Python package installation and dependency management

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v1/skills/python-package-installation-and-dependency-management

Use when when setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that depends on specific versions of auxiliary packages (like spectrum-utils==0.3.5).From its SKILL.md

Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill python-package-installation-and-dependency-management

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SKILL.md

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Python Package Installation and Dependency Management

Summary

Install and configure Python bioinformatics packages with pinned dependencies to ensure reproducible execution of mass spectrometry analysis workflows. This skill addresses version-specific compatibility constraints that arise when combining multiple scientific packages.

When to use

When setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that depends on specific versions of auxiliary packages (like spectrum-utils==0.3.5). Use this skill when the tool's documentation specifies exact version pins and platform constraints (e.g., Linux/OSX only, Python 3.8+ required).

When NOT to use

Environment already has incompatible package versions installed that cannot be reconciled (e.g., spectrum-utils 0.4.0 required by another tool)
Platform is Windows (falcon is documented for Linux and OSX only)
Python version is 3.7 or earlier (falcon requires Python 3.8+)

Inputs

Python 3.8+ runtime environment
pip package manager
Internet access to PyPI package repository
Tool installation specification with pinned dependencies (e.g., from tool README or publication)

Outputs

Installed falcon-ms command-line tool
Installed spectrum-utils==0.3.5 library
Python environment with validated package versions

How to apply

First, verify your Python version meets the minimum requirement (Python 3.8+) and that your operating system is supported (Linux or OSX). Then install the primary tool and its pinned dependencies together using pip, specifying exact versions as documented: pip install falcon-ms spectrum-utils==0.3.5. After installation, verify successful setup by invoking the tool's help or running it on a small test dataset to confirm no import errors or version conflicts occur. Version pinning is critical because spectrum-utils and falcon use feature hashing and nearest neighbor indexing that may break across minor version boundaries.

Related tools

falcon-ms (Primary spectrum clustering tool; installed via pip with pinned dependencies) — https://github.com/bittremieux/falcon
spectrum-utils (Auxiliary library for spectrum handling and preprocessing; pinned to version 0.3.5 for compatibility with falcon)
pip (Package manager used to install falcon-ms and spectrum-utils with exact version specifications)

Examples

pip install falcon-ms spectrum-utils==0.3.5

Evaluation signals

pip install command completes without errors and reports successful installation of both falcon-ms and spectrum-utils==0.3.5
Running falcon --help or falcon -h produces help text without ImportError or version mismatch warnings
Invoking falcon on a small test mzML/mzXML/MGF file runs to completion without exceptions
Installed package versions match documentation requirements: python -c 'import falcon; import spectrum_utils; print(spectrum_utils.__version__)' returns '0.3.5'
Cluster output files (*.csv) are generated with non-empty cluster assignments

Limitations

falcon is restricted to Linux and OSX platforms; Windows users cannot use this tool
Older Python versions (< 3.8) are incompatible; users on legacy environments must upgrade
spectrum-utils version 0.3.5 is a strict requirement; newer or older versions may introduce incompatibilities in feature hashing or vector construction steps
pip requires internet connectivity to download packages from PyPI; offline environments need pre-cached wheels

Evidence

[readme] falcon requires Python 3.8+ and is available on the Linux and OSX platforms: "falcon requires Python 3.8+ and is available on the Linux and OSX platforms."
[readme] pip installation with pinned spectrum-utils version: "You can easily install falcon with pip:

pip install falcon-ms spectrum-utils==0.3.5"
[readme] Feature hashing and nearest neighbor indexing depend on spectrum-utils implementation details: "First, high-resolution spectra are binned and converted to low-dimensional vectors using feature hashing. Next, the spectrum vectors are used to construct nearest neighbor indexes for fast similarity"

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