code formatting, minor refactoring, comments

recOrder/cli/apply_inverse_transfer_function.py

@@ -377,16 +377,16 @@ def apply_inverse_transfer_function_cli(
 
     doPrint = True # CLI prints Job status when used as cmd line
     if unique_id != "": # no unique_id means no job submission info being listened to
-        JM.startClient()
+        JM.start_client()
         i=0
         for j in jobs:           
             job : submitit.Job = j
             job_idx : str = job.job_id
             position = input_position_dirpaths[i]
-            JM.putJobInList(job, unique_id, str(job_idx), position, str(executor.folder.absolute()))
+            JM.put_Job_in_list(job, unique_id, str(job_idx), position, str(executor.folder.absolute()))
             i += 1
-        JM.sendDataThread()
-        JM.setShorterTimeout()
+        JM.send_data_thread()
+        JM.set_shorter_timeout()
         doPrint = False # CLI printing disabled when using GUI
 
     monitor_jobs(jobs, input_position_dirpaths, doPrint)

recOrder/cli/jobs_mgmt.py

@@ -14,20 +14,19 @@
 class JobsManagement():
 
     def __init__(self, *args, **kwargs):
-        self.executor = submitit.AutoExecutor(folder="logs")
         self.clientsocket = None
         self.uIDsjobIDs = {} # uIDsjobIDs[uid][jid] = job        
         self.DATA_QUEUE = []
 
-    def checkForJobIDFile(self, jobID, logsPath, extension="out"):
+    def check_for_jobID_File(self, jobID, logs_path, extension="out"):
 
-        if Path(logsPath).exists():
-            files = os.listdir(logsPath)
+        if Path(logs_path).exists():
+            files = os.listdir(logs_path)
             try:
                 for file in files:
                     if file.endswith(extension):
                         if jobID in file:
-                            file_path = os.path.join(logsPath, file)
+                            file_path = os.path.join(logs_path, file)
                             f = open(file_path, "r")
                             txt = f.read()                    
                             f.close()
@@ -36,22 +35,28 @@ def checkForJobIDFile(self, jobID, logsPath, extension="out"):
                 print(exc.args)
         return ""
 
-    def setShorterTimeout(self):
+    def set_shorter_timeout(self):
         self.clientsocket.settimeout(30)
-
-    def startClient(self):
+    
+    def start_client(self):
         try:
             self.clientsocket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
             self.clientsocket.settimeout(300)
             self.clientsocket.connect(('localhost', SERVER_PORT))
             self.clientsocket.settimeout(None)
 
-            thread = threading.Thread(target=self.stopClient)
+            thread = threading.Thread(target=self.stop_client)
             thread.start()
         except Exception as exc:
             print(exc.args)
 
-    def stopClient(self):
+    # The stopClient() is called right with the startClient() but does not stop 
+    # and essentially is a wait thread listening and is triggered by either a 
+    # connection or timeout. Based on condition triggered by user, reconstruction 
+    # completion or errors the end goal is to close the socket connection which 
+    # would let the CLI exit. I could break it down to 2 parts but the idea was to 
+    # keep the clientsocket.close() call within one method to make it easier to follow.
+    def stop_client(self):
         try:
             time.sleep(2)
             while True:
@@ -73,11 +78,11 @@ def stopClient(self):
                                 job_idx = str(json_obj["jID"])
                                 cmd = json_obj["command"]
                                 if cmd == "clientRelease":
-                                    if self.hasSubmittedJob(u_idx, job_idx):
+                                    if self.has_submitted_job(u_idx, job_idx):
                                         self.clientsocket.close()
                                         break
                                 if cmd == "cancel":
-                                    if self.hasSubmittedJob(u_idx, job_idx):
+                                    if self.has_submitted_job(u_idx, job_idx):
                                         try:
                                             job = self.uIDsjobIDs[u_idx][job_idx]
                                             job.cancel()
@@ -104,7 +109,7 @@ def stopClient(self):
             self.clientsocket.close()
             print(exc.args)
 
-    def checkAllExpJobsCompletion(self, uID):
+    def check_all_ExpJobs_completion(self, uID):
         if uID in SERVER_uIDsjobIDs.keys():
             for jobEntry in SERVER_uIDsjobIDs[uID].keys():
                 job:submitit.Job = SERVER_uIDsjobIDs[uID][jobEntry]["job"]
@@ -115,24 +120,24 @@ def checkAllExpJobsCompletion(self, uID):
                     return False
         return True
 
-    def putJobCompletionInList(self, jobBool, uID: str, jID: str, mode="client"):
+    def put_Job_completion_in_list(self, job_bool, uID: str, jID: str, mode="client"):
         if uID in SERVER_uIDsjobIDs.keys():
             if jID in SERVER_uIDsjobIDs[uID].keys():
-                SERVER_uIDsjobIDs[uID][jID]["bool"] = jobBool
+                SERVER_uIDsjobIDs[uID][jID]["bool"] = job_bool
 
-    def addData(self, data):
+    def add_data(self, data):
         self.DATA_QUEUE.append(data)
 
-    def sendDataThread(self):
-        thread = threading.Thread(target=self.sendData)
+    def send_data_thread(self):
+        thread = threading.Thread(target=self.send_data)
         thread.start()
 
-    def sendData(self):
+    def send_data(self):
         data = "".join(self.DATA_QUEUE)
         self.clientsocket.send(data.encode())
         self.DATA_QUEUE = []
 
-    def putJobInList(self, job, uID: str, jID: str, well:str, log_folder_path:str="", mode="client"):
+    def put_Job_in_list(self, job, uID: str, jID: str, well:str, log_folder_path:str="", mode="client"):
         try:
             well = str(well)
             jID = str(jID)
@@ -148,7 +153,7 @@ def putJobInList(self, job, uID: str, jID: str, well:str, log_folder_path:str=""
                         self.uIDsjobIDs[uID][jID] = job
                 json_obj = {uID:{"jID": str(jID), "pos": well, "log": log_folder_path}}
                 json_str = json.dumps(json_obj)+"\n"                
-                self.addData(json_str)
+                self.add_data(json_str)
             else:
                 # from server side jobs object entry is a None object
                 # this will be later checked as completion boolean for a ExpID which might
@@ -165,7 +170,7 @@ def putJobInList(self, job, uID: str, jID: str, well:str, log_folder_path:str=""
         except Exception as exc:
             print(exc.args)
 
-    def hasSubmittedJob(self, uID: str, jID: str, mode="client")->bool:
+    def has_submitted_job(self, uID: str, jID: str, mode="client")->bool:
         jID = str(jID)
         if mode == "client":
             if uID in self.uIDsjobIDs.keys():

recOrder/cli/monitor.py

@@ -7,17 +7,17 @@
 import sys
 
 
-def _move_cursor_up(n_lines, doPrint=True):
-    if doPrint:
+def _move_cursor_up(n_lines, do_print=True):
+    if do_print:
         sys.stdout.write("\033[F" * n_lines)
 
 
-def _print_status(jobs, position_dirpaths, elapsed_list, print_indices=None, doPrint=True):
+def _print_status(jobs, position_dirpaths, elapsed_list, print_indices=None, do_print=True):
 
     columns = [15, 30, 40, 50]
 
     # header
-    if doPrint:
+    if do_print:
         sys.stdout.write(
             "\033[K"  # clear line
             "\033[96mID"  # cyan
@@ -48,7 +48,7 @@ def _print_status(jobs, position_dirpaths, elapsed_list, print_indices=None, doP
             color = "\033[91m"  # red
 
         if i in print_indices:
-            if doPrint:
+            if do_print:
                 sys.stdout.write(
                     f"\033[K"  # clear line
                     f"{color}{job.job_id}"
@@ -58,7 +58,7 @@ def _print_status(jobs, position_dirpaths, elapsed_list, print_indices=None, doP
                     f"\033[{columns[3]}G {elapsed_list[i]} s\n"
                 )
     sys.stdout.flush()
-    if doPrint:
+    if do_print:
         print(
             f"\033[32m{complete_count}/{len(jobs)} jobs complete. " 
             "<ctrl+z> to move monitor to background. " 
@@ -92,7 +92,7 @@ def _get_jobs_to_print(jobs, num_to_print):
     return job_indices_to_print
 
 
-def monitor_jobs(jobs: list[submitit.Job], position_dirpaths: list[Path], doPrint=True):
+def monitor_jobs(jobs: list[submitit.Job], position_dirpaths: list[Path], do_print=True):
     """Displays the status of a list of submitit jobs with corresponding paths.
 
     Parameters
@@ -113,7 +113,7 @@ def monitor_jobs(jobs: list[submitit.Job], position_dirpaths: list[Path], doPrin
 
     # print all jobs once if terminal is too small
     if shutil.get_terminal_size().lines - NON_JOB_LINES < len(jobs):
-        _print_status(jobs, position_dirpaths, elapsed_list, doPrint)
+        _print_status(jobs, position_dirpaths, elapsed_list, do_print)
 
     # main monitor loop
     try:
@@ -130,15 +130,15 @@ def monitor_jobs(jobs: list[submitit.Job], position_dirpaths: list[Path], doPrin
                 position_dirpaths,
                 elapsed_list,
                 job_indices_to_print,
-                doPrint,
+                do_print,
             )
 
             time.sleep(1)
-            _move_cursor_up(num_jobs_to_print + 2, doPrint)
+            _move_cursor_up(num_jobs_to_print + 2, do_print)
 
         # Print final status
         time.sleep(1)
-        _print_status(jobs, position_dirpaths, elapsed_list, doPrint=doPrint)
+        _print_status(jobs, position_dirpaths, elapsed_list, do_print=do_print)
 
     # cancel jobs if ctrl+c
     except KeyboardInterrupt:

recOrder/plugin/main_widget.py

@@ -90,7 +90,7 @@ def __init__(self, napari_viewer: Viewer):
         # Setup GUI elements
         self.ui = gui.Ui_Form()
         self.ui.setupUi(self)
-        self.ui.tab_reconstruction.setViewer(napari_viewer)
+        self.ui.tab_reconstruction.set_viewer(napari_viewer)
 
         # Override initial tab focus
         self.ui.tabWidget.setCurrentIndex(0)