Verify Command-Line Entry Point Invocation with Help Flag
Summary
Validates that a scientific Python package's command-line entry point script executes successfully and emits help documentation when invoked with the --help flag. This skill confirms the package installation is functional and the CLI interface is available before attempting analysis workflows.
When to use
After installing ChemDistiller or similar Python-based command-line analysis packages, to confirm the package is properly installed in the Python environment and the primary entry point script is accessible and executable. Run this as an immediate post-installation sanity check before attempting to process input data.
When NOT to use
- When the package has already been validated through prior successful analysis runs (redundant check).
- When diagnosing issues with input data processing or annotation results (this skill only verifies CLI availability, not analysis correctness).
- When the package does not expose a command-line interface or requires programmatic import only.
Inputs
- Python package installation directory
- Entry-point script path (e.g., annotate.py)
Outputs
- Help documentation text emitted to standard output
- Exit code 0 indicating successful script completion
How to apply
Locate the main entry-point script (e.g., annotate.py) within the installed package directory. From that directory, invoke the script with Python and the --help flag. Capture and examine the standard output to verify that a non-empty help message describing available command-line arguments and options is emitted. The script should complete without ImportError, SyntaxError, or runtime exceptions. If help documentation is successfully printed to stdout, the installation and entry point are verified functional.
Related tools
- Python (Interpreter for executing annotate.py and other package scripts; required to support ChemDistiller v0.1)
- Anaconda (Recommended Python distribution for managing dependencies (SciPy, NumPy, h5py); simplifies package environment setup) — https://www.anaconda.com/download/
- ChemDistiller (High-throughput tandem MS spectra annotation engine; annotate.py is the primary entry point being verified) — https://github.com/Mrqeoqqt/chemdistiller
Examples
python annotate.py --help
Evaluation signals
- Help output contains a list of command-line arguments (e.g., --help, --test, --ncpu, --delta_mz, --max_results) as described in the README.
- Script execution completes without raising ImportError, ModuleNotFoundError, or SyntaxError.
- Standard output is non-empty and contains human-readable documentation of available options.
- Exit code is 0, indicating successful termination.
- Help text is emitted within a reasonable time (< 5 seconds) with no hanging or timeout.
Limitations
- This skill only verifies that the entry point is invocable and returns help; it does not validate that all dependencies (SciPy, NumPy, h5py, optional RDKit) are correctly installed or functional.
- Successful help output does not guarantee that actual annotation or analysis operations will work correctly or produce correct results.
- The skill assumes the entry-point script supports the --help flag; alternative help invocation patterns (e.g., -h, help subcommand) may not be detected by this method.
Evidence
- [other] Locate the annotate.py script in the ChemDistiller package installation directory. Invoke annotate.py with the --help flag using Python.: "Locate the annotate.py script in the ChemDistiller package installation directory. Invoke annotate.py with the --help flag using Python."
- [other] The annotate.py script can be invoked from the command line with the --help flag to display available options and functionality.: "The annotate.py script can be invoked from the command line with the --help flag to display available options and functionality."
- [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] Capture and validate that the help output is emitted to standard output.: "Capture and validate that the help output is emitted to standard output."
- [readme] ChemDistiller supports Python 2 and 3 (64-bit version recommended) and requires SciPy, NumPy, h5py libraries.: "ChemDistiller supports Python 2 and 3 (64-bit version recommended) and requires SciPy, NumPy, h5py libraries."
1---2name: package-installation-verification3description: Use when after installing ChemDistiller or similar Python-based command-line analysis packages, to confirm the package is properly installed in the Python environment and the primary entry point script is accessible and executable.4license: CC-BY-4.05---67# Verify Command-Line Entry Point Invocation with Help Flag89## Summary1011Validates that a scientific Python package's command-line entry point script executes successfully and emits help documentation when invoked with the --help flag. This skill confirms the package installation is functional and the CLI interface is available before attempting analysis workflows.1213## When to use1415After installing ChemDistiller or similar Python-based command-line analysis packages, to confirm the package is properly installed in the Python environment and the primary entry point script is accessible and executable. Run this as an immediate post-installation sanity check before attempting to process input data.1617## When NOT to use1819- When the package has already been validated through prior successful analysis runs (redundant check).20- When diagnosing issues with input data processing or annotation results (this skill only verifies CLI availability, not analysis correctness).21- When the package does not expose a command-line interface or requires programmatic import only.2223## Inputs2425- Python package installation directory26- Entry-point script path (e.g., annotate.py)2728## Outputs2930- Help documentation text emitted to standard output31- Exit code 0 indicating successful script completion3233## How to apply3435Locate the main entry-point script (e.g., annotate.py) within the installed package directory. From that directory, invoke the script with Python and the --help flag. Capture and examine the standard output to verify that a non-empty help message describing available command-line arguments and options is emitted. The script should complete without ImportError, SyntaxError, or runtime exceptions. If help documentation is successfully printed to stdout, the installation and entry point are verified functional.3637## Related tools3839- **Python** (Interpreter for executing annotate.py and other package scripts; required to support ChemDistiller v0.1)40- **Anaconda** (Recommended Python distribution for managing dependencies (SciPy, NumPy, h5py); simplifies package environment setup) — https://www.anaconda.com/download/41- **ChemDistiller** (High-throughput tandem MS spectra annotation engine; annotate.py is the primary entry point being verified) — https://github.com/Mrqeoqqt/chemdistiller4243## Examples4445```46python annotate.py --help47```4849## Evaluation signals5051- Help output contains a list of command-line arguments (e.g., --help, --test, --ncpu, --delta_mz, --max_results) as described in the README.52- Script execution completes without raising ImportError, ModuleNotFoundError, or SyntaxError.53- Standard output is non-empty and contains human-readable documentation of available options.54- Exit code is 0, indicating successful termination.55- Help text is emitted within a reasonable time (< 5 seconds) with no hanging or timeout.5657## Limitations5859- This skill only verifies that the entry point is invocable and returns help; it does not validate that all dependencies (SciPy, NumPy, h5py, optional RDKit) are correctly installed or functional.60- Successful help output does not guarantee that actual annotation or analysis operations will work correctly or produce correct results.61- The skill assumes the entry-point script supports the --help flag; alternative help invocation patterns (e.g., -h, help subcommand) may not be detected by this method.6263## Evidence6465- [other] Locate the annotate.py script in the ChemDistiller package installation directory. Invoke annotate.py with the --help flag using Python.: "Locate the annotate.py script in the ChemDistiller package installation directory. Invoke annotate.py with the --help flag using Python."66- [other] The annotate.py script can be invoked from the command line with the --help flag to display available options and functionality.: "The annotate.py script can be invoked from the command line with the --help flag to display available options and functionality."67- [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."68- [other] Capture and validate that the help output is emitted to standard output.: "Capture and validate that the help output is emitted to standard output."69- [readme] ChemDistiller supports Python 2 and 3 (64-bit version recommended) and requires _SciPy_, _NumPy_, _h5py_ libraries.: "ChemDistiller supports Python 2 and 3 (64-bit version recommended) and requires _SciPy_, _NumPy_, _h5py_ libraries."
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