changed acmc.py to main.py, convention for cli tool

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