Ecosyste.ms: Issues

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GitHub / jeromekelleher/phylokit issues and pull requests

#44 - CI Failure on `macos-latest`

Issue - State: closed - Opened by Billyzhang1229 5 months ago

#43 - Update github workflow with setup-python@v5

Pull Request - State: closed - Opened by Billyzhang1229 5 months ago - 3 comments

#42 - Add Unit Tests for utility functions

Issue - State: open - Opened by Billyzhang1229 5 months ago

#41 - Likelihood Calculation Felsenstein

Pull Request - State: closed - Opened by Billyzhang1229 5 months ago - 3 comments

#40 - Fix CI and update dependencies

Pull Request - State: closed - Opened by Billyzhang1229 6 months ago - 1 comment

#39 - Add save and open dataset functions

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago

#38 - Add functions to save and open dataset

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 2 comments

#36 - Fix permute tree tests

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#35 - Parallel parsimony score calculation

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#34 - Add get_node_time function

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 2 comments

#33 - Update the xarray dataset dimensions' name

Issue - State: closed - Opened by Billyzhang1229 about 2 years ago

#32 - Fix permute_tree from ds.samples to ds.sample_node

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 3 comments

#31 - Add new feature for visualizing trees

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#30 - Add function to permute tree with specific ordering

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#29 - Add tree visualize function

Issue - State: closed - Opened by Billyzhang1229 about 2 years ago - 4 comments

#28 - Add permute function

Issue - State: open - Opened by jeromekelleher about 2 years ago

#27 - Add parsimony_score function

Issue - State: open - Opened by jeromekelleher about 2 years ago

#26 - Update linkage_matrix_to_dataset() with a jitted function

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#25 - Update _get_node_partition() using numba and numpy arrays

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 5 comments

#24 - Move numba_njit function to jit.py

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#23 - Simpler implementation of the Preorder Traversal

Issue - State: closed - Opened by Billyzhang1229 about 2 years ago

#22 - Circular import when import other module in core.py

Issue - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#21 - Add rf_distance function with tests for distance metrics

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 2 comments

#20 - Add evaluation notebooks for distance metrics and balance metrics

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#19 - Update current work with the new xarray dataset interface

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 4 comments

#18 - Add preorder and postorder functions

Issue - State: open - Opened by jeromekelleher about 2 years ago - 3 comments

#17 - Add MRCA calculation based on Schieber-Vishkin algorithm

Issue - State: open - Opened by jeromekelleher about 2 years ago - 1 comment

#16 - RF distance

Issue - State: open - Opened by jeromekelleher about 2 years ago - 1 comment

#15 - Add mrca, branch_length and kc_distance functions with tests

Pull Request - State: closed - Opened by Billyzhang1229 about 2 years ago - 1 comment

#14 - Update existing functions to use dataset interface

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 1 comment

#13 - Added initial dataset and UPGMA inference

Pull Request - State: closed - Opened by jeromekelleher about 2 years ago - 3 comments

#12 - No-jit coverage

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 2 comments

#11 - Provide some way for numba to be disabled - coverage

Issue - State: closed - Opened by benjeffery over 2 years ago - 3 comments

#10 - Test PR for coverage checks

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 3 comments

#9 - Coverage

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 2 comments

#8 - Add mrca, branch_length and kc_distance functions with tests

Pull Request - State: closed - Opened by Billyzhang1229 over 2 years ago - 8 comments

#7 - Initial CI

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 3 comments

#6 - Add pre-commit config

Pull Request - State: closed - Opened by benjeffery over 2 years ago

#5 - Add b2_index() and tests for tree balance

Pull Request - State: closed - Opened by Billyzhang1229 over 2 years ago - 2 comments

#4 - Initial draft of design document

Pull Request - State: closed - Opened by jeromekelleher over 2 years ago - 4 comments

#3 - Add colless_index and b1_index for tree balance

Pull Request - State: closed - Opened by Billyzhang1229 over 2 years ago - 1 comment

#2 - Add CI

Issue - State: closed - Opened by jeromekelleher over 2 years ago

#1 - Add ROADMAP.md

Issue - State: open - Opened by jeromekelleher over 2 years ago - 1 comment