From 571e3699ef1326cf8f5f04a6ade4be36dc304c1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 14 Feb 2023 13:19:27 +0000
Subject: [PATCH] docs(bin): add gptdocs to cli function
---
src/aliby/bin/run.py | 23 +++++++++++++++++++----
1 file changed, 19 insertions(+), 4 deletions(-)
diff --git a/src/aliby/bin/run.py b/src/aliby/bin/run.py
index e8495580..e918aa56 100644
--- a/src/aliby/bin/run.py
+++ b/src/aliby/bin/run.py
@@ -1,11 +1,26 @@
#!/usr/bin/env jupyter
+import argparse
+from aliby.pipeline import Pipeline, PipelineParameters
def run():
- import argparse
-
- from aliby.pipeline import Pipeline, PipelineParameters
-
+ """
+ Run a default microscopy analysis pipeline.
+
+ Parse command-line arguments and set default parameter values for running a pipeline, then
+ construct and execute the pipeline with the parameters obtained. Command-line arguments can
+ override default parameter values. If a command-line argument is a string representation of
+ an integer, convert it to an integer.
+
+ Returns
+ -------
+ None
+
+ Examples
+ --------
+ FIXME: Add docs.
+ FIXME: GTP-generated. Confirm manually.
+ """
parser = argparse.ArgumentParser(
prog="aliby-run",
description="Run a default microscopy analysis pipeline",
--
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