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benjefferymergify[bot]
benjeffery
authored and
mergify[bot]
committedJun 27, 2022
Update to tskit 1.0.0
·
1.3.31.3.0
1 parent f717961 commit d70abaa

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13 files changed

+35
-35
lines changed

13 files changed

+35
-35
lines changed
 

‎git-submodules/tskit

Submodule tskit updated 102 files

‎lib/dev-tools/dev-cli.c

+1-1
Original file line numberDiff line numberDiff line change
@@ -830,7 +830,7 @@ run_simulate(
830830
if (ret != 0) {
831831
fatal_msprime_error(ret, __LINE__);
832832
}
833-
ret = tsk_treeseq_init(&tree_seq, &tables, TSK_BUILD_INDEXES);
833+
ret = tsk_treeseq_init(&tree_seq, &tables, TSK_TS_INIT_BUILD_INDEXES);
834834
if (ret != 0) {
835835
fatal_tskit_error(ret, __LINE__);
836836
}

‎lib/msprime.c

+2-2
Original file line numberDiff line numberDiff line change
@@ -3446,7 +3446,7 @@ msp_process_input_trees(msp_t *self)
34463446
memset(&ts, 0, sizeof(ts));
34473447
memset(&tree, 0, sizeof(tree));
34483448

3449-
ret = tsk_treeseq_init(&ts, self->tables, TSK_BUILD_INDEXES);
3449+
ret = tsk_treeseq_init(&ts, self->tables, TSK_TS_INIT_BUILD_INDEXES);
34503450
if (ret != 0) {
34513451
ret = msp_set_tsk_error(ret);
34523452
goto out;
@@ -7178,7 +7178,7 @@ msp_set_simulation_model_fixed_pedigree(msp_t *self)
71787178
const tsk_size_t num_nodes = self->tables->nodes.num_rows;
71797179
pedigree_t *pedigree = &self->pedigree;
71807180

7181-
ret = tsk_treeseq_init(&ts, self->tables, TSK_BUILD_INDEXES);
7181+
ret = tsk_treeseq_init(&ts, self->tables, TSK_TS_INIT_BUILD_INDEXES);
71827182
if (ret != 0) {
71837183
ret = msp_set_tsk_error(ret);
71847184
goto out;

‎lib/subprojects/tskit.wrap

+4-4
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
[wrap-file]
2-
directory = tskit-0.99.15
2+
directory = tskit-1.0.0
33

4-
source_url = https://github.com/tskit-dev/tskit/releases/download/C_0.99.15/tskit-0.99.15.tar.xz
5-
source_filename = tskit-0.99.15.tar.xz
6-
source_hash = 83c38e78c1f508cfae9096d89b46421f58b63e1ca71cc1e5c6f981552f33ef87
4+
source_url = https://github.com/tskit-dev/tskit/releases/download/C_1.0.0/tskit-1.0.0.tar.xz
5+
source_filename = tskit-1.0.0.tar.xz
6+
source_hash = f8a085fc6ef170706b76a307e18be4ab425f31a1f50fa9765ab2c2d81eef65c2

‎lib/tests/test_ancestry.c

+5-5
Original file line numberDiff line numberDiff line change
@@ -1219,7 +1219,7 @@ test_mixed_hudson_dtwf(void)
12191219
ret = msp_finalise_tables(&msp);
12201220
CU_ASSERT_EQUAL_FATAL(ret, 0);
12211221

1222-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
1222+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
12231223
CU_ASSERT_EQUAL_FATAL(ret, 0);
12241224
tsk_treeseq_print_state(&ts, _devnull);
12251225
tsk_treeseq_free(&ts);
@@ -1285,7 +1285,7 @@ test_mixed_hudson_smc(void)
12851285
ret = msp_finalise_tables(&msp);
12861286
CU_ASSERT_EQUAL_FATAL(ret, 0);
12871287

1288-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
1288+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
12891289
CU_ASSERT_EQUAL_FATAL(ret, 0);
12901290
tsk_treeseq_print_state(&ts, _devnull);
12911291
tsk_treeseq_free(&ts);
@@ -1357,7 +1357,7 @@ run_gc_simulation(double sequence_length, double gc_rate, double tract_length,
13571357
msp_free(&msp);
13581358

13591359
/* Make sure we can build a tree sequence out of the result */
1360-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
1360+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
13611361
CU_ASSERT_EQUAL_FATAL(ret, 0);
13621362
tsk_treeseq_free(&ts);
13631363

@@ -2852,7 +2852,7 @@ test_simulation_replicates(void)
28522852
CU_ASSERT_EQUAL_FATAL(ret, 0);
28532853
ret = mutgen_generate(&mutgen, 0);
28542854
CU_ASSERT_EQUAL_FATAL(ret, 0);
2855-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
2855+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
28562856
CU_ASSERT_EQUAL_FATAL(ret, 0);
28572857
tsk_treeseq_print_state(&ts, _devnull);
28582858
mutgen_print_state(&mutgen, _devnull);
@@ -3052,7 +3052,7 @@ verify_simulate_from(int model, rate_map_t *recomb_map,
30523052
CU_ASSERT_TRUE(msp_is_completed(&msp));
30533053
ret = msp_finalise_tables(&msp);
30543054
CU_ASSERT_EQUAL_FATAL(ret, 0);
3055-
ret = tsk_treeseq_init(&final, &tables, TSK_BUILD_INDEXES);
3055+
ret = tsk_treeseq_init(&final, &tables, TSK_TS_INIT_BUILD_INDEXES);
30563056
CU_ASSERT_EQUAL_FATAL(ret, 0);
30573057

30583058
ret = tsk_tree_init(&tree, &final, 0);

‎lib/tests/test_core.c

+3-3
Original file line numberDiff line numberDiff line change
@@ -125,9 +125,9 @@ static void
125125
test_tskit_version(void)
126126
{
127127
/* Make sure we don't have any accidental changes to the tskit submodule. */
128-
CU_ASSERT_EQUAL(TSK_VERSION_MAJOR, 0);
129-
CU_ASSERT_EQUAL(TSK_VERSION_MINOR, 99);
130-
CU_ASSERT_EQUAL(TSK_VERSION_PATCH, 15);
128+
CU_ASSERT_EQUAL(TSK_VERSION_MAJOR, 1);
129+
CU_ASSERT_EQUAL(TSK_VERSION_MINOR, 0);
130+
CU_ASSERT_EQUAL(TSK_VERSION_PATCH, 0);
131131
}
132132

133133
static void

‎lib/tests/test_likelihood.c

+8-8
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,7 @@ test_likelihood_errors(void)
5353
ret = tsk_mutation_table_add_row(
5454
&tables.mutations, 0, 1, -1, TSK_UNKNOWN_TIME, "C", 1, NULL, 0);
5555
CU_ASSERT_FATAL(ret >= 0);
56-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
56+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
5757
CU_ASSERT_EQUAL_FATAL(ret, 0);
5858

5959
/* Ne <= 0 is an error */
@@ -91,7 +91,7 @@ test_likelihood_zero_edges(void)
9191
&tables.nodes, TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
9292
CU_ASSERT_FATAL(ret >= 0);
9393

94-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
94+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
9595
CU_ASSERT_EQUAL_FATAL(ret, 0);
9696

9797
/* Zero edges should give a likelihood of zero */
@@ -115,7 +115,7 @@ test_likelihood_zero_edges(void)
115115
ret = tsk_mutation_table_add_row(
116116
&tables.mutations, 0, 0, -1, TSK_UNKNOWN_TIME, "C", 1, NULL, 0);
117117
CU_ASSERT_FATAL(ret >= 0);
118-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
118+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
119119
CU_ASSERT_EQUAL_FATAL(ret, 0);
120120

121121
/* Zero edges should give a likelihood of zero */
@@ -225,7 +225,7 @@ test_likelihood_three_leaves(void)
225225

226226
tsk_population_table_add_row(&tables.populations, NULL, 0);
227227

228-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
228+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
229229
CU_ASSERT_EQUAL_FATAL(ret, 0);
230230

231231
for (i = 0; i < 3; i++) {
@@ -330,7 +330,7 @@ test_likelihood_two_mrcas(void)
330330

331331
tsk_population_table_add_row(&tables.populations, NULL, 0);
332332

333-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
333+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
334334
CU_ASSERT_EQUAL_FATAL(ret, 0);
335335

336336
for (i = 0; i < 3; i++) {
@@ -440,7 +440,7 @@ test_likelihood_material_overhang(void)
440440
CU_ASSERT_FATAL(ret >= 0);
441441

442442
tsk_population_table_add_row(&tables.populations, NULL, 0);
443-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
443+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
444444
CU_ASSERT_EQUAL_FATAL(ret, 0);
445445

446446
for (i = 0; i < 3; i++) {
@@ -564,7 +564,7 @@ test_likelihood_material_gap(void)
564564
CU_ASSERT_FATAL(ret >= 0);
565565

566566
tsk_population_table_add_row(&tables.populations, NULL, 0);
567-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
567+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
568568
CU_ASSERT_EQUAL_FATAL(ret, 0);
569569

570570
for (i = 0; i < 3; i++) {
@@ -698,7 +698,7 @@ test_likelihood_recombination_in_material_gap(void)
698698
CU_ASSERT_FATAL(ret >= 0);
699699

700700
tsk_population_table_add_row(&tables.populations, NULL, 0);
701-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
701+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
702702
CU_ASSERT_EQUAL_FATAL(ret, 0);
703703

704704
for (i = 0; i < 3; i++) {

‎lib/tests/test_pedigrees.c

+6-6
Original file line numberDiff line numberDiff line change
@@ -87,7 +87,7 @@ verify_complete_pedigree_simulation(
8787
ret = msp_finalise_tables(&msp);
8888
CU_ASSERT_EQUAL_FATAL(ret, 0);
8989

90-
ret = tsk_treeseq_init(&ts, &tables_copy, TSK_BUILD_INDEXES);
90+
ret = tsk_treeseq_init(&ts, &tables_copy, TSK_TS_INIT_BUILD_INDEXES);
9191
CU_ASSERT_EQUAL_FATAL(ret, 0);
9292
ret = tsk_tree_init(&tree, &ts, 0);
9393
CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -150,7 +150,7 @@ verify_pedigree(double recombination_rate, unsigned long seed,
150150
verify_complete_pedigree_simulation(&tables, recombination_rate);
151151

152152
/* Is this a valid tree sequence? */
153-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
153+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
154154
CU_ASSERT_EQUAL_FATAL(ret, 0);
155155
/* tsk_table_collection_print_state(&tables, stdout); */
156156

@@ -439,7 +439,7 @@ test_replicates(void)
439439
CU_ASSERT_EQUAL(ret, MSP_EXIT_MODEL_COMPLETE);
440440
msp_verify(&msp, 0);
441441

442-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
442+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
443443
CU_ASSERT_EQUAL_FATAL(ret, 0);
444444
ret = tsk_tree_init(&tree, &ts, 0);
445445
CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -501,7 +501,7 @@ test_replicates_ancient_samples(void)
501501
ret = msp_finalise_tables(&msp);
502502
CU_ASSERT_EQUAL(ret, 0);
503503

504-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
504+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
505505
CU_ASSERT_EQUAL_FATAL(ret, 0);
506506
ret = tsk_tree_init(&tree, &ts, 0);
507507
CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -563,7 +563,7 @@ test_replicates_early_exit(void)
563563
CU_ASSERT_EQUAL(total_offspring, 50);
564564
}
565565

566-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
566+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
567567
CU_ASSERT_EQUAL_FATAL(ret, 0);
568568
ret = tsk_tree_init(&tree, &ts, 0);
569569
CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -609,7 +609,7 @@ test_replicates_exit_coalescence(void)
609609
CU_ASSERT_EQUAL(ret, MSP_EXIT_COALESCENCE);
610610
msp_print_state(&msp, _devnull);
611611

612-
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
612+
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
613613
CU_ASSERT_EQUAL_FATAL(ret, 0);
614614
ret = tsk_tree_init(&tree, &ts, 0);
615615
CU_ASSERT_EQUAL_FATAL(ret, 0);

‎msprime/_msprimemodule.c

+1-1
Original file line numberDiff line numberDiff line change
@@ -3189,7 +3189,7 @@ msprime_log_likelihood_arg(PyObject *self, PyObject *args, PyObject *kwds)
31893189

31903190
/* Note: this will be inefficient here if we're building indexes for large
31913191
* tables. */
3192-
err = tsk_treeseq_init(&ts, tables->tables, TSK_BUILD_INDEXES);
3192+
err = tsk_treeseq_init(&ts, tables->tables, TSK_TS_INIT_BUILD_INDEXES);
31933193
if (err != 0) {
31943194
handle_tskit_library_error(err);
31953195
goto out;

‎requirements/CI-complete/requirements.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -14,4 +14,4 @@ jsonschema<4.0
1414
python_jsonschema_objects==0.4.1
1515
scipy==1.7.3
1616
stdpopsim==0.1.2
17-
tskit==0.4.0
17+
tskit==0.5.0

‎requirements/CI-tests-conda/requirements.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,6 @@
33
# but demes will pull in the latest so we pin here.
44
jsonschema<4.0
55
gsl
6-
tskit==0.4.0
6+
tskit==0.5.0
77
stdpopsim==0.1.2
88
demes==0.2.1

‎requirements/CI-tests-pip/requirements.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -9,4 +9,4 @@ pytest-xdist==2.4.0
99
jsonschema<5.0
1010
python_jsonschema_objects==0.4.1
1111
scipy==1.7.3
12-
tskit==0.4.0
12+
tskit==0.5.0

‎tests/test_lowlevel.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -440,7 +440,7 @@ def test_gsl_error_handler(self):
440440
def test_tsk_library_version(self):
441441
tsk_version = _msprime.get_tskit_c_version()
442442
# Update this when the tskit C library version changes
443-
assert tsk_version == (0, 99, 15)
443+
assert tsk_version == (1, 0, 0)
444444

445445

446446
def get_random_population_models(n):

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