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Co-authored-by: nguyenv <[email protected]>
single-cell-data · Sep 4, 2024 · 6dba46b · 6dba46b
1 parent aa02a85
commit 6dba46b
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Showing 7 changed files with 14 additions and 15 deletions.
diff --git a/apis/python/src/tiledbsoma/soma_dataframe.cc b/apis/python/src/tiledbsoma/soma_dataframe.cc
@@ -148,7 +148,8 @@ void load_soma_dataframe(py::module& m) {
         .def_property_readonly(
             "maybe_soma_joinid_shape", &SOMADataFrame::maybe_soma_joinid_shape)
         .def_property_readonly(
-            "maybe_soma_joinid_maxshape", &SOMADataFrame::maybe_soma_joinid_maxshape)
+            "maybe_soma_joinid_maxshape",
+            &SOMADataFrame::maybe_soma_joinid_maxshape)
         .def_property_readonly(
             "count",
             &SOMADataFrame::count,

diff --git a/apis/python/tests/test_shape.py b/apis/python/tests/test_shape.py
@@ -97,15 +97,14 @@ def test_sparse_nd_array_basics(
         # TODO: make sure this doesn't come through as RuntimeError
         # https://github.com/single-cell-data/TileDB-SOMA/issues/2407
         with pytest.raises((RuntimeError, ValueError)):
-            coords = tuple([arg_shape[i] + 10 for i in range(ndim)])
+            coords = tuple(arg_shape[i] + 10 for i in range(ndim))
             snda.read(coords).tables().concat()
 
     # Test writes out of bounds
     with tiledbsoma.SparseNDArray.open(uri, "w") as snda:
         with pytest.raises(tiledbsoma.SOMAError):
             dikt = {"soma_data": [30]}
-            for i in range(ndim):
-                dikt[dim_names[i]] = [arg_shape[i] + 20]
+            dikt = {name: [shape + 20] for name, shape in zip(dim_names, arg_shape)}
             table = pa.Table.from_pydict(dikt)
             snda.write(table)
 

diff --git a/apis/python/tests/test_sparse_nd_array.py b/apis/python/tests/test_sparse_nd_array.py
@@ -56,8 +56,8 @@ def test_sparse_nd_array_create_ok(
     # https://github.com/single-cell-data/TileDB-SOMA/issues/2407
     assert isinstance(a.maxshape, tuple)
     assert len(a.maxshape) == len(a.shape)
-    for i in range(len(a.shape)):
-        assert a.maxshape[i] >= a.shape[i]
+    for maxshape, shape in zip(a.maxshape, a.shape):
+        assert maxshape >= shape
 
     assert a.is_sparse is True
 

diff --git a/libtiledbsoma/src/soma/soma_array.cc b/libtiledbsoma/src/soma/soma_array.cc
@@ -77,7 +77,7 @@ std::unique_ptr<SOMAArray> SOMAArray::create(
     return std::make_unique<SOMAArray>(ctx, array, timestamp);
 }
 
-std::unique_ptr<SOMAArray> SOMAArray::open( // XXX TOUCH
+std::unique_ptr<SOMAArray> SOMAArray::open(  // XXX TOUCH
     OpenMode mode,
     std::string_view uri,
     std::string_view name,
@@ -143,7 +143,7 @@ SOMAArray::SOMAArray(
     fill_metadata_cache();
 }
 
-SOMAArray::SOMAArray( // XXX TOUCH
+SOMAArray::SOMAArray(  // XXX TOUCH
     OpenMode mode,
     std::string_view uri,
     std::shared_ptr<SOMAContext> ctx,

diff --git a/libtiledbsoma/src/soma/soma_array.h b/libtiledbsoma/src/soma/soma_array.h
@@ -85,7 +85,7 @@ class SOMAArray : public SOMAObject {
      * @param timestamp Optional pair indicating timestamp start and end
      * @return std::unique_ptr<SOMAArray> SOMAArray
      */
-    static std::unique_ptr<SOMAArray> open( // XXX
+    static std::unique_ptr<SOMAArray> open(  // XXX
         OpenMode mode,
         std::string_view uri,
         std::string_view name = "unnamed",
@@ -157,7 +157,7 @@ class SOMAArray : public SOMAObject {
      * @param result_order Result order
      * @param timestamp Timestamp
      */
-    SOMAArray( // XXX TOUCH
+    SOMAArray(  // XXX TOUCH
         OpenMode mode,
         std::string_view uri,
         std::shared_ptr<SOMAContext> ctx,

diff --git a/libtiledbsoma/src/soma/soma_dataframe.cc b/libtiledbsoma/src/soma/soma_dataframe.cc
@@ -68,13 +68,12 @@ std::unique_ptr<SOMADataFrame> SOMADataFrame::open(
         mode, uri, ctx, column_names, result_order, timestamp);
 }
 
-std::unique_ptr<SOMADataFrame> SOMADataFrame::open( // XXX TOUCH
+std::unique_ptr<SOMADataFrame> SOMADataFrame::open(  // XXX TOUCH
     std::string_view uri,
     OpenMode mode,
     std::string_view name,
     std::map<std::string, std::string> platform_config) {
-    return std::make_unique<SOMADataFrame>(
-        mode, uri, name, platform_config);
+    return std::make_unique<SOMADataFrame>(mode, uri, name, platform_config);
 }
 
 bool SOMADataFrame::exists(

diff --git a/libtiledbsoma/src/soma/soma_dataframe.h b/libtiledbsoma/src/soma/soma_dataframe.h
@@ -100,7 +100,7 @@ class SOMADataFrame : public SOMAArray {
      * @param ctx TO WRITE
      * @return std::unique_ptr<SOMADataFrame> SOMADataFrame
      */
-    static std::unique_ptr<SOMADataFrame> open( // XXX
+    static std::unique_ptr<SOMADataFrame> open(  // XXX
         std::string_view uri,
         OpenMode mode,
         std::string_view name,
@@ -155,7 +155,7 @@ class SOMADataFrame : public SOMAArray {
      * @param TO WRITE
      * @param TO WRITE
      */
-    SOMADataFrame( // XXX
+    SOMADataFrame(  // XXX
         OpenMode mode,
         std::string_view uri,
         std::string_view name,