SuchTree 1.3

New for SuchTree v1.3

• Automatic URL/file/NEWICK input no longer broken
• Custom exception classes
• Improved naming conventions of methods & properties
• Refactored node query methods
• Regularized naming and arguments for distance methods
• Refactored topology analysis methods
• More traversal methods
• Refactored graph theory and matrix operations
• Refactored export methods
• Stubs for backward compatibility with deprecation warnings
• Improved test coverage
• Various bug fixes
• Verified commits for GitHub, digital attestations for PiPy
• Renamed master to main
• New logo, website and documentation

Full Changelog: v1.2...v1.3

SuchTree 1.2

New features :

• Support for quartet tests
• Direct NEWICK string input

SuchTree 1.1

This release adds wheels for Linux on ARM and Windows on x86_64, and adds some new features :

• Basic support for support values provided by SuchTree.get_support( node_id )
• Relative evolutionary divergence (RED)
• Bipartitions
• Node generators for in-order and preorder traversal
• Summary of leaf relationships via SuchTree.relationships()

New Contributors

• @mmore500 made their first contribution in #23

Full Changelog: v1.0...v1.1

SuchTree 1.0

SuchTree 1.0 :

• Build system overhaul
• TravisCI -> GitHub Actions
• Standardized module structure
• Automatic wheel builds using cibuildwheel
  • CPython : 3.6, 3.7, 3.8, 3.9, 3.10
  • OS : Linux x86_64, MacOS x86_64, MacOS amd64

Build system overhaul

Not much about SuchTree itself has changed, but the build system has been completely overhauled.

• Migrated build and unit tests from TravisCI to GitHub Actions
• Wheels for Linux on amd64 and MacOS on Intel silicon are now automatically built using cibuildwheel
• Dependencies should now be identified and installed correctly
• Various minor cosmetic fixes

JOSS release

• revised examples notebooks
• new example data for big trees
• added installation instructions
• fixed sundry typos in the documentation

Release for JOSS review

Python3 support. New testing framework. Improved release engineering. Archived with Zenodo.

now, with igraph!

Added support for igraph output from SuchLinkedTrees!

Actual 0.2 release

Some new features and bug fixes to make SuchTree maybe actually useful.