Alignments using C API #3326
Alignments using C API #3326
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #3326 +/- ##
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- Coverage 89.72% 77.86% -11.86%
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Files 29 29
Lines 31181 31220 +39
Branches 5720 5726 +6
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- Hits 27976 24311 -3665
- Misses 1796 5385 +3589
- Partials 1409 1524 +115
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benjeffery
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Slightly uneasy about the API breakage here, although I agree it's the right approach. I guess returning a numpy array is in practise quite similar to returning an iterator? |
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| flat_arr = np.frombuffer( |
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Can you test that this is definitely the same underlying buffer as the low-level version? A copy would be bad here.
| num_nodes = (tsk_size_t) PyArray_DIM(nodes_array, 0); | ||
| nodes = PyArray_DATA(nodes_array); | ||
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| Py_ssize_t total |
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This is a bit convoluted cast-wise, what about
total = (Py_ssize_t)(num_nodes * (tsk_size_t)(right - left)
standard crib about declarations at the top.
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| buf = PyBytes_AS_STRING(buf_obj); | ||
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| Py_BEGIN_ALLOW_THREADS err = tsk_treeseq_decode_alignments(self->tree_sequence, |
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You have to turn off clang format locally to prevent it messing things up around Py_BEGIN_ALLOW_THREADS
I'm 50/50 on it - I don't like that the iterator suggests to the user that this is a memory efficient method, but you're right that it is bit of a break, although |
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But then |
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I think we follow the pattern. We can add another more explicit numpy approach later if needed. Not breaking stuff is what we do. |
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Also iterator pattern would allow us do things like specify a memory budget,which would be quite handy |
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Stacked on #3319