v2.2.0

This minor release mainly changes the PPI prior by including self-interactions (diagonal of the PPI matrix) in the priors, which ensures all TFs are present there. The default setting for the PPI prior is now changed to weighted. Tests are greatly improved, and some performance improvements and minor bugfixes were added under the hood.

Highlights:

• Changes to PPI priors
  • Explicitly include self-interactions
  • Weighted by default
• Greatly expanded tests, all the classes have their own tests now
• Some performance improvements for Ensembl retrieval and motif filtering
• Version of SPONGE can now be queried from the command line
• Fingerprint file includes SPONGE version now

v2.1.0

This minor release enables compatiblity with JASPAR 2026 and adds some minor tweaks to output and tests.

Highlights:

• Ensure compatiblity with JASPAR 2026 TFBS files
• Change repository to src layout
• Update tests
• Change tested Python versions (3.9 out, 3.13 in)

v2.0.6

Trying to fix CI/CD to deduce the version on PyPI correctly.

v2.0.5

This release mainly adds the option to use pixi environments for development and testing.

Highlights:

• Add pixi compatibility to pyproject.toml
• Add license notices to code files
• Update documentation slightly
• Updates to CI/CD pipeline
• Reduced the size of the container

v2.0.4

Alas, release 2.0.3 was not the one to fix all the issues, fingers crossed for this one :)

v2.0.3

Hopefully, this release fixes all the outstanding issues in the new CI/CD pipeline :)

v2.0.2

Minor improvements to SPONGE functionality, documentation and CI/CD.

Highlights:

• Several arguments will now get silently converted into length-1 lists if only given a string (e.g. chromosomes), rather than causing error
• STRING score threshold can now be specified
• Updated documentation regarding the container
• Updated deployment pipeline, which should hopefully prevent issues such as the 2.0.0 release :)

v2.0.1

A new release to fix the PyPI upload.

v2.0.0

This release contains extensive refactoring and some changes to the user interface, but the core functionality is mainly unchanged.

Highlighted changes:

• Options should now be specified using a configuration file in yaml format or directly with a dictionary
• Command line interface options were also simplified
• Changes in default settings:
  • Allow multiple motifs per TF: True
  • Only use physical interactions for PPI: True

v1.1.0

Updated Ensembl BioMart interactions and CD/CI, removed dependency on the biomart module.