantumespresso/ directory. The file follows the structure of the qeapp.yml default configurations file, though it does not strictly require the inclusion of all fields. The custom config.yml file is processed and merged recursively into the object created from processing qeapp.yml.

src/aiidalab_qe/app/configuration/advanced/model.py

@@ -45,7 +45,7 @@ class AdvancedConfigurationSettingsModel(
     electronic_type = tl.Unicode()
     spin_orbit = tl.Unicode()
 
-    clean_workdir = tl.Bool(False)
+    clean_workdir = tl.Bool(DEFAULT["advanced"]["clean_workdir"])
     override = tl.Bool(False)
     total_charge = tl.Float(DEFAULT["advanced"]["tot_charge"])
     van_der_waals_options = tl.List(

src/aiidalab_qe/app/configuration/model.py

@@ -15,6 +15,8 @@
 
 DEFAULT: dict = DEFAULT_PARAMETERS  # type: ignore
 
+NO_RELAXATION_OPTION = ("Structure as is", "none")
+
 
 class ConfigurationStepModel(
     Model,
@@ -23,8 +25,8 @@ class ConfigurationStepModel(
     Confirmable,
 ):
     relax_type_help = tl.Unicode()
-    relax_type_options = tl.List([DEFAULT["workchain"]["relax_type"]])
-    relax_type = tl.Unicode(DEFAULT["workchain"]["relax_type"])
+    relax_type_options = tl.List([NO_RELAXATION_OPTION])
+    relax_type = tl.Unicode(NO_RELAXATION_OPTION[-1], allow_none=True)
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
@@ -60,7 +62,7 @@ def update(self):
                 ),
             )
             relax_type_options = [
-                ("Structure as is", "none"),
+                NO_RELAXATION_OPTION,
                 ("Atomic positions", "positions"),
                 ("Full geometry", "positions_cell"),
             ]
@@ -70,18 +72,23 @@ def update(self):
                 full_relaxation_option="",
             )
             relax_type_options = [
-                ("Structure as is", "none"),
+                NO_RELAXATION_OPTION,
                 ("Atomic positions", "positions"),
             ]
+
+        default = DEFAULT["workchain"]["relax_type"]
+        default_available = [default in [option[1] for option in relax_type_options]]
+        relax_type = default if default_available else relax_type_options[-1][-1]
+
         self._defaults = {
             "relax_type_help": relax_type_help,
             "relax_type_options": relax_type_options,
-            "relax_type": relax_type_options[-1][-1],
+            "relax_type": relax_type,
         }
-        with self.hold_trait_notifications():
-            self.relax_type_help = self._get_default_relax_type_help()
-            self.relax_type_options = self._get_default_relax_type_options()
-            self.relax_type = self._get_default_relax_type()
+
+        self.relax_type_help = self._get_default_relax_type_help()
+        self.relax_type_options = self._get_default_relax_type_options()
+        self.relax_type = self._get_default_relax_type()
 
     def get_model_state(self):
         parameters = {
@@ -148,7 +155,13 @@ def _get_default_relax_type_help(self):
         return self._defaults.get("relax_type_help", "")
 
     def _get_default_relax_type_options(self):
-        return self._defaults.get("relax_type_options", [""])
+        return self._defaults.get("relax_type_options", [NO_RELAXATION_OPTION])
 
     def _get_default_relax_type(self):
-        return self._defaults.get("relax_type", "")
+        options = self._get_default_relax_type_options()
+        relax_type = self._defaults.get("relax_type", NO_RELAXATION_OPTION[-1])
+        return (
+            relax_type
+            if relax_type in [option[1] for option in options]
+            else options[-1][-1]
+        )

src/aiidalab_qe/app/parameters/__init__.py

@@ -1,7 +1,54 @@
+from collections.abc import Mapping
 from importlib import resources
+from pathlib import Path
 
 import yaml
 
 from aiidalab_qe.app import parameters
 
+
+def recursive_merge(d1, d2):
+    """Merge dictionary `d2` into dictionary `d1` recursively.
+
+    - For keys that are in both dictionaries:
+        - If values are dictionaries, merge them recursively.
+        - Otherwise, overwrite the value in `d1` with the value in `d2`.
+    - Keys in `d2` not in `d1` are added to `d1`.
+
+    Parameters
+    ----------
+    `d1` : `dict`
+        The dictionary to merge into.
+    `d2` : `dict`
+        The dictionary to merge from.
+
+    Returns
+    -------
+    `dict`
+        The merged dictionary.
+
+    Examples
+    --------
+    >>> d1 = {'a': 1, 'b': {'c': 2, 'd': 3}}
+    >>> d2 = {'b': {'c': 4, 'e': 5}}
+    >>> recursive_merge(d1, d2)
+    {'a': 1, 'b': {'c': 4, 'd': 3, 'e': 5}}
+    """
+    for key, value in d2.items():
+        if key in d1:
+            if isinstance(d1[key], Mapping) and isinstance(value, Mapping):
+                recursive_merge(d1[key], value)
+            else:
+                d1[key] = value
+        else:
+            d1[key] = value
+    return d1
+
+
 DEFAULT_PARAMETERS = yaml.safe_load(resources.read_text(parameters, "qeapp.yaml"))
+
+
+custom_config_file = Path.home() / ".aiidalab" / "quantumespresso" / "config.yml"
+if custom_config_file.exists():
+    custom_config = yaml.safe_load(custom_config_file.read_text())
+    DEFAULT_PARAMETERS = recursive_merge(DEFAULT_PARAMETERS, custom_config)

src/aiidalab_qe/app/parameters/qeapp.yaml

@@ -15,6 +15,7 @@ workchain:
 
 ## Advanced pw settings
 advanced:
+    clean_workdir: false
     pseudo_family:
         library: SSSP
         version: 1.3