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11 months ago Codecov Report
Attention: 36 lines in your changes are missing coverage. Please review.
Comparison is base (
9f272fc) 79.54% compared to head (60a914e) 79.49%. Report is 2 commits behind head on master.
Additional details and impacted files
```diff @@ Coverage Diff @@ ## master #226 +/- ## ========================================== - Coverage 79.54% 79.49% -0.06% ========================================== Files 89 89 Lines 7948 8050 +102 ========================================== + Hits 6322 6399 +77 - Misses 1626 1651 +25 ``` | [Files](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab) | Coverage Δ | | |---|---|---| | [cassiopeia/data/CassiopeiaTree.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9kYXRhL0Nhc3Npb3BlaWFUcmVlLnB5) | `91.78% <100.00%> (+0.02%)` | :arrow_up: | | [cassiopeia/solver/GreedySolver.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvR3JlZWR5U29sdmVyLnB5) | `98.64% <100.00%> (+0.07%)` | :arrow_up: | | [cassiopeia/solver/HybridSolver.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvSHlicmlkU29sdmVyLnB5) | `74.78% <100.00%> (-0.22%)` | :arrow_down: | | [cassiopeia/solver/NeighborJoiningSolver.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvTmVpZ2hib3JKb2luaW5nU29sdmVyLnB5) | `70.88% <ø> (ø)` | | | [cassiopeia/solver/UPGMASolver.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvVVBHTUFTb2x2ZXIucHk=) | `73.21% <ø> (ø)` | | | [cassiopeia/solver/VanillaGreedySolver.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvVmFuaWxsYUdyZWVkeVNvbHZlci5weQ==) | `100.00% <100.00%> (ø)` | | | [cassiopeia/mixins/utilities.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9taXhpbnMvdXRpbGl0aWVzLnB5) | `91.66% <93.75%> (+11.66%)` | :arrow_up: | | [cassiopeia/solver/DistanceSolver.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvRGlzdGFuY2VTb2x2ZXIucHk=) | `59.32% <16.66%> (-1.21%)` | :arrow_down: | | [cassiopeia/solver/dissimilarity\_functions.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvZGlzc2ltaWxhcml0eV9mdW5jdGlvbnMucHk=) | `84.82% <84.37%> (-0.13%)` | :arrow_down: | | [cassiopeia/plotting/local.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9wbG90dGluZy9sb2NhbC5weQ==) | `88.01% <40.00%> (-1.95%)` | :arrow_down: | | ... and [2 more](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/226?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab) | |:umbrella: View full report in Codecov by Sentry.
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mattjones315
This PR implements two important changes.
Supporting ambiguous alleles in Cassiopeia Greedy algorithm.
Specific changes:
cassiopeia.mixins.utilitiesSupporting parallel dissimilarity matrix
We implement a parallel dissimilarity matrix computation. Due to compatibility issues with
numba, I introduce a wrapper function around the main bones of the dissimilarity map computation, and allow this to operate on batches. I notice a slight slow down for computations that would be numba jit-compatible (on the order of seconds) but I find drastic runtime improvements for computations that are not jit-compatible. This becomes particularly important for cases dealing with ambiguous alleles as currently the cluster dissimilarity function is not able to be compiled innopythonmode. Thus, dramatic speedups - roughly proportional the number of threads, ~10x speedup with 10 threads (as one would expect).I also find that implementing more prescriptive cluster dissimilarity functions (e.g., specific function for
linkage=np.minanddissimilarity_function=weighted_hamming_distance) allows the function to be compiled withnopython=False, forceobj=True, which does speed up the computation noticeably. I retain the original cluster computation to keep it backwards compatible and to allow users to experiment with various linkages and dissimilarity functions on cases where performance is not such an issue.