Various comment updates and small sourcery suggestions

scripts/planktoscope/light.py

@@ -11,11 +11,7 @@ from loguru import logger
 import subprocess  # nosec
 
 # Library to send command over I2C for the light module on the fan
-try:
+import smbus2 as smbus
-    import smbus2 as smbus
-except ModuleNotFoundError:  # We need this to install the library on machine that do not have the module yet
-    subprocess.run("pip3 install smbus2".split())  # nosec
-    import smbus2 as smbus
 
 import enum
 

scripts/planktoscope/module.py

@@ -52,7 +52,7 @@ class ModuleProcess(multiprocessing.Process):
             action = last_message["action"]
         if action == "on":
             # Treat the received messages here
-
+            pass
         elif action != "":
             logger.warning(
                 f"We did not understand the received request {action} - {last_message}"
@@ -92,4 +92,5 @@ class ModuleProcess(multiprocessing.Process):
 
 # This is called if this script is launched directly
 if __name__ == "__main__":
-    # This should be tests of your module
+    # This should be tests of your module
+    pass

scripts/planktoscope/mqtt.py

@@ -86,7 +86,7 @@ class MQTT_Client:
     @logger.catch
     def connect(self):
         logger.info(f"trying to connect to {self.server}:{self.port}")
-        # TODO add try: except ConnectionRefusedError: block here
+        # TODO #104 add try: except ConnectionRefusedError: block here
         # This is a symptom that Mosquitto may have failed to start
         self.client.connect(self.server, self.port, 60)
         self.client.on_connect = self.on_connect

scripts/planktoscope/segmenter/__init__.py

@@ -274,7 +274,7 @@ class SegmenterProcess(multiprocessing.Process):
         h_stddev = np.std(h_channel, where=mask)
         s_stddev = np.std(s_channel, where=mask)
         v_stddev = np.std(v_channel, where=mask)
-        # TODO Add skewness and kurtosis calculation (with scipy) here
+        # TODO #103 Add skewness and kurtosis calculation (with scipy) here
         # using https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.skew.html#scipy.stats.skew
         # and https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kurtosis.html#scipy.stats.kurtosis
         # h_quartiles = np.quantile(h_channel, quartiles)
@@ -789,7 +789,7 @@ class SegmenterProcess(multiprocessing.Process):
         else:
             self.segmenter_client.client.publish(
                 "status/segmenter",
-                f'{{"status":"An exception was raised during the segmentation: {e}."}}',
+                f'{{"status":"An exception was raised during the segmentation: {exception}."}}',
             )
         # Reset process_id
         self.__process_id = ""
@@ -856,6 +856,7 @@ class SegmenterProcess(multiprocessing.Process):
             self.__ecotaxa_path,
             # filename includes project name, timestamp and sample id
             f"ecotaxa_{project}_{date}_{sample}.zip",
+        # TODO #102 sanitize the filename to remove potential problems with spaces and special characters
         )
 
         self.__working_path = path
@@ -978,7 +979,7 @@ class SegmenterProcess(multiprocessing.Process):
 
             elif last_message["action"] != "":
                 logger.warning(
-                    f"We did not understand the received request {action} - {last_message}"
+                    f"We did not understand the received request {last_message}"
                 )
 
     ################################################################################

scripts/planktoscope/segmenter/ecotaxa.py

@@ -205,7 +205,7 @@ def ecotaxa_export(archive_filepath, metadata, image_base_path, keep_files=False
             logger.error("No objects metadata recorded, cannot continue the export")
             return 0
 
-        # fix crappy old camera resolution that was not exported as string
+        # sometimes the camera resolution is not exported as string
         if type(metadata["acq_camera_resolution"]) != str:
             metadata[
                 "acq_camera_resolution"
@@ -216,7 +216,7 @@ def ecotaxa_export(archive_filepath, metadata, image_base_path, keep_files=False
             tsv_line = {}
             tsv_line.update(metadata)
             tsv_line.update(("object_" + k, v) for k, v in roi["metadata"].items())
-            tsv_line.update({"object_id": roi["name"]})
+            tsv_line["object_id"] = roi["name"]
 
             filename = roi["name"] + ".jpg"
 

scripts/planktoscope/segmenter/streamer.py

@@ -50,6 +50,7 @@ class StreamingHandler(http.server.BaseHTTPRequestHandler):
                             )
                             break
                         frame = file.getvalue()
+                        # TODO #101 insert try block here to catch ConnectionResetError: [Errno 104] Connection reset by peer
                         self.wfile.write(b"--FRAME\r\n")
                         self.send_header("Content-Type", "image/jpeg")
                         self.send_header("Content-Length", len(frame))

scripts/planktoscope/stepper.py

@@ -185,6 +185,7 @@ class StepperProcess(multiprocessing.Process):
         if os.path.exists("/home/pi/PlanktoScope/hardware.json"):
             # load hardware.json
             with open("/home/pi/PlanktoScope/hardware.json", "r") as config_file:
+                # TODO #100 insert guard for config_file empty
                 configuration = json.load(config_file)
                 logger.debug(f"Hardware configuration loaded is {configuration}")
         else: