Arbitrary CLI args for shell tasks (#66)

This PR adds the `_CliArgsBaseModel` class (inspired from `_WhenBaseModel`), which replaces the `command_option` and `input_arg_options` of the `ConfigShellTaskSpecs`. Validation is applied on the correctness of the keyword and positional arguments to ensure they start with `-` or `--`.

The three test YAML files are updated accordingly, leading to changes in the pretty-print test text files, which is also part of the PR.

Actually making something useful out of these arguments only happens when the WG is created, so will require #45 to be merged.

src/sirocco/core/workflow.py

@@ -18,7 +18,7 @@
 
 
 class Workflow:
-    """Internal reprensentation of a workflow"""
+    """Internal representation of a workflow"""
 
     def __init__(self, workflow_config: ConfigWorkflow) -> None:
         self.name = workflow_config.name

src/sirocco/parsing/_yaml_data_models.py

@@ -82,6 +82,43 @@ def convert_datetime(cls, value) -> datetime:
         return datetime.fromisoformat(value)
 
 
+class _CliArgsBaseModel(BaseModel):
+    """Base class for cli_arguments specifications"""
+
+    # TODO: Even allow for `str`, or always require list?
+    positional: str | list[str] | None = None
+    # Field needed for child class doing pydantic parsing
+    keyword: dict[str, str] | None = Field(default_factory=dict)
+    flags: str | list[str] | None = None
+    source_file: str | list[str] | None = None
+
+    # TODO: Should we allow users to pass it without the hyphen(s), and prepend them automatically?
+    # TODO: While convenient, it could be a bad idea, if users put in wrong things. Better to be explicit.
+    @field_validator("keyword", mode="before")
+    @classmethod
+    def validate_keyword_args(cls, value):
+        """Ensure keyword arguments start with '-' or '--'."""
+        if value is not None:
+            invalid_keys = [key for key in value if not key.startswith(("-", "--"))]
+            if invalid_keys:
+                invalid_kwarg_exc = f"Invalid keyword arguments: {', '.join(invalid_keys)}"
+                raise ValueError(invalid_kwarg_exc)
+        return value
+
+    @field_validator("flags", mode="before")
+    @classmethod
+    def validate_flag_args(cls, value):
+        """Ensure positional arguments start with '-' or '--'."""
+        if value is not None:
+            if isinstance(value, str):
+                value = [value]
+            invalid_flags = [arg for arg in value if not arg.startswith(("-", "--"))]
+            if invalid_flags:
+                invalid_flags_exc = f"Invalid positional arguments: {', '.join(invalid_flags)}"
+                raise ValueError(invalid_flags_exc)
+        return value
+
+
 class TargetNodesBaseModel(_NamedBaseModel):
     """class for targeting other task or data nodes in the graph
 
@@ -273,9 +310,7 @@ class ConfigRootTask(ConfigBaseTask):
 class ConfigShellTaskSpecs:
     plugin: ClassVar[Literal["shell"]] = "shell"
     command: str = ""
-    command_option: str = ""
-    input_arg_options: dict[str, str] = Field(default_factory=dict)  # noqa: RUF009 Field needed
-    #                                                                        for child class doing pydantic parsing
+    cli_arguments: _CliArgsBaseModel | None = None
     src: str | None = None
 
 

tests/files/configs/test_config_large.yml

@@ -44,7 +44,6 @@ cycles:
             inputs:
               - stream_2:
                   lag: ['P0M', 'P2M', 'P4M', 'P6M', 'P8M', 'P10M']
-                  arg_option: --input
             outputs: [postout_2]
         - store_and_clean_2:
             inputs:
@@ -63,9 +62,11 @@ tasks:
   - extpar:
       plugin: shell  # no extpar plugin available yet
       command: $PWD/examples/files/scripts/extpar
-      command_option: '--verbose'  # todo implement support
-      input_arg_options:
-        obs_data: '--input'
+      cli_arguments:
+        keyword:
+          --input: obs_data
+        flags:
+          - --verbose
       uenv:
         squashfs: path/to/squashfs
         mount_point: runtime/mount/point
@@ -74,10 +75,13 @@ tasks:
   - preproc:
       plugin: shell
       command: $PWD/examples/files/scripts/cleanup.sh
-      input_arg_options:
-        grid_file: '-g'
-        extpar_file : '-p'
-        ERA5: '-e'
+      cli_arguments:
+        positional:
+          - grid_file
+        keyword:
+          -p: extpar_file
+          -e: ERA5
+        source_file: dummy_source_file
       nodes: 4
       walltime: 00:02:00
       uenv:
@@ -86,9 +90,10 @@ tasks:
   - icon:
       plugin: icon
       command: $PWD/examples/files/scripts/icon
-      input_arg_options:
-        grid_file: '-g'
-        icon_input: '--input'
+      cli_arguments:
+        keyword:
+          -g: grid_file
+          --input: icon_input
       nodes: 40
       walltime: 23:59:59
       namelists:
@@ -100,8 +105,9 @@ tasks:
   - postproc_1:
       plugin: shell
       command: $PWD/examples/files/scripts/main_script_ocn.sh
-      input_arg_options:
-        stream_1: '--input'
+      cli_arguments:
+        keyword:
+          --input: stream_1
       nodes: 2
       walltime: 00:05:00
       uenv:
@@ -110,8 +116,12 @@ tasks:
   - postproc_2:
       plugin: shell
       command: $PWD/examples/files/scripts/main_script_atm.sh
-      input_arg_options:
-        stream_2: '--input'
+      cli_arguments:
+        keyword:
+          --input: stream_2
+          # `arg_option` should be in `tasks` section instead
+          # How to implement this? Even needed with keyword-arguments?
+          # arg_option: --input
       nodes: 2
       walltime: 00:05:00
       src: path/to/src/dir
@@ -121,17 +131,19 @@ tasks:
   - store_and_clean_1:
       plugin: shell
       command: $PWD/examples/files/scripts/post_clean.sh
-      input_arg_options:
-        postout_1: '--input'
-        stream_1: '--stream'
-        icon_input: '--icon_input'
+      cli_arguments:
+        keyword:
+          --input: postout_1
+          --stream: stream_1
+          --icon_input: icon_input
       nodes: 1
       walltime: 00:01:00
   - store_and_clean_2:
       plugin: shell
       command: $PWD/examples/files/scripts/post_clean.sh
-      input_arg_options:
-        postout_2: '--input'
+      cli_arguments:
+        keyword:
+          --input: postout_2
       nodes: 1
       walltime: 00:01:00
 data:
@@ -145,6 +157,9 @@ data:
     - ERA5:
         type: file
         src: $PWD/examples/files/data/era5
+    - dummy_source_file:
+        type: file
+        src: $PWD/examples/files/data/dummy_source_file.sh
   generated:
     - extpar_file:
         type: file

tests/files/configs/test_config_parameters.yml

@@ -46,8 +46,9 @@ tasks:
   - icon:
       plugin: shell
       command: $PWD/tests/files/scripts/icon.py
-      input_arg_options:
-        icon_restart: '--restart'
+      cli_arguments:
+        keyword:
+          --restart: icon_restart
       parameters: [foo, bar]
   - statistics_foo:
       plugin: shell

tests/files/configs/test_config_small.yml

@@ -24,8 +24,9 @@ tasks:
   - icon:
       plugin: shell
       command: $PWD/tests/files/scripts/icon.py
-      input_arg_options:
-        icon_restart: '--restart'
+      cli_arguments:
+        keyword:
+          --restart: icon_restart
   - cleanup:
       plugin: shell
       command: $PWD/tests/files/scripts/cleanup.py