snk-cli 0.6.0__tar.gz → 0.6.2__tar.gz

{snk_cli-0.6.0 → snk_cli-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.6.0
+Version: 0.6.2
 Project-URL: Documentation, https://github.com/wytamma/snk-cli#readme
 Project-URL: Issues, https://github.com/wytamma/snk-cli/issues
 Project-URL: Source, https://github.com/wytamma/snk-cli

{snk_cli-0.6.0 → snk_cli-0.6.2}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.6.0"
+__version__ = "0.6.2"

{snk_cli-0.6.0 → snk_cli-0.6.2}/src/snk_cli/config/config.py

@@ -37,6 +37,9 @@ class SnkConfig:
       skip_missing (bool): Whether to skip missing CLI options. Defaults to False.
       additional_snakemake_args (List[str]): List of additional Snakemake command-line arguments. Defaults to an empty list.
       commands (List[str]): List of subcommands to include in the CLI. Defaults to ["run", "script", "env", "profile", "info", "config"].
+      snakefile (Optional[Path]): Path to the Snakefile. Defaults to None.
+      configfile (Optional[Path]): Path to the config file. Defaults to None.
+      min_snk_cli_version (Optional[str]): Minimum version of the SNK CLI required to run the workflow. Defaults to None.
       cli (dict): Dictionary of CLI options and their values. Defaults to an empty dictionary.
       _snk_config_path (Path): The path to the SNK config file. Defaults to None.
 
@@ -73,6 +76,7 @@ class SnkConfig:
     commands: List[str] = field(default_factory=lambda: ["run", "script", "env", "profile", "info", "config"])
     snakefile: Optional[Path] = None
     configfile: Optional[Path] = None
+    min_snk_cli_version: Optional[str] = None
     cli: dict = field(default_factory=dict)
     _snk_config_path: Path = None
 

{snk_cli-0.6.0 → snk_cli-0.6.2}/src/snk_cli/dynamic_typer.py

@@ -8,8 +8,6 @@ from enum import Enum
 from .options import Option
 import sys
 
-def parse_colon_separated_pair(value: str):
-    return tuple(value.split(sep=':', maxsplit=2))
     
 class DynamicTyper:
     app: typer.Typer
@@ -159,13 +157,14 @@ class DynamicTyper:
               except ValueError:
                 raise ValueError(f"Default value '{default}' for option '{option.name}' is not a valid choice.")
             annotation_type = Enum(f'{option.name}', {str(e): annotation_type(e) for e in option.choices})
-        metavar, parser = None, None
+        click_type = None
         if get_origin(annotation_type) is dict or annotation_type is dict:
-            metavar = "KEY:VALUE"
-            parser = parse_colon_separated_pair
+            click_type = Tuple([str, str])
+            if hasattr(annotation_type, '__args__') and len(annotation_type.__args__) == 2:
+                click_type = Tuple([str, annotation_type.__args__[1]])
             annotation_type = List[Tuple]
             if type(default) is dict:
-                default = [f"{k}:{v}" for k, v in default.items()]
+                default = [[k, v] for k, v in default.items()]
         return Parameter(
             option.name,
             kind=Parameter.POSITIONAL_OR_KEYWORD,
@@ -175,8 +174,7 @@ class DynamicTyper:
                 help=f"{option.help}",
                 rich_help_panel="Workflow Configuration",
                 hidden=option.hidden,
-                metavar=metavar,
-                parser=parser,
+                click_type=click_type,
             ),
             annotation=annotation_type,
         )

{snk_cli-0.6.0 → snk_cli-0.6.2}/tests/data/workflow/snk.yaml

@@ -12,14 +12,14 @@ cli:
   KeyValuePair:
     default: ["key", "value"]
     help: A key-value pair
-    type: pair 
+    type: pair[str, str]
   enum:
     choices: [a, b, c]
     default: "a"
   dict:
     help: A dictionary
     type: dict[str, int]
-    default: ["key:1"]
+    default: [["key", 1], ["key2", 2]]
   test:
     another:
       test:

{snk_cli-0.6.0 → snk_cli-0.6.2}/tests/test_types.py

@@ -167,7 +167,7 @@ def test_choices(snakemake_config, annotations, cli_args, expected):
     # dict
     (
         {"example": {"key": "value"}},
-        {"example": {"type": "dict", "default": ["key:value"]}},
+        {"example": {"type": "dict", "default": [["key", "value"]]}},
         [],
         "{'example': {'key': 'value'}}"
     ),
@@ -186,7 +186,7 @@ def test_choices(snakemake_config, annotations, cli_args, expected):
     (
         {},
         {"example": {"type": "dict[str, str]"}},
-        ["--example", "new:2"],
+        ["--example", "new", "2"],
         "{'example': {'new': '2'}}"
     )
     ])