pre-commit formatting fix

machineagency · Oct 14, 2024 · 7b75d41 · 7b75d41
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diff --git a/HTTP_debug.ipynb b/HTTP_debug.ipynb
diff --git a/Untitled.ipynb b/Untitled.ipynb
@@ -0,0 +1,134 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "b656762c-1ca9-4f9c-9ba6-86a3f7190265",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "1127740c-7620-447b-8204-741dfc8fe3cc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import requests\n",
+    "\n",
+    "# ----------- Science Jubilee -------------\n",
+    "from science_jubilee import Machine as Jub\n",
+    "from science_jubilee.tools import HTTPSyringe as syringe\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "64788e2b-4060-4b44-8c87-cf6a880ad318",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "url = 'http://192.168.1.5:5000'\n",
+    "volume = {'volume':5}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "d1be2c94-8669-4bea-b057-a4a3acf035fd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "r = requests.get(url + '/get_status')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "8228ca74-92e4-4761-b4ef-ef0c50fe7381",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "jubilee = Jub.Machine(address='192.168.1.2', simulated = False) "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "c3d3bf61-1aed-476b-b36c-e2c5891f4986",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "jubilee.home_all()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "30f0c9b9-98da-46f9-945c-34607d3abaf5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "deck = jubilee.load_deck('lab_automation_deck.json')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "8378fc8c-b57c-4f31-8acd-f681403444cc",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "AttributeError",
+     "evalue": "'super' object has no attribute '_HTTPSyringe__init'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[13], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m syringe \u001b[38;5;241m=\u001b[39m \u001b[43msyringe\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mHTTPSyringe\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfrom_config\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m/home/brendenpelkie/Code/science-jubilee/src/science_jubilee/tools/configs/10cc_syringe.json\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/Code/science-jubilee/src/science_jubilee/tools/HTTPSyringe.py:47\u001b[0m, in \u001b[0;36mHTTPSyringe.from_config\u001b[0;34m(cls, index, fp)\u001b[0m\n\u001b[1;32m     44\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mopen\u001b[39m(fp) \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m     45\u001b[0m     kwargs \u001b[38;5;241m=\u001b[39m json\u001b[38;5;241m.\u001b[39mload(f)\n\u001b[0;32m---> 47\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mindex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/Code/science-jubilee/src/science_jubilee/tools/HTTPSyringe.py:31\u001b[0m, in \u001b[0;36mHTTPSyringe.__init__\u001b[0;34m(self, index, url)\u001b[0m\n\u001b[1;32m     27\u001b[0m config_r \u001b[38;5;241m=\u001b[39m requests\u001b[38;5;241m.\u001b[39mget(url\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/get_config\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m     29\u001b[0m config \u001b[38;5;241m=\u001b[39m config_r\u001b[38;5;241m.\u001b[39mjson\n\u001b[0;32m---> 31\u001b[0m \u001b[38;5;28;43msuper\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__init\u001b[49m(index, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mconfig, url \u001b[38;5;241m=\u001b[39m url)\n\u001b[1;32m     33\u001b[0m status_r \u001b[38;5;241m=\u001b[39m requests\u001b[38;5;241m.\u001b[39mget(url \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/get_status\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m     35\u001b[0m status \u001b[38;5;241m=\u001b[39m status_r\u001b[38;5;241m.\u001b[39mjson\n",
+      "\u001b[0;31mAttributeError\u001b[0m: 'super' object has no attribute '_HTTPSyringe__init'"
+     ]
+    }
+   ],
+   "source": [
+    "syringe = syringe.HTTPSyringe.from_config(3, \"/home/brendenpelkie/Code/science-jubilee/src/science_jubilee/tools/configs/10cc_syringe.json\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4febab10-2592-4ffa-8435-79944923c1f8",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/building/_static/center_carriage.jpg:Zone.Identifier b/docs/building/_static/center_carriage.jpg:Zone.Identifier
@@ -0,0 +1,4 @@
+[ZoneTransfer]
+ZoneId=3
+ReferrerUrl=https://photos.google.com/
+HostUrl=https://photos.fife.usercontent.google.com/pw/AP1GczNTKqrB6x5tvbBMxMTJFyDbgy_zk3AxiAneT9psVhzxOWMV_G5hJgculg=w1118-h839-s-no?authuser=0
diff --git a/docs/building/_static/manual_tool_load.jpg:Zone.Identifier b/docs/building/_static/manual_tool_load.jpg:Zone.Identifier
@@ -0,0 +1,4 @@
+[ZoneTransfer]
+ZoneId=3
+ReferrerUrl=https://photos.google.com/
+HostUrl=https://photos.fife.usercontent.google.com/pw/AP1GczOZskrK77M2lCCHUA6WmsVrBlFzXpJk3F_SxMnI3xSaLL2wpOspwIOUOg=w755-h839-s-no?authuser=0
diff --git a/docs/building/_static/parking_post_installed.jpg:Zone.Identifier b/docs/building/_static/parking_post_installed.jpg:Zone.Identifier
@@ -0,0 +1,4 @@
+[ZoneTransfer]
+ZoneId=3
+ReferrerUrl=https://photos.google.com/
+HostUrl=https://photos.fife.usercontent.google.com/pw/AP1GczNdml1rYSJs7I5ePvPf3_soG-_yw-1atLrOcG8NfM-14XQY_JKRHXBVGA=w849-h839-s-no?authuser=0
diff --git a/docs/building/_static/pin_alignment.jpg:Zone.Identifier b/docs/building/_static/pin_alignment.jpg:Zone.Identifier
@@ -0,0 +1,4 @@
+[ZoneTransfer]
+ZoneId=3
+ReferrerUrl=https://photos.google.com/
+HostUrl=https://photos.fife.usercontent.google.com/pw/AP1GczOSgRCBeDBH3jrVPtdYDXOI-K-oUlXqCQRL40T92fFPf5QpQnQQbPcCuA=w629-h839-s-no?authuser=0
diff --git a/docs/building/_static/post_wings_alignment.jpg:Zone.Identifier b/docs/building/_static/post_wings_alignment.jpg:Zone.Identifier
@@ -0,0 +1,4 @@
+[ZoneTransfer]
+ZoneId=3
+ReferrerUrl=https://photos.google.com/
+HostUrl=https://photos.fife.usercontent.google.com/pw/AP1GczM2ekpx6LZXizZWJMpK-hmlVSloet7gAPBww-Umlxy0LoZTn6Q0dlf4rA=w1118-h839-s-no?authuser=0
diff --git a/src/science_jubilee/Machine.py b/src/science_jubilee/Machine.py
@@ -3,13 +3,13 @@
 # import websocket # for reading the machine model
 
 import json
+import logging
 import os
 import time
 import warnings
 from functools import wraps
 from pathlib import Path
 from typing import Union
-import logging
 
 import requests  # for issuing commands
 from requests.adapters import HTTPAdapter, Retry
@@ -479,13 +479,17 @@ def gcode(self, cmd: str = "", timeout=None, response_wait: float = 60):
                 reply_response = self.session.get(
                     f"http://{self.address}/rr_model?key=seqs"
                 )
-                logging.debug(f'MODEL response, status: {reply_response.status_code}, headers:{reply_response.headers}, content:{reply_response.content}')
+                logging.debug(
+                    f"MODEL response, status: {reply_response.status_code}, headers:{reply_response.headers}, content:{reply_response.content}"
+                )
 
                 reply_count = reply_response.json()["result"]["reply"]
                 buffer_response = self.session.get(
                     f"http://{self.address}/rr_gcode?gcode={cmd}", timeout=timeout
                 )
-                logging.debug(f'GCODE response, status: {buffer_response.status_code}, headers:{buffer_response.headers}, content:{buffer_response.content}')
+                logging.debug(
+                    f"GCODE response, status: {buffer_response.status_code}, headers:{buffer_response.headers}, content:{buffer_response.content}"
+                )
                 # wait for a response code to be appended
                 # TODO: Implement retry backoff for managing long-running operations to avoid too many requests error. Right now this is handled by the generic exception catch then sleep. Real fix is some sort of backoff for things running longer than a few seconds.
                 tic = time.time()
@@ -496,15 +500,19 @@ def gcode(self, cmd: str = "", timeout=None, response_wait: float = 60):
                             f"http://{self.address}/rr_model?key=seqs"
                         )
 
-                        logging.debug(f'MODEL response, status: {new_reply_response.status_code}, headers:{new_reply_response.headers}, content:{new_reply_response.content}')
+                        logging.debug(
+                            f"MODEL response, status: {new_reply_response.status_code}, headers:{new_reply_response.headers}, content:{new_reply_response.content}"
+                        )
                         new_reply_count = new_reply_response.json()["result"]["reply"]
 
                         if new_reply_count != reply_count:
                             response = self.session.get(
                                 f"http://{self.address}/rr_reply"
                             )
 
-                            logging.debug(f'REPLY response, status: {response.status_code}, headers:{response.headers}, content:{response.content}')
+                            logging.debug(
+                                f"REPLY response, status: {response.status_code}, headers:{response.headers}, content:{response.content}"
+                            )
 
                             response = response.text
                             break
@@ -515,7 +523,7 @@ def gcode(self, cmd: str = "", timeout=None, response_wait: float = 60):
                         try_count += 1
                     except Exception as e:
                         print(f"Connection error ({e}), sleeping 1 second")
-                        logging.debug(f'Error in gcode reply wait loop: {e}')
+                        logging.debug(f"Error in gcode reply wait loop: {e}")
                         time.sleep(2)
                         continue
 
@@ -525,7 +533,6 @@ def gcode(self, cmd: str = "", timeout=None, response_wait: float = 60):
         # TODO: handle this with logging. Also fix so all output goes to logs
         return response
 
-
     def delay_time(self, n):
         """
         Calculate delay time for next request. dumb hard code for now, could be fancy exponential backoff
@@ -541,7 +548,6 @@ def delay_time(self, n):
         else:
             return 1
 
-
     def _set_absolute_positioning(self):
         """Set absolute positioning for all axes except extrusion"""
         self.gcode("G90")

diff --git a/...e/decks/deck_definition/.ipynb_checkpoints/lab_automation_deck_AFL_bolton-checkpoint.json b/...e/decks/deck_definition/.ipynb_checkpoints/lab_automation_deck_AFL_bolton-checkpoint.json
@@ -49,4 +49,4 @@
         "plate": "Aluminum",
         "mask": "Delrin"
     }
-}
+}
diff --git a/src/science_jubilee/decks/deck_definition/lab_automation_deck_AFL_bolton.json b/src/science_jubilee/decks/deck_definition/lab_automation_deck_AFL_bolton.json
@@ -49,4 +49,4 @@
         "plate": "Aluminum",
         "mask": "Delrin"
     }
-}
+}
diff --git a/src/science_jubilee/decks/deck_definition/lab_automation_deck_MA.json b/src/science_jubilee/decks/deck_definition/lab_automation_deck_MA.json
@@ -49,4 +49,4 @@
         "plate": "Aluminum",
         "mask": "Delrin"
     }
-}
+}
diff --git a/...ware/labware_definition/.ipynb_checkpoints/septavialrev1_44_holder_2000ul-checkpoint.json b/...ware/labware_definition/.ipynb_checkpoints/septavialrev1_44_holder_2000ul-checkpoint.json
@@ -544,4 +544,4 @@
         "y": 0,
         "z": 0
     }
-}
+}
diff --git a/src/science_jubilee/labware/labware_definition/septavialrev1_44_holder_2000ul.json b/src/science_jubilee/labware/labware_definition/septavialrev1_44_holder_2000ul.json
@@ -589,4 +589,4 @@
         "y": 0,
         "z": 0
     }
-}
+}
diff --git a/src/science_jubilee/tools/HTTPSyringe.py b/src/science_jubilee/tools/HTTPSyringe.py
@@ -199,7 +199,7 @@ def mix(
         location: Union[Well, Tuple, Location],
         t_hold: int = 1,
         s_aspirate: int = 100,
-        s_dispense: int = 100
+        s_dispense: int = 100,
     ):
         """
         Mixes n times with volume vol
@@ -226,7 +226,9 @@ def mix(
 
         self._machine.safe_z_movement()
         self._machine.move_to(x=x, y=y, wait=True)
-        self._aspirate(500, s_aspirate) #pre-aspirate 500 uL then blow this out at the end to avoid holding onto extra solution 
+        self._aspirate(
+            500, s_aspirate
+        )  # pre-aspirate 500 uL then blow this out at the end to avoid holding onto extra solution
         self._machine.move_to(z=z, wait=True)
 
         for _ in range(n_mix):

diff --git a/src/science_jubilee/tools/configs/10cc_syringe.json b/src/science_jubilee/tools/configs/10cc_syringe.json
@@ -1,4 +1,4 @@
 {
     "url": "http://192.168.1.5:5000",
     "name": "10cc_1"
-}
+}
diff --git a/src/science_jubilee/tools/configs/1cc_1_syringe.json b/src/science_jubilee/tools/configs/1cc_1_syringe.json
@@ -1,4 +1,4 @@
 {
     "url": "http://192.168.1.5:5000",
     "name": "1cc_1"
-}
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -49,4 +49,4 @@ @@
             "plate": "Aluminum",
             "mask": "Delrin"
         }
-    }
+    }