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benjefferybenjeffery
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Fix lint
1 parent 8f7d514 commit 32c2845

5 files changed

Lines changed: 69 additions & 59 deletions

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‎c/tests/test_core.c‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -532,7 +532,7 @@ test_bit_arrays(void)
532532
// NB: This test is only valid for the 32 bit implementation of bit arrays. If we
533533
// were to change the chunk size of a bit array, we'd need to update these tests
534534
tsk_bit_array_t arr;
535-
tsk_id_t items_truth[64] = {0}, items[64] = {0};
535+
tsk_id_t items_truth[64] = { 0 }, items[64] = { 0 };
536536
tsk_size_t n_items = 0, n_items_truth = 0;
537537

538538
// test item retrieval

‎c/tests/test_stats.c‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -348,7 +348,7 @@ verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_flags_t options)
348348

349349
/* test various bin assignments */
350350
for (i = 0; i < N; i++) {
351-
node_bin_map[i] = ((tsk_id_t) (i % B));
351+
node_bin_map[i] = ((tsk_id_t)(i % B));
352352
}
353353
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
354354
index_tuples, T, breakpoints, B, node_bin_map, options, C_B);
@@ -3694,8 +3694,8 @@ static void
36943694
test_pair_coalescence_counts_missing(void)
36953695
{
36963696
tsk_treeseq_t ts;
3697-
tsk_treeseq_from_text(&ts, 5, missing_ex_nodes, missing_ex_edges, NULL,
3698-
NULL, NULL, NULL, NULL, 0);
3697+
tsk_treeseq_from_text(
3698+
&ts, 5, missing_ex_nodes, missing_ex_edges, NULL, NULL, NULL, NULL, NULL, 0);
36993699
verify_pair_coalescence_counts(&ts, 0);
37003700
verify_pair_coalescence_counts(&ts, TSK_STAT_SPAN_NORMALISE);
37013701
tsk_treeseq_free(&ts);

‎c/tests/testlib.c‎

Lines changed: 22 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -373,31 +373,29 @@ const char *empty_ex_nodes = "1 0.0 0 -1\n"
373373
const char *empty_ex_edges = "";
374374

375375
/*** An example of a tree sequence with missing marginal trees. ***/
376-
/*
377-
| 4 | | 4 |
378-
| / \ | | / \ |
379-
| 3 \ | | / 3 |
380-
| / \ \ | | / / \ |
381-
| 0 1 2 | | 0 1 2 |
382-
|-|-----------|-|-----------|-|
383-
0 1 2 3 4 5
376+
/*
377+
| 4 | | 4 |
378+
| / \ | | / \ |
379+
| 3 \ | | / 3 |
380+
| / \ \ | | / / \ |
381+
| 0 1 2 | | 0 1 2 |
382+
|-|-----------|-|-----------|-|
383+
0 1 2 3 4 5
384384
*/
385-
const char *missing_ex_nodes =
386-
"1 0.0 0 -1\n"
387-
"1 0.0 0 -1\n"
388-
"1 0.0 0 -1\n"
389-
"0 1.0 0 -1\n"
390-
"0 2.0 0 -1\n";
391-
392-
const char *missing_ex_edges =
393-
"1.0 2.0 3 0\n"
394-
"1.0 2.0 3 1\n"
395-
"3.0 4.0 3 1\n"
396-
"3.0 4.0 3 2\n"
397-
"3.0 4.0 4 0\n"
398-
"1.0 2.0 4 2\n"
399-
"1.0 2.0 4 3\n"
400-
"3.0 4.0 4 3\n";
385+
const char *missing_ex_nodes = "1 0.0 0 -1\n"
386+
"1 0.0 0 -1\n"
387+
"1 0.0 0 -1\n"
388+
"0 1.0 0 -1\n"
389+
"0 2.0 0 -1\n";
390+
391+
const char *missing_ex_edges = "1.0 2.0 3 0\n"
392+
"1.0 2.0 3 1\n"
393+
"3.0 4.0 3 1\n"
394+
"3.0 4.0 3 2\n"
395+
"3.0 4.0 4 0\n"
396+
"1.0 2.0 4 2\n"
397+
"1.0 2.0 4 3\n"
398+
"3.0 4.0 4 3\n";
401399

402400
/* Simple utilities to parse text so we can write declaritive
403401
* tests. This is not intended as a robust general input mechanism.

‎c/tskit/core.c‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -168,7 +168,8 @@ tsk_strerror_internal(int err)
168168
break;
169169
case TSK_ERR_FILE_VERSION_TOO_OLD:
170170
ret = "tskit file version too old. Please upgrade using the "
171-
"'tskit upgrade' command from tskit version<0.6.2. (TSK_ERR_FILE_VERSION_TOO_OLD)";
171+
"'tskit upgrade' command from tskit version<0.6.2. "
172+
"(TSK_ERR_FILE_VERSION_TOO_OLD)";
172173
break;
173174
case TSK_ERR_FILE_VERSION_TOO_NEW:
174175
ret = "tskit file version is too new for this instance. "

‎python/_tskitmodule.c‎

Lines changed: 41 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -223,7 +223,8 @@ handle_library_error(int err)
223223
const char *not_kas_format_msg
224224
= "File not in kastore format. Either the file is corrupt or it is not a "
225225
"tskit tree sequence file. It may be a legacy HDF file upgradable with "
226-
"`tskit upgrade` from tskit version<0.6.2 or a compressed tree sequence file that can be decompressed "
226+
"`tskit upgrade` from tskit version<0.6.2 or a compressed tree sequence file "
227+
"that can be decompressed "
227228
"with `tszip`.";
228229
const char *ibd_pairs_not_stored_msg
229230
= "Sample pairs are not stored by default "
@@ -8743,38 +8744,38 @@ TreeSequence_get_individuals_nodes(TreeSequence *self)
87438744
}
87448745

87458746
num_individuals = tsk_treeseq_get_num_individuals(self->tree_sequence);
8746-
8747+
87478748
individual_nodes = self->tree_sequence->individual_nodes;
87488749
individual_nodes_length = self->tree_sequence->individual_nodes_length;
8749-
8750-
for (tsk_id_t i = 0; i < (tsk_id_t)num_individuals; i++) {
8750+
8751+
for (tsk_id_t i = 0; i < (tsk_id_t) num_individuals; i++) {
87518752
ploidy = individual_nodes_length[i];
87528753
if (ploidy > max_ploidy) {
87538754
max_ploidy = ploidy;
87548755
}
87558756
}
8756-
8757-
dims[0] = (npy_intp)num_individuals;
8758-
dims[1] = (npy_intp)max_ploidy;
8759-
ret_array = (PyArrayObject *)PyArray_SimpleNew(2, dims, NPY_INT32);
8757+
8758+
dims[0] = (npy_intp) num_individuals;
8759+
dims[1] = (npy_intp) max_ploidy;
8760+
ret_array = (PyArrayObject *) PyArray_SimpleNew(2, dims, NPY_INT32);
87608761
if (ret_array == NULL) {
87618762
goto out;
87628763
}
8763-
8764+
87648765
/* Fill with -1 (TSK_NULL) */
8765-
node_mem = (tsk_id_t *)PyArray_DATA(ret_array);
8766+
node_mem = (tsk_id_t *) PyArray_DATA(ret_array);
87668767
memset(node_mem, 0xFF, PyArray_NBYTES(ret_array));
8767-
8768-
for (tsk_id_t i = 0; i < (tsk_id_t)num_individuals; i++) {
8768+
8769+
for (tsk_id_t i = 0; i < (tsk_id_t) num_individuals; i++) {
87698770
ploidy = individual_nodes_length[i];
87708771
for (j = 0; j < ploidy; j++) {
87718772
node_mem[i * max_ploidy + j] = individual_nodes[i][j];
87728773
}
87738774
}
87748775

8775-
ret = (PyObject *)ret_array;
8776+
ret = (PyObject *) ret_array;
87768777
ret_array = NULL;
8777-
8778+
87788779
out:
87798780
Py_XDECREF(ret_array);
87808781
return ret;
@@ -9771,12 +9772,12 @@ TreeSequence_weighted_stat_vector_method(
97719772
if (result_array == NULL) {
97729773
goto out;
97739774
}
9774-
Py_BEGIN_ALLOW_THREADS
9775-
err = method(self->tree_sequence, w_shape[1], PyArray_DATA(weights_array),
9776-
num_windows, PyArray_DATA(windows_array), num_focal_nodes,
9777-
PyArray_DATA(focal_nodes_array), PyArray_DATA(result_array), options);
9778-
Py_END_ALLOW_THREADS
9779-
if (err != 0) {
9775+
Py_BEGIN_ALLOW_THREADS err
9776+
= method(self->tree_sequence, w_shape[1], PyArray_DATA(weights_array),
9777+
num_windows, PyArray_DATA(windows_array), num_focal_nodes,
9778+
PyArray_DATA(focal_nodes_array), PyArray_DATA(result_array), options);
9779+
Py_END_ALLOW_THREADS if (err != 0)
9780+
{
97809781
handle_library_error(err);
97819782
goto out;
97829783
}
@@ -10800,7 +10801,8 @@ TreeSequence_get_individuals_metadata(TreeSequence *self, void *closure)
1080010801
goto out;
1080110802
}
1080210803
individuals = self->tree_sequence->tables->individuals;
10803-
ret = TreeSequence_make_array(self, individuals.metadata_length, NPY_UINT8, individuals.metadata);
10804+
ret = TreeSequence_make_array(
10805+
self, individuals.metadata_length, NPY_UINT8, individuals.metadata);
1080410806
out:
1080510807
return ret;
1080610808
}
@@ -10891,7 +10893,8 @@ TreeSequence_get_nodes_metadata(TreeSequence *self, void *closure)
1089110893
goto out;
1089210894
}
1089310895
nodes = self->tree_sequence->tables->nodes;
10894-
ret = TreeSequence_make_array(self, nodes.metadata_length, NPY_UINT8, nodes.metadata);
10896+
ret = TreeSequence_make_array(
10897+
self, nodes.metadata_length, NPY_UINT8, nodes.metadata);
1089510898
out:
1089610899
return ret;
1089710900
}
@@ -10982,7 +10985,8 @@ TreeSequence_get_edges_metadata(TreeSequence *self, void *closure)
1098210985
goto out;
1098310986
}
1098410987
edges = self->tree_sequence->tables->edges;
10985-
ret = TreeSequence_make_array(self, edges.metadata_length, NPY_UINT8, edges.metadata);
10988+
ret = TreeSequence_make_array(
10989+
self, edges.metadata_length, NPY_UINT8, edges.metadata);
1098610990
out:
1098710991
return ret;
1098810992
}
@@ -10997,7 +11001,8 @@ TreeSequence_get_edges_metadata_offset(TreeSequence *self, void *closure)
1099711001
goto out;
1099811002
}
1099911003
edges = self->tree_sequence->tables->edges;
11000-
ret = TreeSequence_make_array(self, edges.num_rows + 1, NPY_UINT64, edges.metadata_offset);
11004+
ret = TreeSequence_make_array(
11005+
self, edges.num_rows + 1, NPY_UINT64, edges.metadata_offset);
1100111006
out:
1100211007
return ret;
1100311008
}
@@ -11027,7 +11032,8 @@ TreeSequence_get_sites_metadata(TreeSequence *self, void *closure)
1102711032
goto out;
1102811033
}
1102911034
sites = self->tree_sequence->tables->sites;
11030-
ret = TreeSequence_make_array(self, sites.metadata_length, NPY_UINT8, sites.metadata);
11035+
ret = TreeSequence_make_array(
11036+
self, sites.metadata_length, NPY_UINT8, sites.metadata);
1103111037
out:
1103211038
return ret;
1103311039
}
@@ -11042,7 +11048,8 @@ TreeSequence_get_sites_metadata_offset(TreeSequence *self, void *closure)
1104211048
goto out;
1104311049
}
1104411050
sites = self->tree_sequence->tables->sites;
11045-
ret = TreeSequence_make_array(self, sites.num_rows + 1, NPY_UINT64, sites.metadata_offset);
11051+
ret = TreeSequence_make_array(
11052+
self, sites.num_rows + 1, NPY_UINT64, sites.metadata_offset);
1104611053
out:
1104711054
return ret;
1104811055
}
@@ -11117,7 +11124,8 @@ TreeSequence_get_mutations_metadata(TreeSequence *self, void *closure)
1111711124
goto out;
1111811125
}
1111911126
mutations = self->tree_sequence->tables->mutations;
11120-
ret = TreeSequence_make_array(self, mutations.metadata_length, NPY_UINT8, mutations.metadata);
11127+
ret = TreeSequence_make_array(
11128+
self, mutations.metadata_length, NPY_UINT8, mutations.metadata);
1112111129
out:
1112211130
return ret;
1112311131
}
@@ -11132,7 +11140,8 @@ TreeSequence_get_mutations_metadata_offset(TreeSequence *self, void *closure)
1113211140
goto out;
1113311141
}
1113411142
mutations = self->tree_sequence->tables->mutations;
11135-
ret = TreeSequence_make_array(self, mutations.num_rows + 1, NPY_UINT64, mutations.metadata_offset);
11143+
ret = TreeSequence_make_array(
11144+
self, mutations.num_rows + 1, NPY_UINT64, mutations.metadata_offset);
1113611145
out:
1113711146
return ret;
1113811147
}
@@ -11241,7 +11250,8 @@ TreeSequence_get_migrations_metadata(TreeSequence *self, void *closure)
1124111250
goto out;
1124211251
}
1124311252
migrations = self->tree_sequence->tables->migrations;
11244-
ret = TreeSequence_make_array(self, migrations.metadata_length, NPY_UINT8, migrations.metadata);
11253+
ret = TreeSequence_make_array(
11254+
self, migrations.metadata_length, NPY_UINT8, migrations.metadata);
1124511255
out:
1124611256
return ret;
1124711257
}
@@ -11272,7 +11282,8 @@ TreeSequence_get_populations_metadata(TreeSequence *self, void *closure)
1127211282
goto out;
1127311283
}
1127411284
populations = self->tree_sequence->tables->populations;
11275-
ret = TreeSequence_make_array(self, populations.metadata_length, NPY_UINT8, populations.metadata);
11285+
ret = TreeSequence_make_array(
11286+
self, populations.metadata_length, NPY_UINT8, populations.metadata);
1127611287
out:
1127711288
return ret;
1127811289
}

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