wip: make parameter script work (small script does not anymore

src/sirocco/core.py

@@ -59,7 +59,7 @@ class Task(BaseNode):
     #       keywords and extend it as we support more
     command: str | None = None
     command_option: str | None = None
-    input_arg_options: dict[str, str] | None = None
+    input_arg_options: dict[str, str] = field(default_factory=dict)
     host: str | None = None
     account: str | None = None
     plugin: str | None = None
@@ -94,6 +94,15 @@ def from_config(
             cls_config = dict(config)
             del cls_config["parameters"]
 
+            # We remove the None values in the config, as these are not setted parameters.
+            # This way the default values are not overwritten to None (e.g. for input_arg_options)
+            none_keys = []
+            for key, value in cls_config.items():
+                if value is None:
+                    none_keys.append(key)
+            for key in none_keys:
+                del cls_config[key]
+
             new = cls(
                 parameters=parameters,
                 inputs=inputs,

tests/files/configs/test_config_parameters.yml

@@ -1,6 +1,6 @@
 ---
 start_date: &root_start_date '2026-01-01T00:00'
-end_date: &root_end_date '2028-01-01T00:00'
+end_date: &root_end_date '2026-03-01T00:00'
 
 cycles:
   - bimonthly_tasks:
@@ -39,15 +39,17 @@ cycles:
         - merge:
             inputs:
               - analysis_foo_bar:
-                  lag: ['P0M', 'P2M', 'P4M', 'P6M', 'P8M', 'P10M']
+                  lag: ['P0M']
             outputs: [yearly_analysis]
 
 tasks:
   - icon:
       plugin: shell
       command: $PWD/tests/files/scripts/icon.py
       input_arg_options:
-        icon_restart: '--restart'
+        icon_restart: "--restart"
+        initial_conditions:  "--init"
+        forcing: '--forcing'
       parameters: [foo, bar]
   - statistics_foo:
       plugin: shell
@@ -64,10 +66,10 @@ data:
   available:
     - initial_conditions:
         type: file
-        src: initial_conditions
+        src: $PWD/tests/files/data/initial_conditions
     - forcing:
         type: file
-        src: forcing
+        src: $PWD/tests/files/data/forcing
   generated:
     - icon_output:
         type: file
@@ -89,5 +91,5 @@ data:
         src: yearly_analysis
 
 parameters:
-  foo: [0, 1, 2]
-  bar: {arange: [3, 4, 0.5]}
+  foo: [0, 1]
+  bar: {arange: [3, 4]}

tests/files/data/test_config_parameters.txt

@@ -3,42 +3,42 @@ cycles:
       tasks:
         - icon [date: 2026-01-01 00:00:00, foo: 0, bar: 3.0]:
             input:
-              - initial conditions
+              - initial_conditions
               - forcing
             output:
               - icon_output [date: 2026-01-01 00:00:00, foo: 0, bar: 3.0]
               - icon_restart [date: 2026-01-01 00:00:00, foo: 0, bar: 3.0]
         - icon [date: 2026-01-01 00:00:00, foo: 0, bar: 3.5]:
             input:
-              - initial conditions
+              - initial_conditions
               - forcing
             output:
               - icon_output [date: 2026-01-01 00:00:00, foo: 0, bar: 3.5]
               - icon_restart [date: 2026-01-01 00:00:00, foo: 0, bar: 3.5]
         - icon [date: 2026-01-01 00:00:00, foo: 1, bar: 3.0]:
             input:
-              - initial conditions
+              - initial_conditions
               - forcing
             output:
               - icon_output [date: 2026-01-01 00:00:00, foo: 1, bar: 3.0]
               - icon_restart [date: 2026-01-01 00:00:00, foo: 1, bar: 3.0]
         - icon [date: 2026-01-01 00:00:00, foo: 1, bar: 3.5]:
             input:
-              - initial conditions
+              - initial_conditions
               - forcing
             output:
               - icon_output [date: 2026-01-01 00:00:00, foo: 1, bar: 3.5]
               - icon_restart [date: 2026-01-01 00:00:00, foo: 1, bar: 3.5]
         - icon [date: 2026-01-01 00:00:00, foo: 2, bar: 3.0]:
             input:
-              - initial conditions
+              - initial_conditions
               - forcing
             output:
               - icon_output [date: 2026-01-01 00:00:00, foo: 2, bar: 3.0]
               - icon_restart [date: 2026-01-01 00:00:00, foo: 2, bar: 3.0]
         - icon [date: 2026-01-01 00:00:00, foo: 2, bar: 3.5]:
             input:
-              - initial conditions
+              - initial_conditions
               - forcing
             output:
               - icon_output [date: 2026-01-01 00:00:00, foo: 2, bar: 3.5]
@@ -790,4 +790,4 @@ cycles:
               - analysis_foo_bar [date: 2027-09-01 00:00:00]
               - analysis_foo_bar [date: 2027-11-01 00:00:00]
             output:
-              - yearly_analysis [date: 2027-01-01 00:00:00]
+              - yearly_analysis [date: 2027-01-01 00:00:00]

tests/files/scripts/icon.py

@@ -1,42 +1,62 @@
 #!/usr/bin/env python
+"""usage: icon.py [-h] [--init [INIT]] [--restart [RESTART]] [--forcing [FORCING]]
+
+A script mocking parts of icon in a form of a shell script
+
+options:
+  -h, --help           show this help message and exit
+  --init [INIT]        The icon init file.
+  --restart [RESTART]  The icon restart file.
+  --forcing [FORCING]  The icon forcing file.
+"""
 
 import argparse
 from pathlib import Path
 
+LOG_FILE = Path("icon.log")
+
+def log(text: str):
+    print(text)
+    with LOG_FILE.open("a") as f:
+        f.write(text)
 
 def main():
-    parser = argparse.ArgumentParser(description='A simple script with an optional restart argument.')
-    parser.add_argument('icon_input', type=str, help='The icon input.')
+    parser = argparse.ArgumentParser(description='A script mocking parts of icon in a form of a shell script.')
+    parser.add_argument('--init', nargs='?', type=str, help='The icon init file.')
     parser.add_argument('--restart', nargs='?', type=str, help='The icon restart file.')
+    parser.add_argument('--forcing', nargs='?', type=str, help='The icon forcing file.')
     #parser.add_argument('--restart', nargs='?', const='default', type=str, help='Initiate a restart operation with an optional string argument.')
 
 
     args = parser.parse_args()
+
 
     output = Path('output')
     output.write_text("")
 
-    if args.restart:
+    if args.restart and args.init:
+        raise ValueError("Cannot use '--init' and '--restart' option at the same time.")
+    elif args.restart:
+        if not Path(args.restart).exists():
+            raise FileNotFoundError(f"The icon restart file {args.restart!r} was not found.")
         restart = Path(args.restart)
-        restart.read_text()
-        text = "Restart operation initiated..."
-        print(text)
-        with output.open("a") as f:
-            f.write(text)
-    else:
-        text = "No restart option provided. Continuing without restart."
-        print(text)
-        with output.open("a") as f:
-            f.write(text)
+
+        log(f"Restarting from file {args.restart!r}.")
+    elif args.init:
+        if not Path(args.init).exists():
+            raise FileNotFoundError(f"The icon init file {args.init!r} was not found.")
+
+        log(f"Starting from init file {args.init!r}.")
+    else: 
+        raise ValueError("Please provide a restart or init file with the corresponding option.")
 
     # Main script execution continues here
-    text = "Script execution continues..."
-    print(text)
-    with output.open("a") as f:
-        f.write(text)
+    log("Script finished running calculations")
 
     restart = Path('restart')
     restart.write_text("")
 
 if __name__ == '__main__':
     main()
+
+

tests/test_wc_workflow.py

@@ -21,8 +21,8 @@ def pprinter():
 
 
 @pytest.mark.parametrize("config_path", [
-    "tests/files/configs/test_config_small.yml",
-    #"tests/files/configs/test_config_parameters.yml",
+    #"tests/files/configs/test_config_small.yml",
+    "tests/files/configs/test_config_parameters.yml",
 ])
 def test_run_workgraph(config_path):
     core_workflow = Workflow.from_yaml(config_path)
@@ -46,9 +46,7 @@ def test_parse_config_file(config_case, pprinter):
     if test_str != reference_str:
         new_path = Path(reference_path).with_suffix(".new.txt")
         new_path.write_text(test_str)
-        msg = f"Workflow graph doesn't match serialized data. New graph string dumped to {new_path}."
-        assert reference_str == test_str
-        raise ValueError(msg)
+        assert reference_str == test_str, f"Workflow graph doesn't match serialized data. New graph string dumped to {new_path}."
 
 
 @pytest.mark.skip(reason="don't run it each time, uncomment to regenerate serilaized data")