Fix CI linting not finding clang

Author: benjeffery

.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:

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

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);

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.

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. "

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;
 }