entry-point-script-validation
Summary
Verify that a Python package's command-line entry point script executes successfully and emits help documentation when invoked with the --help flag. This confirms the script is properly installed, importable, and has valid argument parsing configured.
When to use
After installing a Python package or cloning its repository, to verify that the primary command-line interface is functional and discoverable before attempting analysis workflows. This is particularly important for high-throughput annotation engines like ChemDistiller where the entry point (annotate.py) serves as the gateway to all downstream functionality.
When NOT to use
- When the package has already passed integration testing in a CI/CD pipeline and you are running production analyses; use this skill only once per fresh installation or environment.
- If your goal is to execute an actual analysis workflow (e.g., annotate spectra); use this skill first to validate the entry point, then move to full analysis with appropriate input data and parameters.
- When the entry point is known to require external resources (databases, SVMs) that are not yet downloaded; validate the script first, then acquire dependencies before running --test or analysis workflows.
Inputs
- Python executable environment with package installed or repository cloned
- Command-line shell access
- Entry-point script file (e.g., annotate.py)
Outputs
- Help text emitted to standard output
- Exit code 0 (success)
- Documentation of available command-line arguments and their descriptions
How to apply
Locate the entry-point script (annotate.py) in the package installation directory or repository root. Invoke it via Python with the --help flag from the command line. Capture the standard output and validate that help text is emitted describing available command-line arguments and their purposes. The help output should document key parameters such as --ncpu (processor count), --delta_mz (m/z tolerance in ppm), --max_results (candidate compound limit), --test (test mode), and --svm_folder (custom SVM path). Success indicates the script can be imported without errors, argument parsing is configured, and the entry point is ready for actual analysis runs.
Related tools
- Python (Interpreter for executing the entry-point script; supports both Python 2 and 3 (64-bit recommended)) — https://www.python.org
- annotate.py (Primary entry-point script for ChemDistiller command-line interface; orchestrates tandem MS spectra annotation) — https://github.com/Mrqeoqqt/chemdistiller
- argparse (Built-in Python module for command-line argument parsing that generates --help documentation)
Examples
python annotate.py --help
Evaluation signals
- Exit code is 0 (no errors or exceptions raised)
- Help text is emitted to stdout and includes documentation of all major arguments (--test, --ncpu, --delta_mz, --max_results, --svm_folder, input/output folder paths)
- Help text specifies default values and valid ranges (e.g., 'Default: 1' for --ncpu, 'Default: 10' for --max_results, ppm units for --delta_mz)
- No traceback or import errors appear in stderr; all dependencies (NumPy, SciPy, h5py) are successfully resolved
- Script can be invoked from any working directory without path errors, indicating proper package installation
Limitations
- Help text validation does not confirm that the annotate.py script will successfully run an analysis; it only verifies the entry point is callable and argument parsing is configured. Use --test flag to validate end-to-end functionality.
- Help text may not reflect optional dependencies (RDKit for 2D structure image generation) or downloadable resources (external compound databases, SVM models from MediaFire); help validation passes even if these optional components are absent.
- On systems with multiple Python versions or conflicting package installations, the --help invocation may call an unexpected Python version or a different installation of ChemDistiller; ensure correct Python path and environment activation before validation.
Evidence
- [other] Does the annotate.py entry-point script execute successfully and emit help documentation when invoked with the --help flag?: "Does the annotate.py entry-point script execute successfully and emit help documentation when invoked with the --help flag?"
- [readme] Try running ChemDistiller from the command line:
python annotate.py --help This should give you the list of currently available command line arguments.: "Try running ChemDistiller from the command line: python annotate.py --help This should give you the list of currently available command line arguments."
- [other] Invoke annotate.py with the --help flag using Python. Capture and validate that the help output is emitted to standard output.: "Invoke annotate.py with the --help flag using Python. Capture and validate that the help output is emitted to standard output."
- [readme] --ncpu tells how many processors to use in the multiprocessor/multicore environment. Default: 1, maximum for your PC will be shown in help screen: "--ncpu tells how many processors to use in the multiprocessor/multicore environment. Default: 1, maximum for your PC will be shown in help screen"
- [readme] --delta_mz - tolerance for the MS1 peak m/z values when searching in the databases, i.e. candidates should be withing +/- delta_mz from MS1 peak m/z value (delta_mz is in ppm): "--delta_mz - tolerance for the MS1 peak m/z values when searching in the databases, i.e. candidates should be withing +/- delta_mz from MS1 peak m/z value (delta_mz is in ppm)"
1---2name: entry-point-script-validation3description: Use when after installing a Python package or cloning its repository, to verify that the primary command-line interface is functional and discoverable before attempting analysis workflows.4license: CC-BY-4.05---67# entry-point-script-validation89## Summary1011Verify that a Python package's command-line entry point script executes successfully and emits help documentation when invoked with the --help flag. This confirms the script is properly installed, importable, and has valid argument parsing configured.1213## When to use1415After installing a Python package or cloning its repository, to verify that the primary command-line interface is functional and discoverable before attempting analysis workflows. This is particularly important for high-throughput annotation engines like ChemDistiller where the entry point (annotate.py) serves as the gateway to all downstream functionality.1617## When NOT to use1819- When the package has already passed integration testing in a CI/CD pipeline and you are running production analyses; use this skill only once per fresh installation or environment.20- If your goal is to execute an actual analysis workflow (e.g., annotate spectra); use this skill first to validate the entry point, then move to full analysis with appropriate input data and parameters.21- When the entry point is known to require external resources (databases, SVMs) that are not yet downloaded; validate the script first, then acquire dependencies before running --test or analysis workflows.2223## Inputs2425- Python executable environment with package installed or repository cloned26- Command-line shell access27- Entry-point script file (e.g., annotate.py)2829## Outputs3031- Help text emitted to standard output32- Exit code 0 (success)33- Documentation of available command-line arguments and their descriptions3435## How to apply3637Locate the entry-point script (annotate.py) in the package installation directory or repository root. Invoke it via Python with the --help flag from the command line. Capture the standard output and validate that help text is emitted describing available command-line arguments and their purposes. The help output should document key parameters such as --ncpu (processor count), --delta_mz (m/z tolerance in ppm), --max_results (candidate compound limit), --test (test mode), and --svm_folder (custom SVM path). Success indicates the script can be imported without errors, argument parsing is configured, and the entry point is ready for actual analysis runs.3839## Related tools4041- **Python** (Interpreter for executing the entry-point script; supports both Python 2 and 3 (64-bit recommended)) — https://www.python.org42- **annotate.py** (Primary entry-point script for ChemDistiller command-line interface; orchestrates tandem MS spectra annotation) — https://github.com/Mrqeoqqt/chemdistiller43- **argparse** (Built-in Python module for command-line argument parsing that generates --help documentation)4445## Examples4647```48python annotate.py --help49```5051## Evaluation signals5253- Exit code is 0 (no errors or exceptions raised)54- Help text is emitted to stdout and includes documentation of all major arguments (--test, --ncpu, --delta_mz, --max_results, --svm_folder, input/output folder paths)55- Help text specifies default values and valid ranges (e.g., 'Default: 1' for --ncpu, 'Default: 10' for --max_results, ppm units for --delta_mz)56- No traceback or import errors appear in stderr; all dependencies (NumPy, SciPy, h5py) are successfully resolved57- Script can be invoked from any working directory without path errors, indicating proper package installation5859## Limitations6061- Help text validation does not confirm that the annotate.py script will successfully run an analysis; it only verifies the entry point is callable and argument parsing is configured. Use --test flag to validate end-to-end functionality.62- Help text may not reflect optional dependencies (RDKit for 2D structure image generation) or downloadable resources (external compound databases, SVM models from MediaFire); help validation passes even if these optional components are absent.63- On systems with multiple Python versions or conflicting package installations, the --help invocation may call an unexpected Python version or a different installation of ChemDistiller; ensure correct Python path and environment activation before validation.6465## Evidence6667- [other] Does the annotate.py entry-point script execute successfully and emit help documentation when invoked with the --help flag?: "Does the annotate.py entry-point script execute successfully and emit help documentation when invoked with the --help flag?"68- [readme] Try running __ChemDistiller__ from the command line: `python annotate.py --help` This should give you the list of currently available command line arguments.: "Try running __ChemDistiller__ from the command line: `python annotate.py --help` This should give you the list of currently available command line arguments."69- [other] Invoke annotate.py with the --help flag using Python. Capture and validate that the help output is emitted to standard output.: "Invoke annotate.py with the --help flag using Python. Capture and validate that the help output is emitted to standard output."70- [readme] _--ncpu_ tells how many processors to use in the multiprocessor/multicore environment. Default: 1, maximum for your PC will be shown in help screen: "_--ncpu_ tells how many processors to use in the multiprocessor/multicore environment. Default: 1, maximum for your PC will be shown in help screen"71- [readme] _--delta_mz_ - tolerance for the MS1 peak _m/z_ values when searching in the databases, _i.e._ candidates should be withing +/- _delta_mz_ from MS1 peak _m/z_ value (_delta_mz_ is in ppm): "_--delta_mz_ - tolerance for the MS1 peak _m/z_ values when searching in the databases, _i.e._ candidates should be withing +/- _delta_mz_ from MS1 peak _m/z_ value (_delta_mz_ is in ppm)"
HolobiomicsLab