adjust 'output' -> 'output-cwl' for intent clarity

Author: fmigneault

README.md

@@ -32,11 +32,11 @@ click2cwl [-h|--help]
 The typical command to run the CWL convertion is as follows for the desired Python CLI process:
 
 ```shell
-click2cwl --process <path/to/python.py> [--output <path/to/package.cwl>] [--output-format <yaml|json>]
+click2cwl --process <path/to/python.py> [--output-cwl <path/to/package.cwl>] [--output-format <yaml|json>]
 ```
 
 By default, the output CWL is produced as YAML on the standard output with only the `CommandLineTool` definition.
-A file can be generated in YAML or JSON format by specifying the `--output` option.
+A file can be generated in YAML or JSON format by specifying the `--output-cwl` option.
 
 An embedded `CommandLineTool` within a fully defined CWL `Workflow` graph can be generated by
 specifying the `-w|--workflow` shortcut option or explicitly using the `--cwl <clt|cwl>` options.

pyproject.toml

@@ -7,16 +7,15 @@ name = "goldfinch"
 version = "0.1.0"
 description = "Climate service processes defined through CWL."
 authors = [
-    { name = "Francis Charette-Migneault", email = "[email protected]" }
+    { name = "Francis Charette-Migneault", email = "[email protected]" },
+    { name = "David Huard", email = "[email protected]" },
 ]
 readme = "README.md"
 requires-python = ">=3.10"
 license = "Apache-2.0"
 dependencies = [
     "click",
     "click-option-group",
-    # Temporarily use fork until PR is merged upstream (https://github.com/Terradue/click2cwl/pull/4)
-    # "click2cwl @ git+https://github.com/Terradue/click2cwl"
     "click2cwl==0.4.0",
 ]
 

src/goldfinch/utils/click2cwl_cli.py

@@ -163,7 +163,7 @@ def resolve_cli_command(
     multiple=True,
 )
 @click.option(
-    "-o", "--output",
+    "-o", "--output-cwl", "output_cwl",
     type=click.Path(exists=False, dir_okay=False),
     is_flag=False,
     help=(
@@ -322,7 +322,7 @@ def main(ctx: click.Context, **kwargs: str) -> None:
     elif "cwl_type" in kwargs:
         cli_ctx.args.extend(["--dump", kwargs["cwl_type"]])
     if kwargs.get("output"):
-        output_cwl = kwargs["output"]
+        output_cwl = kwargs["output_cwl"]
 
     # add additional parameters to the CWL context
     for req in ["docker", "env", "wall-time", "coresMin", "coresMax", "ramMin", "ramMax", "metadata", "cwl-version"]: