improvements and infrastructure for testing #34
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a start of Phenotype and test_phenotype Add notebook directory and test_seq_to_fitness notebook more detailed install Adds plot to notebook Minor plot changes, removes torch dependency from requirements.txt Update notebook with Jared's code to use fasta, change plot to plotnine Start of fitness mapping normallization Updated plots Start of replay module, test sigmoidal transformation Add torch back to requirements.txt fix pandas dependency, update fitness modeling Add Fitness class, improve organization in replay add missing parameters clean up Fitness and replay (incomplete) Use dataframe for fitness seqs reformat fitness and replay, fix undefineds improve formatting remove Phenotype class add fitness test, fix df traversal modify fitness test add biopython to requirements add torchdms to requirements, catch file path errors import annotations in fitness, replay (for pre-3.9 support) modify Fitness, add ReplayPhenotype class, remove .DS_Store update notebook, improve argument handling update test_fitness Update Fitness (no fasta, fitness mapping func as member variable) formatting, basic proliferator test add proliferators to cycles, modify methods fix imports fix type hints (for python <3.9) formatting, add cell_div_balanced_proliferator fix balanced proliferator, round distance in timescale check add fitness, replay modules to api.rst add uniform fitness method update docstrings & typehints, update balanced proliferator add test, read naive sites file on phenotype initialization split notebook, add more tree tests format notebooks, plot uniform T cell help start plotting phenotype trajectory fix list type hint for python < 3.9 add Selector ABC, ReplaySelector demonstrate leaf alternation, update test_cycles.py change parameter passing to proliferator update notebooks add option to capture full tree refactor, add hotspot-aware mutator rename ReplayPhenotype, ReplaySelector, fix fitness_method typehint fix mutate_S5F Mutator ABC, update notebooks update notebooks, add competition, remove extra node attributes update hotspot-aware mutator, rename replay.py to phenotype.py visualize lineage imbalance in notebook alternative selector add details to selector update three-step selector, visualize both in one round and several cycles move parameters add parameter sweep script with sampling ranked norm3 method, update notebook show uniform selection in notebook update model usage, add one step sweep modify one step sweep Delete .DS_Store Co-authored-by: Alyssa Pratt <[email protected]> Co-authored-by: Erick Matsen <[email protected]>
docformatter --wrap-descriptions 72 --wrap-summaries 72 --in-place gcdyn/*py
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