From 62c283c7c2f4e32f06dd11e80d5cff5ae079c726 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Tue, 18 Feb 2025 21:00:43 +0000
Subject: [PATCH] changed acmc.py to main.py, convention for cli tool
---
tests/test_acmc.py | 34 +++++++++++++++++-----------------
1 file changed, 17 insertions(+), 17 deletions(-)
diff --git a/tests/test_acmc.py b/tests/test_acmc.py
index 1653ca1..bc7c035 100644
--- a/tests/test_acmc.py
+++ b/tests/test_acmc.py
@@ -8,7 +8,7 @@ from pathlib import Path
import trud
import omop
import phen
-import acmc
+import main
# setup logging
from logging_config import setup_logger
@@ -35,29 +35,29 @@ def logger():
def test_phen_init_local_default(tmp_dir, monkeypatch, caplog):
with caplog.at_level(logging.DEBUG):
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "init"])
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "init"])
# Mock input() to return "yes" to the question about reinitialising the directory
monkeypatch.setattr("builtins.input", lambda _: "y")
- acmc.main()
+ main.main()
assert "Phenotype initialised successfully" in caplog.text
def test_phen_init_local_specified(tmp_dir, monkeypatch, caplog):
with caplog.at_level(logging.DEBUG):
phen_path = tmp_dir / "phen"
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "init", "-d", str(phen_path.resolve())])
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "init", "-d", str(phen_path.resolve())])
# Mock input() to return "yes" to the question about reinitialising the directory
monkeypatch.setattr("builtins.input", lambda _: "y")
- acmc.main()
+ main.main()
assert "Phenotype initialised successfully" in caplog.text
def test_phen_workflow(tmp_dir, monkeypatch, caplog):
with caplog.at_level(logging.DEBUG):
phen_path = tmp_dir / "phen"
phen_path = phen_path.resolve()
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "init", "-d", str(phen_path.resolve())])
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "init", "-d", str(phen_path.resolve())])
# Mock input() to return "yes" to the question about reinitialising the directory
monkeypatch.setattr("builtins.input", lambda _: "y")
- acmc.main()
+ main.main()
assert "Phenotype initialised successfully" in caplog.text
with caplog.at_level(logging.DEBUG):
@@ -74,31 +74,31 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog):
shutil.copy(source, destination)
shutil.copy( phen_path / 'config1.json', phen_path / 'config.json')
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "validate", "-d", str(phen_path.resolve())])
- acmc.main()
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "validate", "-d", str(phen_path.resolve())])
+ main.main()
assert "Phenotype validated successfully" in caplog.text
# map phenotype
with caplog.at_level(logging.DEBUG):
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "map", "-d", str(phen_path.resolve()), "-t", "read2", "-tr", "-ve"])
- acmc.main()
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "map", "-d", str(phen_path.resolve()), "-t", "read2", "-tr", "-ve"])
+ main.main()
assert "Phenotype processed successfully" in caplog.text
# publish phenotype
with caplog.at_level(logging.DEBUG):
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "publish", "-d", str(phen_path.resolve())])
- acmc.main()
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "publish", "-d", str(phen_path.resolve())])
+ main.main()
assert "Phenotype published successfully" in caplog.text
# copy phenotype'
with caplog.at_level(logging.DEBUG):
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "copy", "-d", str(phen_path.resolve()), "-td", str(tmp_dir.resolve()), "-v", "v1.0.3"])
- acmc.main()
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "copy", "-d", str(phen_path.resolve()), "-td", str(tmp_dir.resolve()), "-v", "v1.0.3"])
+ main.main()
assert "Phenotype copied successfully" in caplog.text
# diff phenotype
with caplog.at_level(logging.DEBUG):
old_path = tmp_dir / "v1.0.3"
- monkeypatch.setattr(sys, "argv", ["acmc.py", "phen", "diff", "-d", str(phen_path.resolve()), "-old", str(old_path.resolve())])
- acmc.main()
+ monkeypatch.setattr(sys, "argv", ["main.py", "phen", "diff", "-d", str(phen_path.resolve()), "-old", str(old_path.resolve())])
+ main.main()
assert "Phenotypes diff'd successfully" in caplog.text
--
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