new release v2.1.0

[sreichl]

Fix bugs and add features.

[sreichl]

@martin5555555555 please put here a draft for the release notes for v2.1.0. As discussed, I often split it into three sections features, bug fixes and documentation. Have a look at my previous release notes and also consider all commits since the last release (not only yours).

Then write it up in a comprehensive but concise manner here as a comment (you can provide AI with the commit history, your notes, my previous release notes as template etc.).

You can also try using Codex + local git history for a first draft, unsure how well this works.

[martin5555555555]

New release V2.1.0 : Adding Specific terms and retrieval of Greats region hits, extending documentation

Features

• Added summary_specificTerms, highlighting terms that are more specific to one group
• Simplified group-level summary outputs by focusing on summary bubble plots instead of the previous heatmap-based summaries.
• Extended pycisTarget outputs with additional exported tables for:
  • motif hits
  • cistromes
• Extended GREAT result tables with annotated regions and associated genes for relevant terms.
• Added a helper script and example usage for converting feature lists to BED files for region-based enrichment workflows.

Bug fixes

• Improved handling of empty BED/query/background inputs across region-based workflows, including GREAT, LOLA, and GREAT-based region-to-gene association, preventing unnecessary workflow failures on edge cases.
• Fixed the coordinate convention mismatch between BED files and GREAT-derived region-gene association outputs by exporting coordinates in BED-style indexing.
• Improved robustness of aggregation and summary plotting for sparse result sets, including cases with very small matrices or empty outputs.
• Added clearer behavior for empty summary plots so downstream reporting remains stable even when no significant terms are found.

Documentation

• Expanded the documentation with guidance on how to skip selected enrichment tools when they are not needed.
• Added reusable example Snakemake download rules for commonly used enrichment resources and databases.
• Updated the README to reflect the current output structure, including BED indexing conventions and the new summary plot outputs.
• Added publication- and author-related metadata updates.
• Added example of rules to download common databases in a md file in the helper folder