Update example submission script (#227)

Author: ElliottKasoar

docs/source/user_guide/calculations.rst

@@ -123,7 +123,14 @@ They will be converted to AiiDA data types by the script itself.
 
     verdi run submit_singlepoint.py "janus@localhost" --structure "path/to/structure" --model "path/to/model" --device "cpu"
 
-The ``submit_using_config.py`` script can be used to facilitate submission using a config file.
+The ``submit_using_config.py`` script provides an example of submission using a config file.
+
+.. note::
+
+    The structure and model are hard-coded into ``submit_using_config.py`` to avoid
+    issues with relative paths. These should be modified, or removed and set through
+    the configuration file, for your structure and model of interest.
+
 
 Geometry Optimisation calculation
 ---------------------------------

examples/calculations/submit_using_config.py

@@ -2,32 +2,45 @@
 
 from __future__ import annotations
 
+from pathlib import Path
+
 from aiida.engine import run_get_node
 from aiida.orm import load_code
 from aiida.plugins import CalculationFactory
 
+import aiida_mlip
 from aiida_mlip.data.config import JanusConfigfile
-from aiida_mlip.helpers.help_load import load_structure
+from aiida_mlip.helpers.help_load import load_model, load_structure
+
+# __file__ changes depending on where verdi run is called
+DATA_PATH = Path(aiida_mlip.__file__).parent.parent / "tests" / "calculations"
 
 # Add the required inputs for aiida
 metadata = {"options": {"resources": {"num_machines": 1}}}
 code = load_code("janus@localhost")
 
 # This structure will overwrite the one in the config file if present
-structure = load_structure("../tests/calculations/structures/NaCl.cif")
+structure = load_structure(DATA_PATH / "structures" / "NaCl.cif")
+
+# This model will overwrite the one in the config file if present
+model = load_model(
+    model="https://github.com/stfc/janus-core/raw/main/tests/models/mace_mp_small.model",
+    architecture="mace_mp",
+)
 
 # All the other paramenters we want them from the config file
 # We want to pass it as a AiiDA data type for the provenance
-config = JanusConfigfile("../tests/calculations/configs/config_janus.yaml")
+config = JanusConfigfile(DATA_PATH / "configs" / "config_janus.yml")
 
 # Define calculation to run
-SinglepointCalc = CalculationFactory("mlip.sp")
+SinglePointCalc = CalculationFactory("mlip.sp")
 
 # Run calculation
 result, node = run_get_node(
-    SinglepointCalc,
+    SinglePointCalc,
     code=code,
     struct=structure,
+    model=model,
     metadata=metadata,
     config=config,
 )

tests/calculations/test_singlepoint.py

@@ -278,3 +278,22 @@ def test_output_files(fixture_sandbox, generate_calc_job, janus_code, model_fold
     assert isinstance(calc_info.codes_info[0], datastructures.CodeInfo)
     assert sorted(calc_info.codes_info[0].cmdline_params) == sorted(cmdline_params)
     assert sorted(calc_info.retrieve_list) == sorted(retrieve_list)
+
+
+def test_submit_config_example(example_path, janus_code):
+    """Test running calculation using the example submit with config file."""
+    example_file_path = example_path / "submit_using_config.py"
+    command = [
+        "verdi",
+        "run",
+        example_file_path,
+        f"{janus_code.label}@{janus_code.computer.label}",
+    ]
+
+    # Execute the command
+    result = subprocess.run(command, capture_output=True, text=True, check=False)
+    assert result.stderr == ""
+    assert result.returncode == 0
+    assert "results from calculation:" in result.stdout
+    assert "'results_dict': <Dict: uuid:" in result.stdout
+    assert "'xyz_output': <SinglefileData: uuid:" in result.stdout