[c++, python] Apply latest reviews for re-indexer

single-cell-data · Jan 19, 2024 · 08931d3 · 08931d3
1 parent 625f4a2
commit 08931d3
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Showing 7 changed files with 14 additions and 23 deletions.
diff --git a/.github/workflows/r-ci.yml b/.github/workflows/r-ci.yml
@@ -51,9 +51,6 @@ jobs:
       - name: Bootstrap
         run: cd apis/r && tools/r-ci.sh bootstrap
 
-      - name: Install tiledb
-        run: cd apis/r && Rscript -e 'remotes::install_version("tiledb", "0.22.0")'
-
       - name: Install BioConductor package SingleCellExperiment
         run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment
 

diff --git a/apis/python/src/tiledbsoma/_experiment.py b/apis/python/src/tiledbsoma/_experiment.py
@@ -45,6 +45,7 @@ class Experiment(  # type: ignore[misc]  # __eq__ false positive
             A collection of named measurements.
 
     Example:
+        >>> import tiledbsoma
         >>> with tiledbsoma.open("/path/to/experiment") as exp:
         ...     # While users can interact directly with an Experiment's fields:
         ...     obs_df = exp.obs

diff --git a/libtiledbsoma/src/reindexer/example.py b/libtiledbsoma/src/reindexer/example.py
@@ -11,7 +11,7 @@ def main():
     with cellxgene_census.open_soma(**census_s3) as census:
         with census["census_data"]["homo_sapiens"].axis_query(
             measurement_name="RNA",
-            obs_query=soma.AxisQuery(value_filter="""tissue_general == 'eye'"""),
+            obs_query=soma.AxisQuery(value_filter="tissue_general == 'eye'"),
         ) as query:
             query.to_anndata(X_name="raw")
     t2 = perf_counter()

diff --git a/libtiledbsoma/src/reindexer/reindexer.cc b/libtiledbsoma/src/reindexer/reindexer.cc
@@ -5,7 +5,7 @@
  *
  * The MIT License
  *
- * @copyright Copyright (c) 2022 TileDB, Inc.
+ * @copyright Copyright (c) 2024 TileDB, Inc.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -76,11 +76,7 @@ void IntIndexer::map_locations(const int64_t* keys, int size, int threads) {
     int64_t counter = 0;
     // Hash map construction
     for (int i = 0; i < size; i++) {
-        k = kh_put(
-            m64,
-            hash_,
-            keys[i],
-            &ret);  // hash_wrapper<IntType>::put(hash_, key, &ret);
+        k = kh_put(m64, hash_, keys[i], &ret);
         assert(k != kh_end(hash_));
         kh_val(hash_, k) = counter;
         counter++;
@@ -100,10 +96,7 @@ void IntIndexer::lookup(const int64_t* keys, int64_t* results, int size) {
         size));
     if (tiledb_thread_pool_->concurrency_level() == 1) {
         for (int i = 0; i < size; i++) {
-            auto k = kh_get(
-                m64,
-                hash_,
-                keys[i]);  // hash_wrapper<IntType>::get(hash_, keys[i]);
+            auto k = kh_get(m64, hash_, keys[i]);
             if (k == kh_end(hash_)) {
                 // According to pandas behavior
                 results[i] = -1;

diff --git a/libtiledbsoma/src/reindexer/reindexer.h b/libtiledbsoma/src/reindexer/reindexer.h
@@ -5,7 +5,7 @@
  *
  * The MIT License
  *
- * @copyright Copyright (c) 2022 TileDB, Inc.
+ * @copyright Copyright (c) 2024 TileDB, Inc.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -30,7 +30,9 @@
  * This file defines the a pybind11 api into SOMA C++ library.
  */
 
-#pragma once
+#ifndef TILEDBSOMA_REINDEXER_H
+#define TILEDBSOMA_REINDEXER_H
+
 #include <assert.h>
 #include <unistd.h>
 #include <memory>
@@ -97,3 +99,5 @@ class IntIndexer {
 };
 
 }  // namespace tiledbsoma
+
+#endif  // TILEDBSOMA_REINDEXER_H
diff --git a/libtiledbsoma/test/test_indexer.cc b/libtiledbsoma/test/test_indexer.cc
@@ -5,7 +5,7 @@
  *
  * The MIT License
  *
- * @copyright Copyright (c) 2022 TileDB, Inc.
+ * @copyright Copyright (c) 2024 TileDB, Inc.
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -27,7 +27,7 @@
  *
  * @section DESCRIPTION
  *
- * This file manages unit tests for column buffers
+ * This file manages unit tests for re-indexer
  */
 
 #include <reindexer/reindexer.h>

diff --git a/libtiledbsoma/test/test_indexer.py b/libtiledbsoma/test/test_indexer.py
@@ -182,10 +182,6 @@ def indexer_test_pass(keys: np.array, lookups: np.array):
 ]
 
 
-def main():
+def test_indexer():
     for data in test_data:
         indexer_test(data["keys"], data["lookups"], not data["pass"])
-
-
-if __name__ == "__main__":
-    main()