Python Package, Code Refactoring and Documentation #46
Conversation
WalkthroughThis update restructures the project by modularizing code into the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant WebUI (Flask)
participant ConnectionManager
participant Device (USB/WiFi/BLE)
participant LSL/CSV
User->>WebUI (Flask): Connect/Scan/Record/Launch App
WebUI (Flask)->>ConnectionManager: connect_device(protocol, params)
ConnectionManager->>Device: Establish connection (USB/WiFi/BLE)
Device-->>ConnectionManager: Data packets
ConnectionManager->>LSL/CSV: Stream data, optionally record
User->>WebUI (Flask): Stop/Disconnect/Stop Recording
WebUI (Flask)->>ConnectionManager: cleanup()
ConnectionManager->>Device: Close connection
ConnectionManager->>LSL/CSV: Stop streams/recording
Possibly related PRs
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Actionable comments posted: 18
🧹 Nitpick comments (20)
chordspy/gui.py (1)
125-131: PEP-8 spacing & tightermain()interfaceFlake8 rightly flags the missing blank lines.
Also,plot_lsl_data()returns theappobject but the return value is ignored; relying on a global adds coupling.@@ + + def main(): app = plot_lsl_data() # capture the returned QApplication - if inlet: - sys.exit(app.exec_()) + if inlet: + sys.exit(app.exec_()) if __name__ == "__main__": main()Two blank lines before
main()and before the guard satisfy E302/E305 and the explicitappvariable reduces hidden globals.chordspy/csvplotter.py (1)
102-108: Minor PEP-8 spacing deviationInsert two blank lines before
main()and before theif __name__ …guard to silence E302/E305.@@ + + def main(): root = tk.Tk() # Create the main Tkinter root window CSVPlotterApp(root) # Create an instance of the CSVPlotterApp class root.mainloop() # Start the Tkinter main loop + if __name__ == "__main__": main()chordspy/eog.py (1)
186-194: Consistent spacing around newmain()Same PEP-8 blank-line issue as elsewhere; quick fix:
@@ + + def main(): app = QApplication(sys.argv) window = EOGMonitor() print("Note: There will be a 2s calibration delay before peak detection starts.") window.show() sys.exit(app.exec_()) + if __name__ == "__main__": main()chordspy/ffteeg.py (1)
421-428: Good refactoring for modularity, but fix PEP8 formatting issues.The extraction of main execution logic into a dedicated
main()function improves code modularity and follows the consistent pattern applied across the project. However, the static analysis correctly identifies PEP8 formatting violations.Apply this diff to fix the formatting issues:
- + def main(): app = QApplication(sys.argv) window = EEGMonitor() window.show() sys.exit(app.exec_()) + if __name__ == "__main__": main()chordspy/emgenvelope.py (1)
139-146: Consistent refactoring pattern, but address formatting issues.The main function extraction follows the same beneficial pattern as other GUI modules in the project, improving modularity and consistency.
Apply this diff to fix PEP8 formatting:
self.close() - + def main(): app = QApplication(sys.argv) window = EMGMonitor() window.show() sys.exit(app.exec_()) + if __name__ == "__main__": main()chordspy/heartbeat_ecg.py (1)
163-170: Maintain consistency with other modules, fix formatting.The refactoring maintains consistency with the other GUI modules and improves code organization.
Apply this diff to address PEP8 formatting:
self.r_peak_curve.setData(r_peak_times, r_peak_values) # Plot R-peaks as red dots + def main(): app = QApplication(sys.argv) window = ECGMonitor() window.show() sys.exit(app.exec_()) + if __name__ == "__main__": main()chordspy/__init__.py (1)
1-2: Add__all__to clarify intended public APIThe static analysis warnings about unused imports are false positives - these imports are intended to expose the key components (
mainandConnection) at the package level for external use. Consider adding an__all__declaration to make the intended public API explicit:+__all__ = ['main', 'Connection'] + from chordspy.app import main from chordspy.connection import ConnectionThis will clarify that these imports are intentional for the package's public interface and may resolve the static analysis warnings.
chordspy/static/script.js (1)
951-968: Consider consolidating initialization callsThe DOMContentLoaded handler has several initialization calls that could be organized better:
document.addEventListener('DOMContentLoaded', () => { - initializeApplication(); - checkStreamStatus(); - setInterval(checkStreamStatus, 1000); - startTimestampUpdater(); + // Initialize core application functionality + initializeApplication(); + startTimestampUpdater(); + + // Set up periodic status checking + checkStreamStatus(); + setInterval(checkStreamStatus, 1000); // Error handling window.onerror = function(message, source, lineno, colno, error) {This groups related functionality and removes the duplicate
checkStreamStatus()call (sinceinitializeApplication()likely calls it viastartAppStatusChecker()).README.md (1)
3-3: Fix grammatical issues for better clarityAddress the following grammatical improvements flagged by LanguageTool:
-Chords- Python is an open-source bag of tools designed to interface with Micro-controller development boards running [Chords Arduino Firmware](https://github.com/upsidedownlabs/Chords-Arduino-Firmware). Use Upside Down Labs bio-potential amplifiers to read data, visualize it, record data in CSV Files, and stream it via Lab Streaming Layer. +Chords-Python is an open-source bag of tools designed to interface with microcontroller development boards running [Chords Arduino Firmware](https://github.com/upsidedownlabs/Chords-Arduino-Firmware). Use Upside-Down Labs' bio-potential amplifiers to read data, visualize it, record data in CSV files, and stream it via the Lab Streaming Layer.Changes made:
- Fixed spacing in "Chords-Python"
- Added possessive apostrophe for "Upside-Down Labs'"
- Added hyphen to "Upside-Down"
- Added "the" before "Lab Streaming Layer"
- Capitalization consistency for "CSV files"
.github/workflows/release.yaml (1)
133-133: Add newline at end of file.YAML files should end with a newline character for proper formatting.
Add a newline character after the last line.
chordspy/chords_serial.py (3)
108-108: Remove unused variable assignment.The
sampling_ratevariable is assigned but never used.- sampling_rate = self.supported_boards[self.board]["sampling_rate"]If this value is needed for future use, consider storing it as an instance attribute or using it in logging.
16-17: Add blank line before class definition.PEP 8 requires two blank lines before class definitions.
import threading + class Chords_USB:
276-277: Add blank line after class definition.PEP 8 requires two blank lines after class definitions.
last_ten_minute_time = time.time() + if __name__ == "__main__":chordspy/app.py (2)
59-60: Remove unused exception variable.The exception variable
eis not used in the except block.- except Exception as e: + except Exception: return jsonify({'status': 'error', 'message': 'Logging failed'}), 500
200-200: Add missing whitespace after comma.- return jsonify({'status': 'error', 'message': f'{module_name} is already running','code': 'ALREADY_RUNNING'}), 400 + return jsonify({'status': 'error', 'message': f'{module_name} is already running', 'code': 'ALREADY_RUNNING'}), 400chordspy/chords_ble.py (2)
107-111: Remove or use the extracted channel data.The
channelsvariable is extracted but never used. If this is for debugging, consider adding a comment or removing it.- # Extract channel data (2 bytes per channel, big-endian, signed) - channels = [int.from_bytes(sample_data[i:i+2], byteorder='big', signed=True) - for i in range(1, len(sample_data), 2)] + # Extract channel data (2 bytes per channel, big-endian, signed) + # channels = [int.from_bytes(sample_data[i:i+2], byteorder='big', signed=True) + # for i in range(1, len(sample_data), 2)] + # TODO: Process channel data when needed
28-28: Add spaces before inline comment.- CONTROL_CHAR_UUID = "0000ff01-0000-1000-8000-00805f9b34fb" # UUID for control characteristic + CONTROL_CHAR_UUID = "0000ff01-0000-1000-8000-00805f9b34fb" # UUID for control characteristicchordspy/connection.py (3)
2-2: Fix typo in documentation header.Remove the trailing dash in the documentation header.
-CHORDS Data Connection- +CHORDS Data Connection
628-628: Add blank lines for PEP 8 compliance.Add two blank lines before the function definition.
self.cleanup() + def main():
680-681: Add blank line for module-level code separation.Add a blank line after the function definition.
if __name__ == '__main__': main() +
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⛔ Files ignored due to path filters (14)
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📒 Files selected for processing (27)
.github/workflows/release.yaml(1 hunks)MANIFEST.in(1 hunks)README.md(1 hunks)app.py(0 hunks)app_requirements.txt(0 hunks)chords_requirements.txt(0 hunks)chords_serial.py(0 hunks)chordspy/__init__.py(1 hunks)chordspy/app.py(1 hunks)chordspy/beetle.py(1 hunks)chordspy/chords_ble.py(10 hunks)chordspy/chords_serial.py(1 hunks)chordspy/chords_wifi.py(6 hunks)chordspy/connection.py(1 hunks)chordspy/csvplotter.py(1 hunks)chordspy/emgenvelope.py(1 hunks)chordspy/eog.py(1 hunks)chordspy/ffteeg.py(1 hunks)chordspy/game.py(1 hunks)chordspy/gui.py(1 hunks)chordspy/heartbeat_ecg.py(1 hunks)chordspy/keystroke.py(1 hunks)chordspy/static/script.js(3 hunks)chordspy/templates/index.html(5 hunks)connection.py(0 hunks)pyproject.toml(1 hunks)requirements.txt(0 hunks)
💤 Files with no reviewable changes (6)
- requirements.txt
- chords_requirements.txt
- app_requirements.txt
- chords_serial.py
- app.py
- connection.py
🧰 Additional context used
🧬 Code Graph Analysis (6)
chordspy/__init__.py (2)
chordspy/app.py (1)
main(357-366)chordspy/connection.py (2)
main(628-678)Connection(36-626)
chordspy/emgenvelope.py (3)
chordspy/eog.py (1)
main(186-191)chordspy/heartbeat_ecg.py (1)
main(163-167)chordspy/ffteeg.py (1)
main(421-425)
chordspy/chords_serial.py (5)
chordspy/static/script.js (10)
data(177-177)data(194-194)data(573-573)data(692-692)response(34-34)response(129-133)response(171-171)response(191-191)response(563-567)response(691-691)chordspy/test/new_parser.py (7)
connect_hardware(58-122)detect_hardware(125-133)send_command(50-56)cleanup(275-310)start_timer(192-198)log_one_second_data(201-206)log_ten_minute_data(209-219)chordspy/chords_ble.py (1)
cleanup(204-213)chordspy/chords_wifi.py (1)
cleanup(181-193)chordspy/connection.py (1)
cleanup(558-620)
chordspy/connection.py (3)
chordspy/chords_serial.py (5)
Chords_USB(17-275)read_data(161-200)detect_hardware(121-141)send_command(143-159)cleanup(222-231)chordspy/chords_wifi.py (3)
Chords_WIFI(13-199)connect(61-75)cleanup(181-193)chordspy/chords_ble.py (6)
Chords_BLE(13-238)scan_devices(55-69)notification_handler(113-129)connect(215-231)cleanup(204-213)stop(233-238)
chordspy/app.py (5)
chordspy/connection.py (8)
Connection(36-626)cleanup(558-620)connect_usb(524-556)connect_wifi(460-522)connect_ble(399-458)start_csv_recording(140-171)stop_csv_recording(173-195)main(628-678)chordspy/static/script.js (6)
config(40-40)data(177-177)data(194-194)data(573-573)data(692-692)filename(776-776)chordspy/chords_ble.py (1)
cleanup(204-213)chordspy/chords_wifi.py (1)
cleanup(181-193)chordspy/chords_serial.py (1)
cleanup(222-231)
chordspy/chords_wifi.py (3)
chordspy/chords_ble.py (1)
cleanup(204-213)chordspy/chords_serial.py (1)
cleanup(222-231)chordspy/connection.py (1)
cleanup(558-620)
🪛 Flake8 (7.2.0)
chordspy/__init__.py
[error] 1-1: 'chordspy.app.main' imported but unused
(F401)
[error] 2-2: 'chordspy.connection.Connection' imported but unused
(F401)
chordspy/eog.py
[error] 186-186: expected 2 blank lines, found 1
(E302)
[error] 193-193: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/heartbeat_ecg.py
[error] 163-163: expected 2 blank lines, found 1
(E302)
[error] 169-169: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/csvplotter.py
[error] 102-102: expected 2 blank lines, found 1
(E302)
[error] 107-107: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/gui.py
[error] 125-125: expected 2 blank lines, found 1
(E302)
[error] 130-130: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/emgenvelope.py
[error] 139-139: expected 2 blank lines, found 1
(E302)
[error] 145-145: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/ffteeg.py
[error] 421-421: expected 2 blank lines, found 1
(E302)
[error] 427-427: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/chords_serial.py
[error] 17-17: expected 2 blank lines, found 1
(E302)
[error] 70-70: at least two spaces before inline comment
(E261)
[error] 108-108: local variable 'sampling_rate' is assigned to but never used
(F841)
[error] 256-256: global missing_samples is unused: name is never assigned in scope
(F824)
[error] 265-265: global supported_boards is unused: name is never assigned in scope
(F824)
[error] 265-265: global board is unused: name is never assigned in scope
(F824)
[error] 277-277: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/chords_ble.py
[error] 28-28: at least two spaces before inline comment
(E261)
[error] 108-108: local variable 'channels' is assigned to but never used
(F841)
[error] 109-109: continuation line under-indented for visual indent
(E128)
[error] 240-240: expected 2 blank lines, found 1
(E302)
chordspy/connection.py
[error] 36-36: expected 2 blank lines, found 1
(E302)
[error] 264-264: local variable 'estimated_rate' is assigned to but never used
(F841)
[error] 264-264: at least two spaces before inline comment
(E261)
[error] 428-428: continuation line under-indented for visual indent
(E128)
[error] 628-628: expected 2 blank lines, found 1
(E302)
[error] 680-680: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/app.py
[error] 25-25: redefinition of unused 'logging' from line 17
(F811)
[error] 41-41: expected 2 blank lines, found 1
(E302)
[error] 59-59: local variable 'e' is assigned to but never used
(F841)
[error] 63-63: expected 2 blank lines, found 1
(E302)
[error] 81-81: expected 2 blank lines, found 1
(E302)
[error] 87-87: expected 2 blank lines, found 1
(E302)
[error] 95-95: at least two spaces before inline comment
(E261)
[error] 110-110: expected 2 blank lines, found 1
(E302)
[error] 122-122: continuation line under-indented for visual indent
(E128)
[error] 129-129: expected 2 blank lines, found 1
(E302)
[error] 140-140: expected 2 blank lines, found 1
(E302)
[error] 152-152: expected 2 blank lines, found 1
(E302)
[error] 166-166: expected 2 blank lines, found 1
(E302)
[error] 182-182: expected 2 blank lines, found 1
(E302)
[error] 200-200: missing whitespace after ','
(E231)
[error] 216-216: expected 2 blank lines, found 1
(E302)
[error] 234-234: expected 2 blank lines, found 1
(E302)
[error] 293-293: expected 2 blank lines, found 1
(E302)
[error] 300-300: global connection_manager is unused: name is never assigned in scope
(F824)
[error] 309-309: expected 2 blank lines, found 1
(E302)
[error] 316-316: global connection_manager is unused: name is never assigned in scope
(F824)
[error] 337-337: expected 2 blank lines, found 1
(E302)
[error] 344-344: global connection_manager is unused: name is never assigned in scope
(F824)
[error] 357-357: expected 2 blank lines, found 1
(E302)
[error] 368-368: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/chords_wifi.py
[error] 11-11: 'scipy.signal.butter' imported but unused
(F401)
[error] 11-11: 'scipy.signal.filtfilt' imported but unused
(F401)
[error] 13-13: expected 2 blank lines, found 1
(E302)
[error] 126-126: local variable 'sps' is assigned to but never used
(F841)
[error] 127-127: local variable 'fps' is assigned to but never used
(F841)
[error] 128-128: local variable 'bps' is assigned to but never used
(F841)
[error] 201-201: expected 2 blank lines after class or function definition, found 1
(E305)
🪛 Ruff (0.11.9)
chordspy/__init__.py
1-1: chordspy.app.main imported but unused; consider removing, adding to __all__, or using a redundant alias
(F401)
2-2: chordspy.connection.Connection imported but unused; consider removing, adding to __all__, or using a redundant alias
(F401)
chordspy/chords_serial.py
108-108: Local variable sampling_rate is assigned to but never used
Remove assignment to unused variable sampling_rate
(F841)
chordspy/chords_ble.py
108-108: Local variable channels is assigned to but never used
Remove assignment to unused variable channels
(F841)
chordspy/connection.py
161-161: Use a context manager for opening files
(SIM115)
264-264: Local variable estimated_rate is assigned to but never used
Remove assignment to unused variable estimated_rate
(F841)
668-669: Use a single if statement instead of nested if statements
(SIM102)
chordspy/app.py
25-25: Redefinition of unused logging from line 17
Remove definition: logging
(F811)
59-59: Local variable e is assigned to but never used
Remove assignment to unused variable e
(F841)
chordspy/chords_wifi.py
11-11: scipy.signal.butter imported but unused
Remove unused import
(F401)
11-11: scipy.signal.filtfilt imported but unused
Remove unused import
(F401)
126-126: Local variable sps is assigned to but never used
Remove assignment to unused variable sps
(F841)
127-127: Local variable fps is assigned to but never used
Remove assignment to unused variable fps
(F841)
128-128: Local variable bps is assigned to but never used
Remove assignment to unused variable bps
(F841)
🪛 LanguageTool
README.md
[uncategorized] ~3-~3: The adjective “Upside-Down” is spelled with a hyphen.
Context: ...edownlabs/Chords-Arduino-Firmware). Use Upside Down Labs bio-potential amplifiers to read d...
(UPSIDE_DOWN)
[uncategorized] ~3-~3: It seems likely that a singular genitive (’s) apostrophe is missing.
Context: ...ords-Arduino-Firmware). Use Upside Down Labs bio-potential amplifiers to read data, ...
(AI_HYDRA_LEO_APOSTROPHE_S_XS)
[uncategorized] ~3-~3: You might be missing the article “the” here.
Context: ...rd data in CSV Files, and stream it via Lab Streaming Layer. > [!NOTE] > **Fir...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
🪛 actionlint (1.7.7)
.github/workflows/release.yaml
128-128: the runner of "softprops/action-gh-release@v1" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
130-130: property "details" is not defined in object type {pypi_publish: {outputs: {}; result: string}; setup_and_build: {outputs: {}; result: string}}
(expression)
🪛 YAMLlint (1.37.1)
.github/workflows/release.yaml
[error] 133-133: no new line character at the end of file
(new-line-at-end-of-file)
🪛 Pylint (3.3.7)
chordspy/chords_serial.py
[refactor] 17-17: Too many instance attributes (8/7)
(R0902)
[error] 258-258: Undefined variable 'missing_samples'
(E0602)
[error] 269-269: Undefined variable 'supported_boards'
(E0602)
[error] 269-269: Undefined variable 'board'
(E0602)
chordspy/connection.py
[refactor] 36-36: Too many instance attributes (27/7)
(R0902)
[refactor] 161-161: Consider using 'with' for resource-allocating operations
(R1732)
[error] 290-290: Instance of 'Chords_BLE' has no 'data_available' member
(E1101)
[error] 295-295: Instance of 'Chords_BLE' has no 'get_latest_sample' member
(E1101)
[refactor] 287-319: Too many nested blocks (6/5)
(R1702)
[error] 331-331: Instance of 'Chords_WIFI' has no 'data_available' member
(E1101)
[error] 336-336: Instance of 'Chords_WIFI' has no 'get_latest_sample' member
(E1101)
[refactor] 328-357: Too many nested blocks (6/5)
(R1702)
[refactor] 366-397: Too many nested blocks (6/5)
(R1702)
[refactor] 558-558: Too many branches (15/12)
(R0912)
chordspy/app.py
[refactor] 207-207: Consider using 'with' for resource-allocating operations
(R1732)
[refactor] 226-230: Unnecessary "else" after "return", remove the "else" and de-indent the code inside it
(R1705)
[error] 267-267: Assigning result of a function call, where the function has no return
(E1111)
[error] 278-278: Possibly using variable 'success' before assignment
(E0606)
chordspy/chords_wifi.py
[refactor] 13-13: Too many instance attributes (14/7)
(R0902)
[refactor] 34-34: Too many arguments (6/5)
(R0913)
[refactor] 34-34: Too many positional arguments (6/5)
(R0917)
[refactor] 88-88: Too many branches (15/12)
(R0912)
[refactor] 88-88: Too many statements (58/50)
(R0915)
🪛 ast-grep (0.38.1)
chordspy/app.py
[warning] 365-365: Detected Flask app with debug=True. Do not deploy to production with this flag enabled as it will leak sensitive information. Instead, consider using Flask configuration variables or setting 'debug' using system environment variables.
Context: app.run(debug=True, use_reloader=False, host='0.0.0.0', port=5000)
Note: [CWE-489] Active Debug Code. [REFERENCES]
- https://labs.detectify.com/2015/10/02/how-patreon-got-hacked-publicly-exposed-werkzeug-debugger/
(debug-enabled-python)
🔇 Additional comments (12)
pyproject.toml (2)
32-33: Console script entry point is well-defined.The console script configuration properly maps the
chordspycommand to the main application entry point.
12-31: Verify dependency security using pip-audit with correct invocationThe Poetry migration is solid—next, ensure all fixed versions are free of known vulnerabilities. Since
pip-auditmay install to~/.local/bin(outside your PATH), invoke it like this:# Create a temporary requirements file cat > temp_requirements.txt << EOF numpy==2.1.3 pylsl==1.16.2 pyserial==3.5 bleak==0.22.3 pyqtgraph==0.13.7 PyQt5==5.15.11 keyboard==0.13.5 scipy==1.14.1 pygame==2.6.1 neurokit2==0.2.10 plotly==5.24.1 pandas==2.2.3 tk==0.1.0 PyAutoGUI==0.9.54 Flask==3.1.1 psutil==6.1.1 websocket-client==1.8.0 PyYAML==6.0.2 EOF # Install pip-audit if needed pip install --user pip-audit # Run vulnerability scan via module to avoid PATH issues python3 -m pip_audit --requirement temp_requirements.txt # Cleanup rm temp_requirements.txt• Ensure the scan completes without errors.
• Review any reported CVEs and update versions as necessary.
• Once all vulnerabilities are addressed, merge the Poetry changes.MANIFEST.in (1)
1-5: Well-structured manifest for Flask web applicationThe MANIFEST.in file correctly includes all necessary resources for the Flask web interface:
- Essential documentation files (
requirements.txt,README.md)- Web application assets (
templates,static)- Configuration files (
config)This ensures the package will work correctly when installed via pip.
chordspy/static/script.js (2)
115-118: Clean implementation of launch button functionalityThe inline
onclickapproach works well for the dynamic button generation. ThelaunchAppfunction properly handles different response scenarios including already running apps.
127-149: Robust error handling in launchApp functionGood implementation with:
- Proper async/await usage
- Specific handling of ALREADY_RUNNING status
- Comprehensive error catching and logging
- Clear user feedback through alerts
README.md (2)
16-32: Excellent simplification of installation processThe new installation instructions are much clearer and more user-friendly compared to the previous multi-step process. The virtual environment setup with platform-specific activation commands is particularly helpful.
35-38: Updated usage reflects new package structureThe change from
python app.pytochordspycommand correctly reflects the new console script entry point defined in the package configuration.chordspy/templates/index.html (2)
3-5: Excellent documentation enhancementThe added HTML comments throughout the template significantly improve code maintainability by clearly explaining:
- The purpose of each major section
- UI component functionality
- Dark mode configuration
- Interactive element behavior
This documentation will be valuable for future developers working on the frontend.
177-181: Clear Tailwind configuration documentationThe comment explaining the class-based dark mode configuration is helpful for understanding the styling approach used throughout the application.
chordspy/chords_ble.py (1)
1-52: Excellent documentation improvements!The added docstrings and comments significantly improve code readability and maintainability.
chordspy/chords_wifi.py (1)
1-43: Well-documented class and methods!The added docstrings provide excellent clarity on the WiFi client's functionality and usage.
chordspy/connection.py (1)
161-161: Current file handling approach is appropriate.The file needs to remain open across multiple method calls for continuous recording, so a context manager is not suitable here. The existing error handling and cleanup in
stop_csv_recording()ensures proper resource management.
PayalLakra
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Actionable comments posted: 2
♻️ Duplicate comments (3)
chordspy/app.py (2)
365-365: Disable debug mode for production deployment.Running Flask with
debug=Trueis a security risk as it exposes sensitive information and enables the interactive debugger.Consider using environment variables to control debug mode:
- app.run(debug=True, use_reloader=False, host='0.0.0.0', port=5000) + debug_mode = os.environ.get('FLASK_DEBUG', 'False').lower() == 'true' + app.run(debug=debug_mode, use_reloader=False, host='0.0.0.0', port=5000)
258-284: Fix connection return value handling in run_connection.The connection methods are expected to return boolean values, but based on the static analysis and past review comments, these methods don't consistently return success/failure status. This causes issues where
successmay beNoneeven when connections succeed.For WiFi connections specifically, the method doesn't return a value, so
successbecomesNone:elif protocol == 'wifi': - success = connection_manager.connect_wifi() + connection_manager.connect_wifi() + success = True # WiFi connection starts background threadsThis ensures the success variable is properly set for all connection types.
chordspy/chords_wifi.py (1)
125-128: Log or use the calculated rates.The sample rate (sps), frame rate (fps), and byte rate (bps) are calculated but never used or logged, making this computation wasteful.
# Calculate samples, packets, and bytes per second sps = self.calculate_rate(self.sample_size, elapsed_time) fps = self.calculate_rate(self.packet_size, elapsed_time) bps = self.calculate_rate(self.data_size, elapsed_time) + + # Log the rates for monitoring + print(f"Rates - Samples: {sps:.1f}/s, Packets: {fps:.1f}/s, Bytes: {bps:.1f}/s")Alternatively, if these rates aren't needed, consider removing the calculations entirely.
🧹 Nitpick comments (6)
.github/workflows/release.yaml (1)
133-133: Add missing newline at end of file.The file is missing a newline character at the end, which violates YAML formatting standards.
generate_release_notes: true +chordspy/app.py (1)
58-58: Remove unused exception variable.The exception variable
eis assigned but never used in the except block.except Exception as e: - return jsonify({'status': 'error', 'message': 'Logging failed'}), 500 + return jsonify({'status': 'error', 'message': 'Logging failed'}), 500Or utilize the exception for better error reporting:
except Exception as e: - return jsonify({'status': 'error', 'message': 'Logging failed'}), 500 + return jsonify({'status': 'error', 'message': f'Logging failed: {str(e)}'}), 500chordspy/connection.py (4)
44-44: Fix typo in docstring.There's a typo "monitorin" that should be "monitoring".
- - Sample validation and rate monitorin + - Sample validation and rate monitoring
36-36: Add missing blank lines before class definition.Python PEP 8 requires 2 blank lines before class definitions.
+ class Connection:
628-628: Add missing blank lines before function definition.Python PEP 8 requires 2 blank lines before top-level function definitions.
+ def main():
680-681: Add missing blank lines after function definition.Python PEP 8 requires 2 blank lines after class or function definitions at module level.
if __name__ == '__main__': main() + +
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.github/workflows/release.yaml(1 hunks)chordspy/app.py(1 hunks)chordspy/chords_wifi.py(6 hunks)chordspy/connection.py(1 hunks)
🧰 Additional context used
🧬 Code Graph Analysis (1)
chordspy/connection.py (3)
chordspy/chords_serial.py (5)
Chords_USB(17-275)read_data(161-200)detect_hardware(121-141)send_command(143-159)cleanup(222-231)chordspy/chords_wifi.py (3)
Chords_WIFI(12-198)connect(60-74)cleanup(180-192)chordspy/chords_ble.py (6)
Chords_BLE(13-238)scan_devices(55-69)notification_handler(113-129)connect(215-231)cleanup(204-213)stop(233-238)
🪛 ast-grep (0.38.1)
chordspy/app.py
[warning] 364-364: Detected Flask app with debug=True. Do not deploy to production with this flag enabled as it will leak sensitive information. Instead, consider using Flask configuration variables or setting 'debug' using system environment variables.
Context: app.run(debug=True, use_reloader=False, host='0.0.0.0', port=5000)
Note: [CWE-489] Active Debug Code. [REFERENCES]
- https://labs.detectify.com/2015/10/02/how-patreon-got-hacked-publicly-exposed-werkzeug-debugger/
(debug-enabled-python)
🪛 Ruff (0.11.9)
chordspy/app.py
58-58: Local variable e is assigned to but never used
Remove assignment to unused variable e
(F841)
chordspy/connection.py
161-161: Use a context manager for opening files
(SIM115)
264-264: Local variable estimated_rate is assigned to but never used
Remove assignment to unused variable estimated_rate
(F841)
668-669: Use a single if statement instead of nested if statements
(SIM102)
chordspy/chords_wifi.py
125-125: Local variable sps is assigned to but never used
Remove assignment to unused variable sps
(F841)
126-126: Local variable fps is assigned to but never used
Remove assignment to unused variable fps
(F841)
127-127: Local variable bps is assigned to but never used
Remove assignment to unused variable bps
(F841)
🪛 Flake8 (7.2.0)
chordspy/app.py
[error] 40-40: expected 2 blank lines, found 1
(E302)
[error] 58-58: local variable 'e' is assigned to but never used
(F841)
[error] 62-62: expected 2 blank lines, found 1
(E302)
[error] 80-80: expected 2 blank lines, found 1
(E302)
[error] 86-86: expected 2 blank lines, found 1
(E302)
[error] 94-94: at least two spaces before inline comment
(E261)
[error] 109-109: expected 2 blank lines, found 1
(E302)
[error] 121-121: continuation line under-indented for visual indent
(E128)
[error] 128-128: expected 2 blank lines, found 1
(E302)
[error] 139-139: expected 2 blank lines, found 1
(E302)
[error] 151-151: expected 2 blank lines, found 1
(E302)
[error] 165-165: expected 2 blank lines, found 1
(E302)
[error] 181-181: expected 2 blank lines, found 1
(E302)
[error] 199-199: missing whitespace after ','
(E231)
[error] 215-215: expected 2 blank lines, found 1
(E302)
[error] 233-233: expected 2 blank lines, found 1
(E302)
[error] 292-292: expected 2 blank lines, found 1
(E302)
[error] 299-299: global connection_manager is unused: name is never assigned in scope
(F824)
[error] 308-308: expected 2 blank lines, found 1
(E302)
[error] 315-315: global connection_manager is unused: name is never assigned in scope
(F824)
[error] 336-336: expected 2 blank lines, found 1
(E302)
[error] 343-343: global connection_manager is unused: name is never assigned in scope
(F824)
[error] 356-356: expected 2 blank lines, found 1
(E302)
[error] 367-367: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/connection.py
[error] 36-36: expected 2 blank lines, found 1
(E302)
[error] 264-264: local variable 'estimated_rate' is assigned to but never used
(F841)
[error] 264-264: at least two spaces before inline comment
(E261)
[error] 428-428: continuation line under-indented for visual indent
(E128)
[error] 628-628: expected 2 blank lines, found 1
(E302)
[error] 680-680: expected 2 blank lines after class or function definition, found 1
(E305)
chordspy/chords_wifi.py
[error] 12-12: expected 2 blank lines, found 1
(E302)
[error] 125-125: local variable 'sps' is assigned to but never used
(F841)
[error] 126-126: local variable 'fps' is assigned to but never used
(F841)
[error] 127-127: local variable 'bps' is assigned to but never used
(F841)
[error] 200-200: expected 2 blank lines after class or function definition, found 1
(E305)
🪛 Pylint (3.3.7)
chordspy/app.py
[refactor] 206-206: Consider using 'with' for resource-allocating operations
(R1732)
[refactor] 225-229: Unnecessary "else" after "return", remove the "else" and de-indent the code inside it
(R1705)
[error] 266-266: Assigning result of a function call, where the function has no return
(E1111)
[error] 277-277: Possibly using variable 'success' before assignment
(E0606)
chordspy/connection.py
[refactor] 36-36: Too many instance attributes (27/7)
(R0902)
[refactor] 161-161: Consider using 'with' for resource-allocating operations
(R1732)
[error] 290-290: Instance of 'Chords_BLE' has no 'data_available' member
(E1101)
[error] 295-295: Instance of 'Chords_BLE' has no 'get_latest_sample' member
(E1101)
[refactor] 287-319: Too many nested blocks (6/5)
(R1702)
[error] 331-331: Instance of 'Chords_WIFI' has no 'data_available' member
(E1101)
[error] 336-336: Instance of 'Chords_WIFI' has no 'get_latest_sample' member
(E1101)
[refactor] 328-357: Too many nested blocks (6/5)
(R1702)
[refactor] 366-397: Too many nested blocks (6/5)
(R1702)
[refactor] 558-558: Too many branches (15/12)
(R0912)
chordspy/chords_wifi.py
[refactor] 12-12: Too many instance attributes (14/7)
(R0902)
[refactor] 33-33: Too many arguments (6/5)
(R0913)
[refactor] 33-33: Too many positional arguments (6/5)
(R0917)
[refactor] 87-87: Too many branches (15/12)
(R0912)
[refactor] 87-87: Too many statements (58/50)
(R0915)
🪛 YAMLlint (1.37.1)
.github/workflows/release.yaml
[error] 133-133: no new line character at the end of file
(new-line-at-end-of-file)
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Actionable comments posted: 0
♻️ Duplicate comments (9)
chordspy/chords_serial.py (1)
241-276: Fix global variable issues in timer methods.The timer methods reference undefined global variables which will cause
NameErrorexceptions at runtime. These should be instance variables initialized in__init__and accessed viaself.def __init__(self): """ Initialize the Chords_USB client and sets up serial connection attributes, data buffer, and installs signal handler for clean exit on interrupt signals. """ self.ser = None # Serial connection object self.buffer = bytearray() # Buffer for incoming data self.retry_limit = 4 # Maximum connection retries self.packet_length = None # Expected packet length for current board self.num_channels = None # Number of data channels for current board self.data = None # Numpy array for storing channel data self.board = "" # Detected board name self.streaming_active = False # Streaming state flag + + # Timer and logging attributes + self.start_time = None + self.last_ten_minute_time = None + self.total_packet_count = 0 + self.cumulative_packet_count = 0 + self.samples_per_second = 0 + self.missing_samples = 0 def start_timer(self): """ Start the timer for packet counting and logging. """ - global start_time, last_ten_minute_time, total_packet_count, cumulative_packet_count current_time = time.time() - start_time = current_time # Session start time - last_ten_minute_time = current_time # 10-minute interval start time - total_packet_count = 0 # Counter for packets in current second - cumulative_packet_count = 0 # Counter for all packets + self.start_time = current_time # Session start time + self.last_ten_minute_time = current_time # 10-minute interval start time + self.total_packet_count = 0 # Counter for packets in current second + self.cumulative_packet_count = 0 # Counter for all packets def log_one_second_data(self): """ Log data for one second intervals and displays: Number of packets received in the last second, Number of missing samples (if any) """ - global total_packet_count, samples_per_second, missing_samples - samples_per_second = total_packet_count - print(f"Data count for the last second: {total_packet_count} samples, "f"Missing samples: {missing_samples}") - total_packet_count = 0 # Reset for next interval + self.samples_per_second = self.total_packet_count + print(f"Data count for the last second: {self.total_packet_count} samples, "f"Missing samples: {self.missing_samples}") + self.total_packet_count = 0 # Reset for next interval def log_ten_minute_data(self): """ Log data for 10-minute intervals and displays: Total packets received, Actual sampling rate, Drift from expected rate """ - global cumulative_packet_count, last_ten_minute_time, supported_boards, board - print(f"Total data count after 10 minutes: {cumulative_packet_count}") - sampling_rate = cumulative_packet_count / (10 * 60) # Calculate actual sampling rate + print(f"Total data count after 10 minutes: {self.cumulative_packet_count}") + sampling_rate = self.cumulative_packet_count / (10 * 60) # Calculate actual sampling rate print(f"Sampling rate: {sampling_rate:.2f} samples/second") - expected_sampling_rate = supported_boards[board]["sampling_rate"] + expected_sampling_rate = self.supported_boards[self.board]["sampling_rate"] drift = ((sampling_rate - expected_sampling_rate) / expected_sampling_rate) * 3600 # Calculate drift from expected rate print(f"Drift: {drift:.2f} seconds/hour") # Reset counters - cumulative_packet_count = 0 - last_ten_minute_time = time.time() + self.cumulative_packet_count = 0 + self.last_ten_minute_time = time.time()chordspy/connection.py (8)
36-95: Consider refactoring to reduce class complexity.The Connection class has 27 instance attributes and handles multiple responsibilities (protocol management, LSL streaming, CSV recording, rate monitoring, thread management). This violates the Single Responsibility Principle.
Consider breaking this into separate classes:
ConnectionManager(main orchestrator)LSLStreamer(handles LSL operations)CSVRecorder(handles file recording)RateMonitor(handles sample rate calculations)This would improve modularity, testability, and maintainability.
169-169: Use context manager for file operations.The file is opened without a context manager, which could lead to resource leaks if an exception occurs.
Since the file needs to remain open for recording duration, implement a proper context manager pattern:
class Connection: def __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): self.cleanup()Or ensure robust error handling in cleanup methods.
272-272: Complete rate checker implementation.The method calculates
estimated_ratebut never uses it, making the calculation ineffective.if filtered_diffs: estimated_rate = 1 / np.mean(filtered_diffs) # Rate = 1/average interval between samples + print(f"\nLSL stream rate verification: {estimated_rate:.2f} Hz") + return estimated_rate else: print("\nAll timestamps had zero difference (invalid).") + return None else: print("\nNot enough timestamps collected to estimate rate.") + return None
290-327: Fix references to non-existent BLE methods.The BLE data handler references
self.ble_connection.data_availableandself.ble_connection.get_latest_sample()which don't exist in theChords_BLEclass.Based on the relevant code snippets, the
Chords_BLEclass doesn't expose these methods. Either:
- Implement missing methods in
Chords_BLE:@property def data_available(self) -> bool: # Check if samples are available in internal buffer return len(self.sample_buffer) > 0 def get_latest_sample(self) -> list: # Return and remove the latest sample if self.sample_buffer: return self.sample_buffer.popleft() return None
- Or modify the handler to use existing BLE notification mechanisms.
331-365: Fix references to non-existent WiFi methods.Similar to BLE, the WiFi handler references
self.wifi_connection.data_availableandself.wifi_connection.get_latest_sample()which don't exist in theChords_WIFIclass.The
Chords_WIFIclass needs these methods implemented or the handler needs to be updated to use existing WiFi data processing methods.
407-467: Consolidate BLE data handling approach.The BLE connection creates a custom notification handler that processes data while also starting a
ble_data_handlerthread, causing duplicate data processing logic and potential race conditions.Consolidate the data handling by either:
- Using only the notification handler approach and removing the
ble_data_handlerthread logic- Storing incoming data in a thread-safe queue in the notification handler and letting
ble_data_handlerprocess itAlso fix the indentation issue:
channels = [int.from_bytes(sample_data[i:i+2], byteorder='big', signed=True) - for i in range(1, len(sample_data), 2)] + for i in range(1, len(sample_data), 2)]
468-531: Consolidate WiFi data handling approach.The WiFi connection processes data in its own loop while also starting a
wifi_data_handlerthread, creating inconsistent data handling architecture.Move all data receiving and processing logic from the main loop into the
wifi_data_handlerthread for consistency. The mainconnect_wifimethod should only manage connection setup and teardown.
671-683: Fix inconsistent error handling for WiFi connection.The WiFi connection doesn't check the return value like USB and BLE connections do, and uses nested if statements.
# WiFi Protocol Handling elif args.protocol == 'wifi': - if manager.connect_wifi(): # Attempt WiFi connection - while manager.running: # Main execution loop - time.sleep(1) # Prevent CPU overutilization + manager.connect_wifi() # WiFi handles its own loop # BLE Protocol Handling elif args.protocol == 'ble': - if manager.connect_ble(args.ble_address): # Attempt BLE connection - while manager.running: # Main execution loop - time.sleep(1) # Prevent CPU overutilization + if not manager.connect_ble(args.ble_address): # Attempt BLE connection + print("Failed to connect to BLE device") + return + while manager.running: # Main execution loop + time.sleep(1) # Prevent CPU overutilization
🧹 Nitpick comments (2)
chordspy/chords_serial.py (1)
108-108: Remove unused variable assignment.The
sampling_ratevariable is assigned but never used in this method.- sampling_rate = self.supported_boards[self.board]["sampling_rate"] + # sampling_rate = self.supported_boards[self.board]["sampling_rate"] # Available if neededchordspy/connection.py (1)
44-44: Fix typo in docstring.There's a typo in "monitorin" - should be "monitoring".
- - Sample validation and rate monitorin + - Sample validation and rate monitoring
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chordspy/chords_serial.py(1 hunks)chordspy/connection.py(1 hunks)
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🧬 Code Graph Analysis (1)
chordspy/connection.py (3)
chordspy/chords_serial.py (5)
Chords_USB(17-275)read_data(161-200)detect_hardware(121-141)send_command(143-159)cleanup(222-231)chordspy/chords_wifi.py (3)
Chords_WIFI(12-198)connect(60-74)cleanup(180-192)chordspy/chords_ble.py (6)
Chords_BLE(13-238)scan_devices(55-69)notification_handler(113-129)connect(215-231)cleanup(204-213)stop(233-238)
🪛 Ruff (0.12.2)
chordspy/chords_serial.py
108-108: Local variable sampling_rate is assigned to but never used
Remove assignment to unused variable sampling_rate
(F841)
chordspy/connection.py
169-169: Use a context manager for opening files
(SIM115)
272-272: Local variable estimated_rate is assigned to but never used
Remove assignment to unused variable estimated_rate
(F841)
679-680: Use a single if statement instead of nested if statements
(SIM102)
🔇 Additional comments (3)
chordspy/chords_serial.py (1)
17-240: LGTM! Well-structured USB communication class.The class implementation is comprehensive and well-documented. The packet parsing logic, error handling, and resource management are all properly implemented. The signal handling and cleanup mechanisms ensure graceful shutdown.
chordspy/connection.py (2)
532-567: LGTM! Well-implemented USB connection method.The USB connection method properly handles device detection, configuration, and thread management. The error handling and resource management are appropriate.
569-637: LGTM! Comprehensive cleanup implementation.The cleanup method properly handles resource deallocation in the correct order, with appropriate error handling and timeout management for thread termination.
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Actionable comments posted: 2
♻️ Duplicate comments (1)
chordspy/chords_serial.py (1)
241-276: Remove global variable declarations and fix undefined variable references.These timer methods still have the issues previously identified:
- Remove all
globaldeclarations as you're using instance attributes- Line 258:
missing_samplesis undefined and never calculated- Line 269: Use
self.boardinstead of undefinedboardApply these fixes:
def start_timer(self): """ Start the timer for packet counting and logging. """ - global start_time, last_ten_minute_time, total_packet_count, cumulative_packet_count current_time = time.time() self.start_time = current_time # Session start time self.last_ten_minute_time = current_time # 10-minute interval start time self.total_packet_count = 0 # Counter for packets in current second self.cumulative_packet_count = 0 # Counter for all packets def log_one_second_data(self): """ Log data for one second intervals and displays: Number of packets received in the last second, Number of missing samples (if any) """ - global total_packet_count, samples_per_second, missing_samples - self.samples_per_second = total_packet_count - print(f"Data count for the last second: {total_packet_count} samples, "f"Missing samples: {missing_samples}") + self.samples_per_second = self.total_packet_count + # Calculate missing samples based on expected sampling rate + expected_samples = self.supported_boards[self.board]["sampling_rate"] + missing_samples = max(0, expected_samples - self.total_packet_count) + print(f"Data count for the last second: {self.total_packet_count} samples, " + f"Missing samples: {missing_samples}") self.total_packet_count = 0 # Reset for next interval def log_ten_minute_data(self): """ Log data for 10-minute intervals and displays: Total packets received, Actual sampling rate, Drift from expected rate """ - global cumulative_packet_count, last_ten_minute_time, supported_boards, board print(f"Total data count after 10 minutes: {self.cumulative_packet_count}") sampling_rate = self.cumulative_packet_count / (10 * 60) # Calculate actual sampling rate print(f"Sampling rate: {sampling_rate:.2f} samples/second") - expected_sampling_rate = self.supported_boards[board]["sampling_rate"] + expected_sampling_rate = self.supported_boards[self.board]["sampling_rate"] drift = ((sampling_rate - expected_sampling_rate) / expected_sampling_rate) * 3600 # Calculate drift from expected rate print(f"Drift: {drift:.2f} seconds/hour") # Reset counters self.cumulative_packet_count = 0 self.last_ten_minute_time = time.time()
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chordspy/chords_serial.py(1 hunks)
🧰 Additional context used
🪛 Ruff (0.12.2)
chordspy/chords_serial.py
108-108: Local variable sampling_rate is assigned to but never used
Remove assignment to unused variable sampling_rate
(F841)
🔇 Additional comments (6)
chordspy/chords_serial.py (6)
1-58: Well-structured class definition with comprehensive documentation.The imports are appropriate, and the class structure with protocol constants and supported boards dictionary provides a clean, maintainable design.
59-75: Proper initialization with thread-safe signal handling.Good practice to check for the main thread before installing the signal handler. All attributes are correctly initialized as instance variables.
121-142: Effective hardware auto-detection implementation.The method systematically tries all ports and baud rates, providing good user feedback during the detection process.
143-160: Robust command sending with proper buffer management.Good practice to flush buffers before sending commands and handle Unicode decode errors gracefully.
161-201: Well-implemented packet parsing with robust error handling.The method effectively handles packet synchronization, validation, and data extraction. The rolling buffer approach for data storage is efficient.
202-240: Clean streaming control with proper resource management.The streaming methods provide clear start/stop control with robust cleanup and signal handling for graceful shutdown.
| if __name__ == "__main__": | ||
| client = Chords_USB() # Create and run the USB client | ||
| client.detect_hardware() # Detect and connect to hardware | ||
| client.start_streaming() # Start streaming data No newline at end of file |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add error handling for hardware detection failure.
The script should handle the case where hardware detection fails to prevent crashes.
if __name__ == "__main__":
client = Chords_USB() # Create and run the USB client
- client.detect_hardware() # Detect and connect to hardware
- client.start_streaming() # Start streaming data
+ if client.detect_hardware(): # Detect and connect to hardware
+ client.start_streaming() # Start streaming data
+ else:
+ print("Failed to detect hardware. Exiting.")
+ sys.exit(1)Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In chordspy/chords_serial.py around lines 277 to 280, the code calls
detect_hardware() without handling potential failures, which can cause crashes
if hardware detection fails. Add error handling around the detect_hardware()
call to catch exceptions or check for failure returns, and handle these cases
gracefully by logging an error message and exiting or retrying as appropriate.
| self.board = response | ||
| print(f"{response} detected at {port} with baudrate {baudrate}") | ||
| self.num_channels = self.supported_boards[self.board]["Num_channels"] | ||
| sampling_rate = self.supported_boards[self.board]["sampling_rate"] |
There was a problem hiding this comment.
Remove unused variable assignment.
The sampling_rate variable is assigned but never used in this method.
-sampling_rate = self.supported_boards[self.board]["sampling_rate"]📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| sampling_rate = self.supported_boards[self.board]["sampling_rate"] |
🧰 Tools
🪛 Ruff (0.12.2)
108-108: Local variable sampling_rate is assigned to but never used
Remove assignment to unused variable sampling_rate
(F841)
🤖 Prompt for AI Agents
In chordspy/chords_serial.py at line 108, the variable sampling_rate is assigned
but never used. Remove the assignment of sampling_rate entirely from this line
to clean up the code and avoid unused variable warnings.
|
@PayalLakra Thank you so much for your contributions, I am merging this now. |
2 participants
I have made the following changes:
Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Refactor
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