AD-SDL · caseystone · Jan 6, 2026 · Nov 4, 2025 · Nov 4, 2025 · Nov 4, 2025
diff --git a/.gitignore b/.gitignore
@@ -160,3 +160,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# VS Code
+.vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,9 +1,8 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
-      - id: check-json
       - id: check-toml
       - id: check-ast
       - id: check-merge-conflict
@@ -12,15 +11,19 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.9
+    rev: v0.14.2
     hooks:
       # Run the linter.
       - id: ruff
         args: [--fix]
       # Run the formatter.
       - id: ruff-format
+  - repo: https://gitlab.com/bmares/check-json5
+    rev: v1.0.0
+    hooks:
+    - id: check-json5
diff --git a/Dockerfile b/Dockerfile
diff --git a/README.md b/README.md
@@ -1,118 +1,127 @@
-# BMG module 
+# BMG Module
 
-A WEI-powered module for controlling BMG Microplate Readers, currently tested with the VANTAstar model.
+A MADSci-powered module for controlling BMG microplate readers, currently tested with the VANTAstar model.
 
-Contains a BMG driver (bmg_driver.py) and BMG REST Node (bmg_rest_node.py). 
+Contains a BMG driver (bmg_driver.py), BMG Object Thread Class (bmg_object_thread.py), and BMG REST Node (bmg_rest_node.py).
 
-### Assay Setup on BMG microplate reader
+### Assay Setup on a BMG Microplate Reader
 
-In order to run an assay on the BMG plate reader, you first need to create the assay using the BMG Smart Control software (not the Voyager software). Once the assay is created and saved, it needs to be exported and the .TCS file should be placed inside the BMG directory that contains the assay database .db file ("C:\Program Files (x86)\BMG\CLARIOstar\User\Definit" with default BMG Smart Control on Windows). Once the .TCS file for your assay has been saved into the database directory, it can be accessed by our BMG driver and REST Node by assay name. 
+To run an assay on the BMG plate reader, you must first create the assay using the BMG SMART Control software (not the Voyager software). Once the assay is created and saved, it must be exported, and the .TCS file should be placed inside the BMG directory that contains the assay database .db file ("C:\Program Files (x86)\BMG\CLARIOstar\User\Definit" with default BMG SMART Control on Windows).
 
-### Running instructions
+Once the .TCS file for your assay has been saved into the database directory, it can be accessed by the BMG driver and REST Node by assay name.
 
-The BMG driver and REST Node can only connect to the device if run with **32-bit python**. In the following commands, be sure that you're running the correct python version, replacing 'python' with the complete path to your 32-bit python .exe file if necessary. 
+### Running Instructions
+
+The BMG driver and REST Node can only connect to the device when run with **32-bit Python** on a Windows machine. When creating your Python virtual environment in the commands below, replace 'python.exe' with the path to a 32-bit Python executable.
 
 #### Installation
 
-When running the last line of these install instructions, be sure to pip install using your 32-bit python. An example of how to do this is below but make sure to replace python.exe with the path to your 32-bit python .exe.
+Clone the repository:
 
-    python.exe -m pip install -e .
+    git clone https://github.com/AD-SDL/bmg_module.git
+    cd bmg_module
 
-General install instructions: 
+Create a virtual environment with 32-bit Python, then activate it. Be sure to use your 32-bit Python path:
+
+    python.exe -m venv .venv
+    .venv\Scripts\activate
+
+Install the dependencies using PDM or pip:
+
+    pdm install
+
+or
 
-    git clone https://github.com/AD-SDL/bmg_module.git
-    cd bmg_module 
     pip install -e .
 
-If you're having trouble installing the requirements or wei due to an issue installing httptools, use the Visual Studio Installer (download this if you don't have it already), and either modify or install Visual Studio Community 2022 to include "Desktop development with C++".
+If you're having trouble installing the requirements or MADSci due to an issue installing httptools, use the Visual Studio Installer (download it if you do not already have it), and either modify or install Visual Studio Community 2022 to include Desktop development with C++.
 
-#### Running the driver
+#### Running the Interface
+
+Inside the bmg_module directory, run the following commands to test the connection to the BMG device through the BMG interface.
 
-    cd bmg_module
     cd src
-    python bmg_driver.py
+    python bmg_interface.py
+
+This will print the current BMG LABTECH Remote Control version number if the driver is able to connect successfully to the BMG device.
 
-This will print out the current BMG LABTECH Remote Control Version Number if the driver is able to connect correctly to the BMG device.
+You can also use the driver in other programs. The example Python program below uses the BMG driver to open and close the plate tray, set the temperature, and run an assay named ASSAY_NAME.
 
-You can also use the driver in other programs. See the below python program uses the bmg driver to open and close the plate tray, then sets the temperature and runs an assay named ASSAY_TEST. When connecting, the model must be CLARIOstar even when using a VANTAstar model.
+When instantiating the bmg_device, the model name must be entered as "CLARIOstar" even if you own a BMG VANTAstar device. Also, be sure to replace the protocol_database_path and data_output_directory values with your correct paths.
+
+If you own a BMG device with extended temperature range (10.0 deg C to 60.0 deg C), you will need to specify this when instantiating your BMG device in the code below.
 
     import bmg_interface
 
-    bmg_device = bmg_interface.BmgCom("CLARIOstar")
+    bmg_device = bmg_interface.BmgCom(control_name = "CLARIOstar")
+    # for extended temperature range models, use the instantiation below instead.
+    # bmg_device = bmg_interface.BmgCom(
+    #    control_name = "CLARIOstar",
+    #    extended_temperature_range_model = True,
+    # )
     bmg_device.plate_out()
     bmg_device.plate_in()
     bmg_device.set_temp(30.0)
     bmg_device.run_assay(
         protocol_name = "ASSAY_NAME",
         protocol_database_path = "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Definit" ,
         data_output_directory = "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Data",
-        data_output_file_name = "assya_data.txt",
+        data_output_file_name = "assay_data.txt",
     )
 
-Be sure to replace the protocol_database_path and data_output_directory with your correct paths.  
-
 
 #### Running the REST Node
 
-The REST Node can be started with a command in the format below
-
-    python.exe bmg_rest_node.py --port <your_port> --db_directory_path <(optional) path to bmg db directory containing assay .TCS files> --output_path <(optional) path to directory for saving data output files>
+The REST Node can be started with a command in the format below.
 
+    python bmg_rest_node.py --node_url <(str, optional) address for your LiCONiC MADSci REST Node> --db_directory_path <(str, optional) path to bmg db directory containing assay .TCS files> --data_output_directory_path <(str, optional) path to directory for saving data output files> --extended_temperature_range_model <(bool, optional) True if your BMG device has an extended temperature range of 10.0 deg C to 60.0 deg C, False if your BMG device has a temperature range of 25.0 deg C to 45.0 deg C>
 
---db_directory_path will default to "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Definit" unless specified \
-and -- output_path will default to "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Data" unless specified.
+--node_url will default to "http://127.0.0.1:2000" \
+--db_directory_path will default to "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Definit" \
+--data_output_directory_path will default to "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Data" \
+and --extended_temperature_range_model will default to False.
 
-Example usage with no optional arguments (remember to use 32-bit python): 
 
+Example usage with no optional arguments:
 
-    python.exe bmg_rest_node.py --port 3003
 
+    python bmg_rest_node.py
 
-Example usage with all optional arguments: 
 
+Example usage with all optional arguments:
 
-    python.exe bmg_rest_node.py --port 3003 --db_directory_path "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Definit" --output_path "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Data"
+    python bmg_rest_node.py --node_url "http://127.0.0.1:3003" --db_directory_path "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Definit" --data_output_directory_path "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Data" --extended_temperature_range_model False
 
+### Example Usage in MADSci Workflow YAML file
 
-### Example Usage in WEI Workflow YAML file
+Below is an example of a MADSci YAML workflow file that interacts with the BMG REST Node. Replace "ASSAY_NAME","ASSAY_DATA.txt", and "YOUR/DATA/OUTPUT/PATH/" with the name of the assay you wish to run on the BMG, the desired output data file name, and the path to the directory where the output data will be stored.
 
-Below is an example of a YAML WEI Workflow file that could interact with the BMG REST Node. 
+    name: Test Workflow
 
-    name: BMG Example
-    author: RPL 
-    info: An example WEI workflow to show available BMG actions
-    version: '0.1'
+    metadata:
+        author: Casey Stone
+        info: Example MADSci workflow for BMG actions
+        version: 0.1
 
-    flowdef:
-    - name: open bmg
-      module: bmg
+    steps:
+    - name: open BMG
+      node: bmg
       action: open
 
     - name: close bmg
-      module: bmg
+      node: bmg
       action: close
 
     - name: set temp
-      module: bmg
+      node: bmg
       action: set_temp
       args:
         temp: 30.0
 
     - name: Run bmg
-      module: bmg
+      node: bmg
       action: run_assay
-      args: 
-        assay_name: Assay_name
-        data_output_file_name: assay_data.txt
-
-
-
-
-
-
-
-
-
-
-
-
+      args:
+        assay_name: ASSAY_NAME
+        data_output_file_name: ASSAY_DATA.txt
+        data_output_directory_path: YOUR/DATA/OUTPUT/PATH/
diff --git a/compose.yaml b/compose.yaml