From 50a4a993d67a640461374366f7cd2e4ec958667d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 24 Jan 2023 14:48:29 +0000
Subject: [PATCH] feat(aliby): add run script for cli upon install
---
bin/run.py | 47 --------------------------------------
src/aliby/bin/__init__.py | 1 +
src/aliby/bin/run.py | 48 +++++++++++++++++++++++++++++++++++++++
3 files changed, 49 insertions(+), 47 deletions(-)
delete mode 100644 bin/run.py
create mode 100644 src/aliby/bin/__init__.py
create mode 100644 src/aliby/bin/run.py
diff --git a/bin/run.py b/bin/run.py
deleted file mode 100644
index 230b934b..00000000
--- a/bin/run.py
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env jupyter
-
-import argparse
-
-from aliby.pipeline import Pipeline, PipelineParameters
-
-parser = argparse.ArgumentParser(
- prog="aliby-run", description="Run a default microscopy analysis pipeline"
-)
-
-param_values = {
- "expt_id": None,
- "distributed": 2,
- "tps": 2,
- "directory": "./data",
- "filter": 0,
- "host": None,
- "username": None,
- "password": None,
-}
-
-
-def _cast_str(x: str or None):
- """
- Cast string as int if possible. If Nonetype return None.
- """
- if x:
- try:
- return int(x)
- except:
- return x
-
-
-for k in param_values:
- parser.add_argument(f"--{k}", action="store")
-
-args = parser.parse_args()
-
-for k in param_values:
- if passed_value := _cast_str(getattr(args, k)):
-
- param_values[k] = passed_value
-
-params = PipelineParameters.default(general=param_values)
-p = Pipeline(params)
-
-p.run()
diff --git a/src/aliby/bin/__init__.py b/src/aliby/bin/__init__.py
new file mode 100644
index 00000000..a051bb08
--- /dev/null
+++ b/src/aliby/bin/__init__.py
@@ -0,0 +1 @@
+#!/usr/bin/env jupyter
diff --git a/src/aliby/bin/run.py b/src/aliby/bin/run.py
new file mode 100644
index 00000000..e8495580
--- /dev/null
+++ b/src/aliby/bin/run.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env jupyter
+
+
+def run():
+ import argparse
+
+ from aliby.pipeline import Pipeline, PipelineParameters
+
+ parser = argparse.ArgumentParser(
+ prog="aliby-run",
+ description="Run a default microscopy analysis pipeline",
+ )
+
+ param_values = {
+ "expt_id": None,
+ "distributed": 2,
+ "tps": 2,
+ "directory": "./data",
+ "filter": 0,
+ "host": None,
+ "username": None,
+ "password": None,
+ }
+
+ def _cast_str(x: str or None):
+ """
+ Cast string as int if possible. If Nonetype return None.
+ """
+ if x:
+ try:
+ return int(x)
+ except:
+ return x
+
+ for k in param_values:
+ parser.add_argument(f"--{k}", action="store")
+
+ args = parser.parse_args()
+
+ for k in param_values:
+ if passed_value := _cast_str(getattr(args, k)):
+
+ param_values[k] = passed_value
+
+ params = PipelineParameters.default(general=param_values)
+ p = Pipeline(params)
+
+ p.run()
--
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