Paper Freeze (#39)

* Refactor: Cleanup for Digital Discovery Paper * testing resetting with errors * Fix: reset state on reconnect --------- Co-authored-by: Dozgulbas <[email protected]>
AD-SDL · Oct 11, 2023 · 893f1e3 · 893f1e3
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diff --git a/Makefile b/Makefile
@@ -1,6 +1,6 @@
 .DEFAULT_GOAL := all
-isort = isort ot2_driver
-black = black --target-version py39 ot2_driver
+isort = python -m isort .
+black = python -m black --target-version py39 .
 
 .PHONY: format
 format:
@@ -10,15 +10,15 @@ format:
 .PHONY: lint
 lint:
 	$(black) --check --diff
-	flake8 ot2_driver/
-	pydocstyle ot2_driver/ --count
+	python -m flake8 .
+	python -m pydocstyle . --count
 
 
 
 .PHONY: mypy
 mypy:
-	mypy --config-file setup.cfg --package ot2_driver/
-	mypy --config-file setup.cfg ot2_driver/
+	mypy --config-file setup.cfg --package .
+	mypy --config-file setup.cfg .
 
 .PHONY: all
 all: format lint
diff --git a/README.md b/README.md
@@ -1,28 +1,30 @@
-### Installation 
-1. `git clone https://github.com/KPHippe/ot2_driver.git`
-2. Switch to my dev branch `git checkout dev-kyle`
-3. I would recommend a conda/venv environment. The following assusumes conda. 
-    1. `conda create -n ot2-driver python=3.9`
-    1. `conda activate ot2-driver`
-    1. `pip install -r requirements.txt` 
-    1. `pip install -e .`
-    
+### Installation
+
+```
+git clone https://github.com/AD-SDL/ot2_module.git
+cd ot2_module
+pip install -r requirements.txt
+pip install -e .
+```
+
 *This installs ot2_driver as a package*
 
+Note: This module was developed using Python 3.9
+
 ### Getting the OT2 setup for ssh
-*This is not required (or used) for the HTTP driver* 
+*This is not required (or used) for the HTTP driver*
 When setting up an ssh key to connect to the opentrons, it is helpful to make a new one without a passphrase. For more information on setting up an ssh connection see:
 
 *Note, you have to have the Opentrons App installed*
 
 - https://support.opentrons.com/en/articles/3203681-setting-up-ssh-access-to-your-ot-2
 - https://support.opentrons.com/en/articles/3287453-connecting-to-your-ot-2-with-ssh
 
-For prototyping in the RPL, connect via the wire and wait for the robot to become visible on the application. Click `settings` then `network settings` and if you intend on running via the wire, use the `wired-ip` in the robot configuration file. If you intend to use the wireless IP, you must connect to the `snowcrash` network, but this does not have internet access. 
+For prototyping in the RPL, connect via the wire and wait for the robot to become visible on the application. Click `settings` then `network settings` and if you intend on running via the wire, use the `wired-ip` in the robot configuration file. If you intend to use the wireless IP, you must connect to the `snowcrash` network, but this does not have internet access.
 
-### Robot config 
+### Robot config
 
-Below is an example of what I refer to as the `robot_config` 
+Below is an example of what I refer to as the `robot_config`
 ```
 # OT2 in lab
 - ip: IP.ADDRESS
@@ -32,7 +34,7 @@ Below is an example of what I refer to as the `robot_config`
 
 ```
 
-### Running the driver 
+### Running the driver
 
 If you would like to use the script as I have made it, I have provided command line descriptions and example commands below
 
@@ -57,27 +59,27 @@ optional arguments:
 
 ```
 
-To run the `protopiler/example_configs/basic_config.yaml` with verbose settings and default outs, run the following 
+To run the `protopiler/example_configs/basic_config.yaml` with verbose settings and default outs, run the following
 ```
 python ot2_driver_ssh.py -rc [insert/robot/config/path] -pc protopiler/example_configs/basic_config.yaml -v
 ```
-To run the `protopiler/example_configs/basic_config.yaml` with verbose settings and specify the output files, run the following 
+To run the `protopiler/example_configs/basic_config.yaml` with verbose settings and specify the output files, run the following
 
 ```
-python ot2_driver_ssh.py -rc [insert/robot/config/path] -pc protopiler/example_configs/basic_config.yaml -po ./test_protocol.py -ro ./test_resources.json -v 
+python ot2_driver_ssh.py -rc [insert/robot/config/path] -pc protopiler/example_configs/basic_config.yaml -po ./test_protocol.py -ro ./test_resources.json -v
 ```
 
 To run your own protocol.py file, replace data in the `-pc` option with the path to your protocol.py file
 ```
 python ot2_driver_ssh.py -rc [insert/robot/config/path] -pc ./test_protocol.py
 ```
 
-*The process is the same for the HTTP driver* 
+*The process is the same for the HTTP driver*
 
 If you would like to write your own code using the ot2 driver you can start with something like this
 ```python
 # would have to specify path to ot2_driver_ssh.py if not in directory
-from ot2_driver_ssh import OT2_Driver 
+from ot2_driver_ssh import OT2_Driver
 
 # Load one ot2
 for ot2_raw_cfg in yaml.safe_load(open(`robot_config_path`)):
@@ -92,22 +94,22 @@ if "py" not in str(`protocol_config`):
         protocol_out=`protocol_out`,
         resource_out=`resource_out`,
     )
-
 
-# Transfer the protocol to the ot2 
+
+# Transfer the protocol to the ot2
 transfer_returncode = ot2.transfer(protocol_file)
 if returncode:
     print("Exception raised when transferring...")
 
-# Execute the protocol 
+# Execute the protocol
 ot2.execute(protocol_file)
 
 ```
 ### Updating the Code on node computer
-1.  `cd ~/wei_ws/src/ot2_driver`
+1.  `cd ~/wei_ws/src/ot2_module`
 2.  `git pull`
 3.  `pip install -e .`
-### Running Dev Tools 
- 
+### Running Dev Tools
+
 1. Install `pip install -r requirements/dev.txt`
 2. Run `make` in project root
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -6,16 +6,16 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import datetime
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
 import sys
-import datetime
 
 sys.path.insert(0, os.path.abspath("../.."))
-import ot2_driver
 
 # -- Project information -----------------------------------------------------
 

diff --git a/ot2_driver/__init__.py b/ot2_driver/__init__.py
@@ -1,3 +1,3 @@
 """Test descriptions, I am in the `ot2_driver.__init__`"""
 
-__version__ = "0.0.1a1"
+__version__ = "0.2.0"
diff --git a/ot2_driver/config.py b/ot2_driver/config.py
@@ -1,10 +1,10 @@
 """Stores dataclasses/args/config for the ot2 drivers"""
-import yaml
 import json
 from argparse import ArgumentParser, Namespace
 from pathlib import Path
-from typing import Union, Optional, Type, TypeVar
+from typing import Optional, Type, TypeVar, Union
 
+import yaml
 from pydantic import BaseModel as _BaseModel
 
 _T = TypeVar("_T")
@@ -13,7 +13,7 @@
 
 
 class BaseModel(_BaseModel):
-    """Allows any sub-class to inherit methods allowing for programatic description of protocols
+    """Allows any sub-class to inherit methods allowing for programmatic description of protocols
     Can load a yaml into a class and write a class into a yaml file.
     """
 
@@ -48,7 +48,7 @@ def json(self, **kwargs) -> str:
         return super().json(**kwargs)
 
     def write_yaml(self, cfg_path: PathLike) -> None:
-        """Allows programatic creation of ot2util objects and saving them into yaml.
+        """Allows programmatic creation of ot2util objects and saving them into yaml.
         Parameters
         ----------
         cfg_path : PathLike

diff --git a/ot2_driver/ot2_driver_http.py b/ot2_driver/ot2_driver_http.py
@@ -3,13 +3,13 @@
 import time
 from enum import Enum
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Any
+from typing import Any, Dict, List, Optional, Tuple
 
 import requests
 import yaml
 from urllib3 import Retry
 
-from ot2_driver.config import PathLike, parse_ot2_args, OT2_Config
+from ot2_driver.config import OT2_Config, PathLike, parse_ot2_args
 from ot2_driver.protopiler.protopiler import ProtoPiler
 
 
@@ -77,7 +77,12 @@ def __init__(
             self.change_lights_status(status=True)
 
     def compile_protocol(
-        self, config_path, resource_file=None, resource_path=None, payload: Optional[Dict[str, Any]] = None, protocol_out_path=None
+        self,
+        config_path,
+        resource_file=None,
+        resource_path=None,
+        payload: Optional[Dict[str, Any]] = None,
+        protocol_out_path=None,
     ) -> Tuple[str, str]:
         """Compile the protocols via protopiler
 
@@ -97,14 +102,20 @@ def compile_protocol(
         """
         if ".py" not in str(config_path):
             self.protopiler.load_config(
-                config_path=config_path, resource_file=resource_file, resource_path=resource_path, protocol_out_path=protocol_out_path
+                config_path=config_path,
+                resource_file=resource_file,
+                resource_path=resource_path,
+                protocol_out_path=protocol_out_path,
             )
             print("resource_file = {}".format(str(resource_file)))
             (
                 protocol_out_path,
                 protocol_resource_file,
             ) = self.protopiler.yaml_to_protocol(
-                config_path, resource_file=resource_file, resource_file_out=resource_path, payload=payload
+                config_path,
+                resource_file=resource_file,
+                resource_file_out=resource_path,
+                payload=payload,
             )
 
             return protocol_out_path, protocol_resource_file
@@ -258,10 +269,10 @@ def get_robot_status(self) -> RobotStatus:
         Status
             Either IDLE or RUNNING
         """
-        runs = self.get_runs() 
-        if runs is None: 
+        runs = self.get_runs()
+        if runs is None:
             return RobotStatus.OFFLINE.value
-        
+
         for run in runs:
             run_status = run["status"]
             if (

diff --git a/ot2_driver/protocol_20230221-123810.py b/ot2_driver/protocol_20230221-123810.py
@@ -1,15 +1,14 @@
 from opentrons import protocol_api
 
-
 metadata = {
     "protocolName": "Color Mixing all",
     "author": "Kyle [email protected]",
     "description": "Mixing red colors",
-    "apiLevel": "2.12"
+    "apiLevel": "2.12",
 }
 
-def run(protocol: protocol_api.ProtocolContext):
 
+def run(protocol: protocol_api.ProtocolContext):
     deck = {}
     pipettes = {}
 
@@ -20,8 +19,12 @@ def run(protocol: protocol_api.ProtocolContext):
     deck["7"] = protocol.load_labware("opentrons_6_tuberack_nest_50ml_conical", "7")
     deck["10"] = protocol.load_labware("opentrons_96_tiprack_300ul", "10")
     deck["11"] = protocol.load_labware("opentrons_96_tiprack_20ul", "11")
-    pipettes["left"] = protocol.load_instrument("p300_single_gen2", "left", tip_racks=[deck["10"]])
-    pipettes["right"] = protocol.load_instrument("p20_single_gen2", "right", tip_racks=[deck["11"]])
+    pipettes["left"] = protocol.load_instrument(
+        "p300_single_gen2", "left", tip_racks=[deck["10"]]
+    )
+    pipettes["right"] = protocol.load_instrument(
+        "p20_single_gen2", "right", tip_racks=[deck["11"]]
+    )
 
     ####################
     # execute commands #
@@ -60,7 +63,6 @@ def run(protocol: protocol_api.ProtocolContext):
     pipettes["left"].blow_out()
     pipettes["left"].drop_tip()
 
-
     # Mix color 2
     pipettes["left"].pick_up_tip(deck["10"].wells()[3])
     pipettes["left"].well_bottom_clearance.aspirate = 1.0
@@ -94,7 +96,6 @@ def run(protocol: protocol_api.ProtocolContext):
     pipettes["right"].blow_out()
     pipettes["right"].drop_tip()
 
-
     # Mix color 3
     pipettes["right"].pick_up_tip(deck["11"].wells()[2])
     pipettes["right"].well_bottom_clearance.aspirate = 1.0

diff --git a/ot2_driver/protopiler/config.py b/ot2_driver/protopiler/config.py
@@ -110,9 +110,10 @@ class Transfer(CommandBase):
     """blow out from tip into current location"""
     drop_tip: Union[bool, List[bool]] = True
     """Drop the tip once a transfer is done"""
-    return_tip:Union[bool, List[bool]] = False
+    return_tip: Union[bool, List[bool]] = False
     """puts tip back into tip box"""
 
+
 class Multi_Transfer(CommandBase):
     multi_source: Union[str, List[List[str]]]
     """List of sources to be aspirated, each list within matrix presumed to be in single column"""
@@ -133,6 +134,7 @@ class Multi_Transfer(CommandBase):
     multi_drop_tip: Union[bool, List[bool]] = True
     """Drop the tip once a transfer is done"""
 
+
 class Mix(CommandBase):
     reps: Union[int, List[int]]
     """how many mix cycles"""
@@ -141,26 +143,32 @@ class Mix(CommandBase):
     location: Union[List[str], str]
     """mixing destination"""
 
+
 class Deactivate(CommandBase):
     deactivate: bool
     """Deactivates current module"""
 
+
 class Temperature_Set(CommandBase):
     change_temp: int
     """Temperature to set temperature module to"""
 
+
 class Replace_Tip(CommandBase):
     replace_tip: bool
     """Place tip back into tip rack"""
 
+
 class Clear_Pipette(CommandBase):
     clear: bool
     """Blowout and remove any tip on pipette over trash"""
 
+
 class Move_Pipette(CommandBase):
     move_to: int
     """Moves pipette to given deck position"""
 
+
 # metadata container
 class Metadata(BaseSettings):
     """Container for the run metadata"""
@@ -182,7 +190,19 @@ class ProtocolConfig(BaseSettings):
     """The additional resources (currently xls, xlsx files) to be used when compiling a protocol"""
     equipment: List[Union[Labware, Pipette]]
     """A list of the equipment you want to use on the OT2"""
-    commands: List[Union[Transfer, Multi_Transfer, Mix, Deactivate, Temperature_Set, Replace_Tip, Clear_Pipette, Move_Pipette, CommandBase]]
+    commands: List[
+        Union[
+            Transfer,
+            Multi_Transfer,
+            Mix,
+            Deactivate,
+            Temperature_Set,
+            Replace_Tip,
+            Clear_Pipette,
+            Move_Pipette,
+            CommandBase,
+        ]
+    ]
     """Commands to execute during run"""
     metadata: Metadata
-    """Information about the run"""
+    """Information about the run"""