Parallelization

.github/workflows/python-package.yml

@@ -1,5 +1,5 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
 name: Python package
 
@@ -16,19 +16,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        python setup.py install
+        pip install ".[dev]"
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

CHANGELOG.md

@@ -0,0 +1,64 @@
+# CHANGELOG
+
+<!-- ## 0.0.XX (2025-XX-XX)
+
+Features:
+
+- 
+
+Fixes:
+
+-  -->
+
+## 0.0.13 (2025-03-31)
+
+Features:
+
+- Added new functions for parallel mutations extraction
+- Outgroup now is optional node in the tree; ingroup now is just the sister node of outgroup and outgroup is the node that grow up from the root
+
+Fixes:
+
+- Repair package; pyproject.toml is work now. Setup.py deprecated, but simplified version saved.
+- circular imports fixed
+- all scripts now have main func
+
+## 0.0.11 (2024-10-24)
+
+Features:
+
+- Edges sampling by @kpotoh in https://github.com/mitoclub/PyMutSpec/pull/9
+- added barplots with errorbars
+- citation added to readme
+
+Fixes:
+
+- fixed bug that allow short sequences be used in expected freqs calculation
+
+**Full Changelog**: https://github.com/mitoclub/PyMutSpec/compare/0.0.10...0.0.11
+
+## 0.0.10 (2024-04-14)
+
+Features:
+
+- added availability to collect non-syn mutational spectrum
+- added a couple of arguments to calculate_mutspec func: scale, drop_underrepresented (this will drop mut types less than 0.9 by default)
+
+Fixes:
+
+- drop Times New Roman from default font for spectrum barplots
+- deleted legacy log/doc files from repo
+- added few tests for expected mutations collecting funcs
+- fix scripts/calculate_mutspec.py : previously it failed when there was no mutations on branches, and reduced mutnum thresholds
+
+## 0.0.8 (2023-11-13)
+
+Features:
+
+- Added little tests for plot functions
+- Added few new functions from analysis notebooks, that used to tree spectra analysis
+
+Fixes:
+
+- Fixed uncertainty coefficient (phylocoef) calculation: based on only ingroup and geometric mean of distances from root to leaves
+- General test for collect_mutations.py main class

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2018 The Python Packaging Authority
+Copyright (c) 2025 mitofungen.com
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

pymutspec/__init__.py

@@ -1,4 +1 @@
-from pymutspec import annotation, draw, io, constants, utils
-
-# Define the pymutspec version
-__version__ = "0.0.12"
+__version__ = "0.0.13"

pymutspec/annotation/__init__.py

@@ -1,5 +1,5 @@
 from .auxiliary import lbl2lbl_id, lbl_id2lbl, rev_comp, transcriptor
-from .tree import iter_tree_edges, node_parent, calc_phylocoefs, get_ingroup_root, get_tree_len, get_tree_outgrp_name
+from .tree import iter_tree_edges, node_parent, calc_phylocoefs, get_ingroup_root, get_tree_len
 from .spectra import (
     calculate_mutspec, collapse_mutspec, calc_edgewise_spectra, 
     complete_sbs192_columns, jackknife_spectra_sampling, collapse_sbs192,