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Merge pull request #2282 from fernweh-3/cobrarrow
Add initCobrarrow, Fix MATLAB Version Compatibility, Update Documentation
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,154 +1,77 @@ | ||
| # Instructions for Using MATLAB API | ||
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| This guide will walk you through setting up and running the MATLAB API. | ||
| ## Step 1: Run `initCobrarrow` | ||
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| ## Step 1: Install Python and Create a Virtual Environment | ||
| 1. In the MATLAB command window, run the following command: | ||
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| If Python is not installed on your system, download and install a compatible version as specified by [MathWorks](https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/python-support.pdf). | ||
| ```matlab | ||
| initCobrarrow() | ||
| ``` | ||
| 2. If you encounter an error while running `initCobrarrow`, it may be because Python is not installed on your system or the installed version is not compatible with MATLAB. | ||
| ### 1.1 Create a Virtual Environment | ||
| - **Solution**: Download and install a compatible version of Python as specified by [MathWorks Python Compatibility](https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/python-support.pdf). | ||
| - For detailed instructions on installing and configuring Python, refer to the following MathWorks documentation: | ||
| - [Configure Your System to Use Python](https://uk.mathworks.com/help/matlab/matlab_external/install-supported-python-implementation.html) | ||
| Ensure you use a Python version compatible with your MATLAB installation. For this example, we'll use Python 3.9. | ||
| ```sh | ||
| # Specify Python version when you create the virtual environment | ||
| python3.9 -m venv python_env | ||
| ``` | ||
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| ### 1.2 Activate the Virtual Environment | ||
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| Activate the virtual environment you just created: | ||
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| - **On Windows:** | ||
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| ```sh | ||
| .\python_env\Scripts\activate | ||
| ``` | ||
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| - **On macOS and Linux:** | ||
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| ```sh | ||
| source python_env/bin/activate | ||
| ``` | ||
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| ## Step 2: Install Dependencies | ||
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| Once the virtual environment is activated, install the required dependencies using the `requirements.txt` file provided with the MATLAB API: | ||
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| ```sh | ||
| pip install -r requirements.txt | ||
| ``` | ||
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| ## Step 3: Set MATLAB to Use the Python Environment | ||
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| To ensure MATLAB uses this Python environment every time it starts: | ||
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| 1. **Locate or Create the MATLAB Startup File**: | ||
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| - On Windows: The `startup.m` file is usually located in the `Documents\MATLAB` folder. | ||
| - On macOS or Linux: The file is also named `startup.m` and is located in the MATLAB user folder, typically `~/Documents/MATLAB`. | ||
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| If the file doesn't exist, create a new `startup.m` file in the appropriate directory. | ||
| 2. **Edit the Startup File**: | ||
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| Add the following lines to the `startup.m` file, replacing the path with the full path to your virtual environment's Python executable: | ||
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| ```matlab | ||
| % Set the Python environment for MATLAB | ||
| pyenv('Version', fullfile('path_to_your_virtual_env', 'python')); | ||
| ``` | ||
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| For example: | ||
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| ```matlab | ||
| pyenv('Version', fullfile('C:\COBRArrow\client\MATLAB_API\python_env\Scripts\python.exe')); | ||
| ``` | ||
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| Or on macOS/Linux: | ||
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| ```matlab | ||
| pyenv('Version', fullfile('~/Document/COBRArrow/client/MATLAB_API/python_env/bin/python')); | ||
| ``` | ||
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| 3. **Save and Restart MATLAB**: | ||
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| Save the `startup.m` file. When you restart MATLAB, it will automatically use the specified Python environment. | ||
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| ## Step 4: MATLAB API is ready to use. | ||
| ## Step 2: MATLAB API is ready to use. | ||
| ### Example Use of Calling MATLAB APIs | ||
| Refer to MATLAB script `testMatlab.m` that uses the MATLAB API to perform some operations. | ||
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| ```matlab | ||
| % Example MATLAB script to use the MATLAB API | ||
| % load the model | ||
| recon3D_model = load('../models/Recon3D_301.mat').Recon3D; | ||
| model = recon3D_model; | ||
| schemaName = 'Recon3D'; | ||
| % Load the model | ||
| file = load('path/to/your_model.mat'); | ||
| model = file.yourModel; | ||
| schemaName = 'yourModelName'; | ||
| % Create an instance of the COBRArrow class | ||
| host = 'localhost'; | ||
| port = 443; | ||
| host = 'cobrarrowServerHost'; | ||
| port = cobrarrowServerPort; % port is optional if you use a domain name for host | ||
| client = COBRArrow(host, port); | ||
| % Login | ||
| client = client.login('johndoe', '123456'); | ||
| client = client.login('username', 'password'); | ||
| % Send the model to the server | ||
| client.sendModel(model, schemaName); | ||
| % Persist the model in DuckDB | ||
| client.persistModel(schemaName, true); | ||
| % Read the model back for general purposes | ||
| fetchedModel = client.fetchModel(schemaName); | ||
| disp('Fetched Model:'); | ||
| disp(fetchedModel); | ||
| % For example, fetchedModel can be used to do simulations using COBRA Toolbox | ||
| initCobraToolbox; | ||
| solution = optimizeCbModel(fetchedModel); | ||
| disp('solution:'); | ||
| disp(solution); | ||
| % Read the model back for FBA analysis | ||
| FBAmodel = client.fetchModelForFBAAnalysis(schemaName); | ||
| disp('FBA Model:'); | ||
| disp(FBAmodel); | ||
| % Set solver for using remote optimization service | ||
| arrowSolver = COBRArrowSolver('GLPK'); | ||
| arrowSolver.setParameter('tol', 1e-9); | ||
| % Perform optimization | ||
| resultStruct = client.optimizeModel(schemaName,arrowSolver); | ||
| % Display results | ||
| disp('Optimization Results:'); | ||
| disp(resultStruct); | ||
| % Perform optimization | ||
| resultStruct = client.optimizeModel(schemaName, arrowSolver); | ||
| % Example of sending an individual field | ||
| fieldName = 'rxns'; | ||
| fieldData = model.rxns; | ||
| % Example of sending flux value(an individual field) for animation | ||
| fieldName = 'flux'; | ||
| fieldData = resultStruct.flux; | ||
| client.sendField(schemaName, fieldName, fieldData); | ||
| % Read the field back | ||
| readData = client.readField(schemaName, fieldName); | ||
| disp('Read Field Data:'); | ||
| disp(readData); | ||
| readData = client.fetchField(schemaName, fieldName); | ||
| % List all flight information in a schema on server | ||
| % List all flight information in a schema on the server | ||
| flightsList = client.listAllFlights(schemaName); | ||
| disp('Flights List in schema:'); | ||
| disp(flightsList); | ||
| % List all flight information on server | ||
| % List all flight information on the server | ||
| flightsList = client.listAllFlights(); | ||
| disp('All Flights List:'); | ||
| disp(flightsList); | ||
| % Get all unique identifier of the flights in a schema | ||
| % Get all unique identifiers of the flights in a schema | ||
| descriptors = client.getAllDescriptors(schemaName); | ||
| disp('Descriptors:'); | ||
| disp(descriptors); | ||
| ``` |
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| function initCobrarrow() | ||
| % Display MATLAB version | ||
| ver = version; | ||
| fprintf('MATLAB Version: %s\n', ver); | ||
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| % Check if Python is installed and display details | ||
| pyEnvInfo = pyenv; | ||
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| if isempty(pyEnvInfo.Executable) | ||
| showInstruction(); | ||
| else | ||
| fprintf('Python is installed. Version: '); | ||
| disp(pyEnvInfo.Version); | ||
| fprintf('Python Executable: \n'); | ||
| disp(pyEnvInfo.Executable); | ||
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| % test Python version compatibility | ||
| try | ||
| py.math.sqrt(16); | ||
| catch ME | ||
| showInstruction(); | ||
| rethrow(ME); | ||
| end | ||
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| % Get the current directory where the MATLAB script is located | ||
| currentFile = mfilename('fullpath'); | ||
| currentDir = fileparts(currentFile); | ||
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| % Construct the full path to the requirements.txt file | ||
| requirementsPath = fullfile(currentDir, 'requirements.txt'); | ||
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| % Use python -m pip install to ensure pip is invoked correctly | ||
| cmd = sprintf('"%s" -m pip install -r "%s"', pyEnvInfo.Executable, requirementsPath); | ||
| status = system(cmd); | ||
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| if status == 0 | ||
| % test if pyarrow package works | ||
| py.pyarrow.table(py.dict(pyargs('column1', {1, 2, 3, 4}))); | ||
| disp('Python package pyarrow installed successfully.'); | ||
| else | ||
| error('Failed to install packages.'); | ||
| end | ||
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| fprintf("\nNow you can use the COBRArrow API in MATLAB.\n\n"); | ||
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| end | ||
| end | ||
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| function showInstruction() | ||
| versionLink = 'https://uk.mathworks.com/support/requirements/python-compatibility.html?s_tid=srchtitle_site_search_1_python%20compatibility'; | ||
| versionLabel = 'Versions of Python Compatible with MATLAB'; | ||
| configLink = 'https://uk.mathworks.com/help/matlab/matlab_external/install-supported-python-implementation.html'; | ||
| configLabel = 'Configure Your System to Use Python'; | ||
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| fprintf('Python is not installed or not set up in MATLAB.\n'); | ||
| fprintf('Please install the correct version of Python according to '); | ||
| fprintf('<a href="%s">%s</a>. \n', versionLink, versionLabel); | ||
| fprintf('Please refer to <a href="%s">%s</a> to config Python in MATLAB. \n', configLink,configLabel); | ||
| end |