Add macros to LsHmm_forward_matrix and LsHmm_backward_matrix

szhan commented 9 months ago

Fixes #2841

codecov[bot] commented 9 months ago

Codecov Report

Merging #2853 (c5ccb42) into main (25116f6) will decrease coverage by 0.19%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #2853      +/-   ##
==========================================
- Coverage   89.94%   89.76%   -0.19%     
==========================================
  Files          28       30       +2     
  Lines       22849    29907    +7058     
  Branches     4621     5803    +1182     
==========================================
+ Hits        20552    26845    +6293     
- Misses       1281     1755     +474     
- Partials     1016     1307     +291

Flag	Coverage Δ
c-tests	`86.15% <ø> (ø)`
lwt-tests	`80.78% <ø> (ø)`
python-c-tests	`67.90% <100.00%> (?)`
python-tests	`98.92% <ø> (ø)`

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Files	Coverage Δ
python/_tskitmodule.c	`88.69% <100.00%> (ø)`

... and 4 files with indirect coverage changes

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jeromekelleher commented 9 months ago

The linter is stupid here and doing the wrong thing. The only solution is to put in some comments to force it not to join lines that shouldn't be joined (see other usages of PyBEGIN etc)

szhan commented 9 months ago

lint is doing it in other places like

    Py_BEGIN_ALLOW_THREADS err = tsk_treeseq_genealogical_nearest_neighbours(
        self->tree_sequence, PyArray_DATA(focal_array), num_focal, reference_sets,
        reference_set_size, num_reference_sets, 0, PyArray_DATA(ret_array));
    Py_END_ALLOW_THREADS if (err != 0)
    {
        handle_library_error(err);
        goto out;
    }

szhan commented 9 months ago

I'm not sure how to test that the macros are working here. I guess we could add tests that look like the ones in test_threading.py, but I'm not sure if it is testing what we want in this case.

jeromekelleher commented 9 months ago

I think we should drop this and do your multi-threaded matching using processes instead @szhan

tskit-dev / tskit

Add macros to LsHmm_forward_matrix and LsHmm_backward_matrix #2853

Codecov Report