diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index fb443fbc1a..99169f1b7c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -22,9 +22,10 @@ jobs: - name: install clang-format if: steps.clang_format.outputs.cache-hit != 'true' run: | - python -m venv env - source env/bin/activate - pip install clang-format==6.0.1 + pip install setuptools clang-format==6.0.1 + clang-format -version + sudo cp /opt/hostedtoolcache/Python/3.12.10/x64/bin/clang-format /opt/hostedtoolcache/Python/3.12.10/x64/bin/clang-format-6.0 + clang-format-6.0 -version - uses: pre-commit/action@v3.0.1 benchmark: diff --git a/c/tests/test_core.c b/c/tests/test_core.c index eed22fc1ca..6a14ecc655 100644 --- a/c/tests/test_core.c +++ b/c/tests/test_core.c @@ -532,7 +532,7 @@ test_bit_arrays(void) // NB: This test is only valid for the 32 bit implementation of bit arrays. If we // were to change the chunk size of a bit array, we'd need to update these tests tsk_bit_array_t arr; - tsk_id_t items_truth[64] = {0}, items[64] = {0}; + tsk_id_t items_truth[64] = { 0 }, items[64] = { 0 }; tsk_size_t n_items = 0, n_items_truth = 0; // test item retrieval diff --git a/c/tests/test_stats.c b/c/tests/test_stats.c index f55cdcee50..22faf2256c 100644 --- a/c/tests/test_stats.c +++ b/c/tests/test_stats.c @@ -348,7 +348,7 @@ verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_flags_t options) /* test various bin assignments */ for (i = 0; i < N; i++) { - node_bin_map[i] = ((tsk_id_t) (i % B)); + node_bin_map[i] = ((tsk_id_t)(i % B)); } ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I, index_tuples, T, breakpoints, B, node_bin_map, options, C_B); @@ -3694,8 +3694,8 @@ static void test_pair_coalescence_counts_missing(void) { tsk_treeseq_t ts; - tsk_treeseq_from_text(&ts, 5, missing_ex_nodes, missing_ex_edges, NULL, - NULL, NULL, NULL, NULL, 0); + tsk_treeseq_from_text( + &ts, 5, missing_ex_nodes, missing_ex_edges, NULL, NULL, NULL, NULL, NULL, 0); verify_pair_coalescence_counts(&ts, 0); verify_pair_coalescence_counts(&ts, TSK_STAT_SPAN_NORMALISE); tsk_treeseq_free(&ts); diff --git a/c/tests/testlib.c b/c/tests/testlib.c index 1f05178627..637a59e681 100644 --- a/c/tests/testlib.c +++ b/c/tests/testlib.c @@ -373,31 +373,29 @@ const char *empty_ex_nodes = "1 0.0 0 -1\n" const char *empty_ex_edges = ""; /*** An example of a tree sequence with missing marginal trees. ***/ -/* - | 4 | | 4 | - | / \ | | / \ | - | 3 \ | | / 3 | - | / \ \ | | / / \ | - | 0 1 2 | | 0 1 2 | - |-|-----------|-|-----------|-| - 0 1 2 3 4 5 +/* + | 4 | | 4 | + | / \ | | / \ | + | 3 \ | | / 3 | + | / \ \ | | / / \ | + | 0 1 2 | | 0 1 2 | + |-|-----------|-|-----------|-| + 0 1 2 3 4 5 */ -const char *missing_ex_nodes = - "1 0.0 0 -1\n" - "1 0.0 0 -1\n" - "1 0.0 0 -1\n" - "0 1.0 0 -1\n" - "0 2.0 0 -1\n"; - -const char *missing_ex_edges = - "1.0 2.0 3 0\n" - "1.0 2.0 3 1\n" - "3.0 4.0 3 1\n" - "3.0 4.0 3 2\n" - "3.0 4.0 4 0\n" - "1.0 2.0 4 2\n" - "1.0 2.0 4 3\n" - "3.0 4.0 4 3\n"; +const char *missing_ex_nodes = "1 0.0 0 -1\n" + "1 0.0 0 -1\n" + "1 0.0 0 -1\n" + "0 1.0 0 -1\n" + "0 2.0 0 -1\n"; + +const char *missing_ex_edges = "1.0 2.0 3 0\n" + "1.0 2.0 3 1\n" + "3.0 4.0 3 1\n" + "3.0 4.0 3 2\n" + "3.0 4.0 4 0\n" + "1.0 2.0 4 2\n" + "1.0 2.0 4 3\n" + "3.0 4.0 4 3\n"; /* Simple utilities to parse text so we can write declaritive * tests. This is not intended as a robust general input mechanism. diff --git a/c/tskit/core.c b/c/tskit/core.c index 2b0078bf08..175505439e 100644 --- a/c/tskit/core.c +++ b/c/tskit/core.c @@ -168,7 +168,8 @@ tsk_strerror_internal(int err) break; case TSK_ERR_FILE_VERSION_TOO_OLD: ret = "tskit file version too old. Please upgrade using the " - "'tskit upgrade' command from tskit version<0.6.2. (TSK_ERR_FILE_VERSION_TOO_OLD)"; + "'tskit upgrade' command from tskit version<0.6.2. " + "(TSK_ERR_FILE_VERSION_TOO_OLD)"; break; case TSK_ERR_FILE_VERSION_TOO_NEW: ret = "tskit file version is too new for this instance. " diff --git a/python/_tskitmodule.c b/python/_tskitmodule.c index e79a876467..a9ee1ba188 100644 --- a/python/_tskitmodule.c +++ b/python/_tskitmodule.c @@ -223,7 +223,8 @@ handle_library_error(int err) const char *not_kas_format_msg = "File not in kastore format. Either the file is corrupt or it is not a " "tskit tree sequence file. It may be a legacy HDF file upgradable with " - "`tskit upgrade` from tskit version<0.6.2 or a compressed tree sequence file that can be decompressed " + "`tskit upgrade` from tskit version<0.6.2 or a compressed tree sequence file " + "that can be decompressed " "with `tszip`."; const char *ibd_pairs_not_stored_msg = "Sample pairs are not stored by default " @@ -9715,12 +9716,12 @@ TreeSequence_weighted_stat_vector_method( if (result_array == NULL) { goto out; } - Py_BEGIN_ALLOW_THREADS - err = method(self->tree_sequence, w_shape[1], PyArray_DATA(weights_array), - num_windows, PyArray_DATA(windows_array), num_focal_nodes, - PyArray_DATA(focal_nodes_array), PyArray_DATA(result_array), options); - Py_END_ALLOW_THREADS - if (err != 0) { + Py_BEGIN_ALLOW_THREADS err + = method(self->tree_sequence, w_shape[1], PyArray_DATA(weights_array), + num_windows, PyArray_DATA(windows_array), num_focal_nodes, + PyArray_DATA(focal_nodes_array), PyArray_DATA(result_array), options); + Py_END_ALLOW_THREADS if (err != 0) + { handle_library_error(err); goto out; } @@ -10744,7 +10745,8 @@ TreeSequence_get_individuals_metadata(TreeSequence *self, void *closure) goto out; } individuals = self->tree_sequence->tables->individuals; - ret = TreeSequence_make_array(self, individuals.metadata_length, NPY_UINT8, individuals.metadata); + ret = TreeSequence_make_array( + self, individuals.metadata_length, NPY_UINT8, individuals.metadata); out: return ret; } @@ -10835,7 +10837,8 @@ TreeSequence_get_nodes_metadata(TreeSequence *self, void *closure) goto out; } nodes = self->tree_sequence->tables->nodes; - ret = TreeSequence_make_array(self, nodes.metadata_length, NPY_UINT8, nodes.metadata); + ret = TreeSequence_make_array( + self, nodes.metadata_length, NPY_UINT8, nodes.metadata); out: return ret; } @@ -10926,7 +10929,8 @@ TreeSequence_get_edges_metadata(TreeSequence *self, void *closure) goto out; } edges = self->tree_sequence->tables->edges; - ret = TreeSequence_make_array(self, edges.metadata_length, NPY_UINT8, edges.metadata); + ret = TreeSequence_make_array( + self, edges.metadata_length, NPY_UINT8, edges.metadata); out: return ret; } @@ -10941,7 +10945,8 @@ TreeSequence_get_edges_metadata_offset(TreeSequence *self, void *closure) goto out; } edges = self->tree_sequence->tables->edges; - ret = TreeSequence_make_array(self, edges.num_rows + 1, NPY_UINT64, edges.metadata_offset); + ret = TreeSequence_make_array( + self, edges.num_rows + 1, NPY_UINT64, edges.metadata_offset); out: return ret; } @@ -10971,7 +10976,8 @@ TreeSequence_get_sites_metadata(TreeSequence *self, void *closure) goto out; } sites = self->tree_sequence->tables->sites; - ret = TreeSequence_make_array(self, sites.metadata_length, NPY_UINT8, sites.metadata); + ret = TreeSequence_make_array( + self, sites.metadata_length, NPY_UINT8, sites.metadata); out: return ret; } @@ -10986,7 +10992,8 @@ TreeSequence_get_sites_metadata_offset(TreeSequence *self, void *closure) goto out; } sites = self->tree_sequence->tables->sites; - ret = TreeSequence_make_array(self, sites.num_rows + 1, NPY_UINT64, sites.metadata_offset); + ret = TreeSequence_make_array( + self, sites.num_rows + 1, NPY_UINT64, sites.metadata_offset); out: return ret; } @@ -11061,7 +11068,8 @@ TreeSequence_get_mutations_metadata(TreeSequence *self, void *closure) goto out; } mutations = self->tree_sequence->tables->mutations; - ret = TreeSequence_make_array(self, mutations.metadata_length, NPY_UINT8, mutations.metadata); + ret = TreeSequence_make_array( + self, mutations.metadata_length, NPY_UINT8, mutations.metadata); out: return ret; } @@ -11076,7 +11084,8 @@ TreeSequence_get_mutations_metadata_offset(TreeSequence *self, void *closure) goto out; } mutations = self->tree_sequence->tables->mutations; - ret = TreeSequence_make_array(self, mutations.num_rows + 1, NPY_UINT64, mutations.metadata_offset); + ret = TreeSequence_make_array( + self, mutations.num_rows + 1, NPY_UINT64, mutations.metadata_offset); out: return ret; } @@ -11185,7 +11194,8 @@ TreeSequence_get_migrations_metadata(TreeSequence *self, void *closure) goto out; } migrations = self->tree_sequence->tables->migrations; - ret = TreeSequence_make_array(self, migrations.metadata_length, NPY_UINT8, migrations.metadata); + ret = TreeSequence_make_array( + self, migrations.metadata_length, NPY_UINT8, migrations.metadata); out: return ret; } @@ -11216,7 +11226,8 @@ TreeSequence_get_populations_metadata(TreeSequence *self, void *closure) goto out; } populations = self->tree_sequence->tables->populations; - ret = TreeSequence_make_array(self, populations.metadata_length, NPY_UINT8, populations.metadata); + ret = TreeSequence_make_array( + self, populations.metadata_length, NPY_UINT8, populations.metadata); out: return ret; }