Brief summary

• define a list of core modules to be installed, per default
• only install module specific dependencies on request

Auto-generated Summary

This pull request improves dependency management and documentation for optional features in the project. It introduces an all optional dependency group in pyproject.toml for non-core analysis modules, updates documentation and example notebooks to install both core and optional dependencies, and adds clearer error messages when optional dependencies are missing. Additionally, it updates the __init__.py files to provide better import structure and user guidance.

Dependency management and installation:

• Added an all optional dependency group in pyproject.toml to bundle all non-core analysis dependencies (e.g., biopython, lifelines, networkx, kmapper, snfpy, etc.), making it easier for users to install optional features with pip install "acore[all]".
• Updated the main dependencies and organized them by theme (core, scientific computing, enrichment analysis, batch correction, IO, types), and moved vuecore to the docs group for documentation visualization. [1] [2]

Documentation and examples:

• Updated all example notebooks and scripts to instruct users to install both acore and vuecore (and, by implication, other optional dependencies) for full functionality, using %pip install acore vuecore. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10]

Improved error handling for optional dependencies:

• Added try/except blocks in __init__.py files of optional modules (e.g., kaplan_meier_analysis, network_analysis, publications_analysis, tda_analysis) to raise informative errors if required optional dependencies are missing, guiding users to install them via the appropriate pip command. [1] [2] [3] [4]

Codebase and import improvements:

• Updated src/acore/__init__.py to explicitly import all submodules and include them in __all__, improving discoverability and import structure.

Minor updates:

• Updated jupytext_version metadata in example scripts for consistency. [1] [2] [3] [4]

These changes make the project easier to install, use, and troubleshoot, especially when working with optional analysis modules.- in the future with the default dependencies

Checks

• Look at CONTRIBUTING.md for guidance on how to contribute.