Merge pull request #577 from czbiohub-sf/cli_entrypoints

Add entry points for CLI

Author: NicholasBratvold

setup.py

@@ -59,4 +59,12 @@ def readme():
         ]
     },
     classifiers=["CZ Biohub :: Bioengineering"],
+    entry_points={
+        "console_scripts": [
+            "remo-run=ulc_mm_package.QtGUI.oracle:main",
+            "remo-dev=ulc_mm_package.QtGUI.dev_run:main",
+            "remo-fix-focus=ulc_mm_package.utilities.coarse_focus_utility:main",
+            "remo-pneumatic-calibration=ulc_mm_package.utilities.pneumatic_utility:main",
+        ]
+    },
 )

ulc_mm_package/QtGUI/dev_run.py

@@ -1179,7 +1179,7 @@ def closeEvent(self, event):
         self.close()
 
 
-if __name__ == "__main__":
+def main():
     if path.isfile(LOCKFILE):
         print(
             f"Terminating run. Lockfile ({LOCKFILE}) exists, so scope is locked while another run is in progress."
@@ -1197,3 +1197,7 @@ def closeEvent(self, event):
         app.exec_()
     finally:
         main_window.mscope.shutoff()
+
+
+if __name__ == "__main__":
+    main()

ulc_mm_package/QtGUI/oracle.py

@@ -128,8 +128,9 @@ def __init__(self):
             mkdir(log_dir)
 
         # Setup logger
+        logger_config_path = Path(__file__).resolve().parent.parent / "logger.config"
         fileConfig(
-            fname="../logger.config",
+            fname=str(logger_config_path),
             defaults={
                 "filename": path.join(log_dir, f"{self.datetime_str}.log"),
                 "fileHandlerLevel": "DEBUG" if VERBOSE else "INFO",
@@ -474,7 +475,7 @@ def liveview_exit_handler(self):
     def error_handler(self, title, text, behavior, QR_code):
         if QR_code is not QR.NONE.value:
             if behavior == ERROR_BEHAVIORS.RELOAD.value:
-                QR_msg = "\n\Try loading a new flow cell. If problem persists, scan QR code to troubleshoot."
+                QR_msg = "\nTry loading a new flow cell. If problem persists, scan QR code to troubleshoot."
             else:
                 QR_msg = "\n\nScan QR code to troubleshoot."
         else:
@@ -863,7 +864,7 @@ def emergency_shutoff(self):
             self.logger.info("EMERGENCY ORACLE SHUT OFF SUCCESSFUL.")
 
 
-if __name__ == "__main__":
+def main():
     app = ShutoffApplication(sys.argv)
     oracle = Oracle()
 
@@ -884,3 +885,7 @@ def shutoff_excepthook(type, value, traceback):
     sys.excepthook = shutoff_excepthook
 
     app.exec()
+
+
+if __name__ == "__main__":
+    main()