Add launch.json debug config file

Add launch.json debug config file and minor main.py function descriptions
niklases · Dec 10, 2023 · e9b1373 · e9b1373
1 parent c926041
commit e9b1373
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Showing 2 changed files with 53 additions and 2 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -0,0 +1,34 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: PyPEF Help",
+            "type": "python",
+            "request": "launch",
+            "program": "${workspaceFolder}/pypef/main.py",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "args": [
+                "--help"
+            ]
+        },
+        {
+            "name": "Python: PyPEF MKLSTS",
+            "type": "python",
+            "request": "launch",
+            "program": "${workspaceFolder}/pypef/main.py",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "cwd": "${workspaceFolder}/datasets/ANEH/",
+            "args": [
+                "mklsts", 
+                "--wt", "${workspaceFolder}/datasets/ANEH/Sequence_WT_ANEH.fasta", 
+                "--input", "${workspaceFolder}/datasets/ANEH/37_ANEH_variants.csv"
+            ]
+        }
+
+    ]
+}
diff --git a/pypef/main.py b/pypef/main.py
@@ -324,7 +324,6 @@
 ch.setFormatter(formatter)
 logger.addHandler(ch)
 
-
 schema = Schema({
     Optional('--all'): bool,
     Optional('--conc'): bool,
@@ -398,6 +397,22 @@
 
 
 def validate(args):
+    """
+    Validate (docopt) arguments.
+    
+    Parameters
+    ----------
+    args: dict
+        Key-value pairs of arguments,
+        e.g.,
+        {'mklsts': True,
+         '--wt': 'WT_Seq.fasta',
+         '--input': 'Variant-Fitness.csv'}
+
+    Returns
+    -------
+    None
+    """
     try:
         args = schema.validate(args)
         return args
@@ -408,6 +423,8 @@ def validate(args):
 def run_main():
     """
     Entry point for pip-installed version.
+    Arguments are created from Docstring using docopt that 
+    creates an argument dict.
     """
     arguments = docopt(__doc__, version=__version__)
     start_time = time.time()
@@ -424,7 +441,7 @@ def run_main():
     else:
         run_pypef_utils(arguments)
 
-    elapsed = str(timedelta(seconds=time.time()-start_time)).split(".")[0]
+    elapsed = str(timedelta(seconds=time.time() - start_time)).split(".")[0]
     elapsed = f'{elapsed.split(":")[0]} h {elapsed.split(":")[1]} min {elapsed.split(":")[2]} s'
     logger.info(f'Done! (Run time: {elapsed})')