Conda environment setup and activation

Skill HolobiomicsLab/asb-skill-collections/packs/metabolomics/ms-imaging/skills/conda-environment-setup-and-activation

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npx -y skills add HolobiomicsLab/asb-skill-collections --skill conda-environment-setup-and-activation

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Use when preparing a fresh system or user account to run MSIGen for mass spectrometry imaging data processing, or when you need to isolate MSIGen installation from other Python projects to avoid dependency conflicts.

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SKILL.md

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conda-environment-setup-and-activation

Summary

Create and activate a isolated Conda Python environment with pinned version constraints to ensure reproducible installation of MSIGen and its dependencies (Python >=3.9 and <=3.11). This skill is essential before installing MSIGen or its optional prerequisites like pyBaf2Sql.

When to use

Apply this skill when preparing a fresh system or user account to run MSIGen for mass spectrometry imaging data processing, or when you need to isolate MSIGen installation from other Python projects to avoid dependency conflicts. Specifically required before installing MSIGen via pip or before installing pyBaf2Sql for Bruker .baf data support.

When NOT to use

MSIGen is already installed in a working environment and you are only running analysis code — activation of an existing environment is not a 'setup' operation.
You are using a different package manager (pip venv, Poetry, Docker) as the primary environment isolation strategy; mixing conda create with non-Conda virtual environments can cause confusion.
Your system Python version is already 3.11 and you have manually installed all MSIGen dependencies globally — environment isolation is then optional (but not recommended for reproducibility).

Inputs

Anaconda or Miniconda installation on system PATH
Command-line interface (Anaconda Prompt on Windows, Terminal on macOS/Linux)

Outputs

Activated Conda environment named 'MSIGen' with Python 3.11 (or specified 3.9–3.11 version)
Shell/prompt prefix indicating active environment (e.g., '(MSIGen) C:>')

How to apply

Using Anaconda or Miniconda, execute conda create with explicit Python version pinning (3.9–3.11 range; 3.11 is recommended) and environment name 'MSIGen', then activate the environment using conda activate. The version constraint ensures compatibility with MSIGen's codebase and avoids breaking changes in Python 3.12+. After activation, the prompt will prefix with (MSIGen), confirming the environment is active. All subsequent pip install commands for MSIGen, pyBaf2Sql, Jupyter Notebook, or other tools must be run within this activated environment to install packages into the isolated namespace rather than the system Python.

Related tools

Anaconda (Conda distribution and package manager; provides conda create and conda activate commands to build isolated Python environments) — https://www.anaconda.com/download
Miniconda (Lightweight alternative to Anaconda; provides only Conda and Python without pre-bundled packages; smaller download for environment setup) — https://www.anaconda.com/download/success

Examples

conda create --name MSIGen python=3.11 -y && conda activate MSIGen && python --version

Evaluation signals

Conda environment 'MSIGen' is listed in conda env list output.
Command-line prompt displays '(MSIGen)' prefix after running conda activate MSIGen, confirming environment is active.
Running python --version within the active environment returns Python 3.9–3.11 (e.g., 'Python 3.11.x'), not the system Python version.
Subsequent pip install MSIGen or pip install git+https://github.com/gtluu/pyBaf2Sql commands complete without version constraint conflicts.
Running conda list in the active environment shows installed packages are isolated to that environment, not the base or system Python.

Limitations

Python 3.12+ is not supported; MSIGen requires <=3.11 due to potential breaking changes in newer Python major versions.
Anaconda and Miniconda must be installed and available on system PATH before conda commands can be executed; users without prior Conda installation must download and install it separately.
Environment activation is terminal/shell-specific and does not persist across new terminal sessions; users must re-run conda activate MSIGen in each new shell or configure a shell profile to auto-activate.
Creating the environment requires network access to download Python packages from Conda repositories; offline or air-gapped systems may require pre-cached package archives.

Evidence

[methods] Using an environment with python version >=3.9 and <=3.11: "Using an environment with python version >=3.9 and <=3.11"
[methods] If you do not have Python installed, we recommend installing the Anaconda distribution of Python: "If you do not have Python installed, we recommend installing the Anaconda distribution of Python"
[readme] conda create --name MSIGen python=3.11 -y; conda activate MSIGen: "conda create --name MSIGen python=3.11 -y conda activate MSIGen"
[methods] you can instead download Miniconda from https://www.anaconda.com/download/success: "you can instead download Miniconda from https://www.anaconda.com/download/success"