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Refactor plotting functions, improve tests, and update README - #16

Merged

kpotoh merged 21 commits into

masterfrom

modify-package

Jul 16, 2026

Merged

Refactor plotting functions, improve tests, and update README#16
kpotoh merged 21 commits into
masterfrom
modify-package

Commits on Mar 31, 2025
- src-layout and manual upload of 14 version
  kpotoh
  committed
  eb568c6
Commits on Feb 19, 2026
- add support of latest version of seaborn
  kpotoh
  committed
  822872d
- Update README and refactor plotting functions for mutational spectra
  kpotoh
  committed
  0621c3d
- fix TODO
  kpotoh
  committed
  6803723
- Merge branch 'seaborn-fix' into modify-package
  kpotoh
  committed
  7ef7f7e
Commits on Feb 20, 2026
- Initial plan
  Copilot
  committed
  57ece97
- Fix broken tests, add docstrings, improve test coverage
  
  Copilot
  and
  kpotoh
  committed
  53f0356
- Address code review: improve assertion messages and docstring pattern notation
  
  Copilot
  and
  kpotoh
  committed
  973023e
- Revert sbs_orders.py to commented state; fix KK label support in plot_mutspec
  
  Copilot
  and
  kpotoh
  committed
  759695c
- Improve README with comprehensive user guide based on chordata notebooks
  
  Copilot
  and
  kpotoh
  committed
  a19e3f8
- Initial plan
  Copilot
  committed
  d844e38
- Merge pull request #14 from mitoclub/copilot/improve-tests-and-docs
  kpotoh
  authored
  81fd6e2
- Replace ete3 with custom PhyloNode/PhyloTree using BioPython
  
  Copilot
  and
  kpotoh
  committed
  78c7b98
- Rename PhyloNode/PhyloTree to TreeNode/Tree; add ete3 comparison tests
  
  Copilot
  and
  kpotoh
  committed
  1d4e725
- Merge branch 'modify-package' into copilot/remove-ete3-replace-with-biopython
  kpotoh
  authored
  8fe8717
- Merge pull request #15 from mitoclub/copilot/remove-ete3-replace-with-biopython
  kpotoh
  authored
  14f7b8a
- check tests after ete3 replacement
  kpotoh
  committed
  2d83677
Commits on Jul 15, 2026
- lints and some devs before new changes
  kpotoh
  committed
  7402a36
Commits on Jul 16, 2026

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Refactor plotting functions, improve tests, and update README - #16

Refactor plotting functions, improve tests, and update README#16
kpotoh merged 21 commits into
masterfrom
modify-package

Commits on Mar 31, 2025

src-layout and manual upload of 14 version

Commits on Feb 19, 2026

add support of latest version of seaborn

Update README and refactor plotting functions for mutational spectra

fix TODO

Merge branch 'seaborn-fix' into modify-package

Commits on Feb 20, 2026

Initial plan

Fix broken tests, add docstrings, improve test coverage

Address code review: improve assertion messages and docstring pattern notation

Revert sbs_orders.py to commented state; fix KK label support in plot_mutspec

Improve README with comprehensive user guide based on chordata notebooks

Initial plan

Merge pull request #14 from mitoclub/copilot/improve-tests-and-docs

Replace ete3 with custom PhyloNode/PhyloTree using BioPython

Rename PhyloNode/PhyloTree to TreeNode/Tree; add ete3 comparison tests

Merge branch 'modify-package' into copilot/remove-ete3-replace-with-biopython

Merge pull request #15 from mitoclub/copilot/remove-ete3-replace-with-biopython

check tests after ete3 replacement

Commits on Jul 15, 2026

lints and some devs before new changes

Commits on Jul 16, 2026

test on all versions using tox and pyenv

remove tqdm from deps; remove requirement of CDS be divisible by 3

remove "assert tree.name != 'ROOT'" to fix phylocoef calc AND rename tree_len to tree_heigth