Remove autocompletion, path bugged

Author: Corentin

README.md

@@ -31,8 +31,7 @@ Using pip, you can simply install MyoQuant in a python environment with a simple
 ## How to Use
 
 To use the command-line tool, first activate your venv in which MyoQuant is installed: `source .venv/bin/activate`  
-Then you can perform SDH or HE analysis. You can use the command `myoquant --help` to list available commands.  
-💡 For confort, you can run `myoquant --install-completion [bash|zsh|fish|powershell|pwsh]` to install auto-completion for the commands and arguments ! 🙂
+Then you can perform SDH or HE analysis. You can use the command `myoquant --help` to list available commands.
 
 - **For SDH Image Analysis** the command is:  
   `myoquant sdh-analysis IMAGE_PATH`  

myoquant/__main__.py

@@ -10,42 +10,53 @@
 
 app = typer.Typer(
     name="MyoQuant",
-    add_completion=True,
+    add_completion=False,
     help="MyoQuant Analysis Command Line Interface",
     pretty_exceptions_show_locals=False,
 )
 
 
-def check_file_exists(ctx: typer.Context, path):
-    if ctx.resilient_parsing:
-        return
-    if path is None:
-        return path
-    if not path.exists():
-        console.print(f"The path you've supplied {path} does not exist.", style="red")
-        raise typer.Exit(code=1)
-    return path
-
-
 @app.command()
 def sdh_analysis(
     image_path: Path = typer.Argument(
-        ..., help="The image file path to analyse.", callback=check_file_exists
+        ...,
+        help="The image file path to analyse.",
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     mask_path: Path = typer.Option(
         None,
         help="The path to a binary mask to hide slide region during analysis.",
-        callback=check_file_exists,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     model_path: Path = typer.Option(
         None,
         help="The SDH model path to use for analysis. Will download latest one if no path provided.",
-        callback=check_file_exists,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     cellpose_path: Path = typer.Option(
         None,
         help="The pre-computed CellPose mask to use for analysis. Will run Cellpose if no path provided. Required as an image file.",
-        callback=check_file_exists,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     output_path: Path = typer.Option(
         None,
@@ -175,22 +186,44 @@ def sdh_analysis(
 @app.command()
 def he_analysis(
     image_path: Path = typer.Argument(
-        ..., help="The image file path to analyse.", callback=check_file_exists
+        ...,
+        help="The image file path to analyse.",
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     mask_path: Path = typer.Option(
         None,
         help="The path to a binary mask to hide slide region during analysis.",
-        callback=check_file_exists,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     cellpose_path: Path = typer.Option(
         None,
         help="The pre-computed CellPose mask to use for analysis. Will run Cellpose if no path provided. Required as an image file.",
-        callback=check_file_exists,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     stardist_path: Path = typer.Option(
         None,
         help="The pre-computed Stardist mask to use for analysis. Will run Stardist if no path provided. Required as an image file.",
-        callback=check_file_exists,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
     ),
     output_path: Path = typer.Option(
         None,