Maintain all pending index entries.

CHANGELOG.rst

@@ -15,6 +15,8 @@ Change Log
 
 *Fixed:*
 
+* Write all pending index entries to the file when `gsd_flush()` is called after `gsd_write_chunk()`
+  and before `gsd_end_frame()` (`#319 <https://github.com/glotzerlab/gsd/pull/319>`__).
 * Readthedocs builds with pandas 2.2.0
   (`#322 <https://github.com/glotzerlab/gsd/pull/322>`__).
 

gsd/gsd.c

@@ -2012,7 +2012,7 @@ int gsd_flush(struct gsd_handle* handle)
                 {
                 handle->frame_index.data[i]
                     = handle->frame_index
-                          .data[handle->frame_index.size - handle->pending_index_entries];
+                          .data[handle->frame_index.size - handle->pending_index_entries + i];
                 }
             }
 

gsd/test/test_fl.py

@@ -1146,3 +1146,29 @@ def test_file_exists_error():
             schema_version=[1, 2],
         ):
             pass
+
+
+def test_pending_index_entries(tmp_path):
+    """Ensure that gsd preserves pending index entries."""
+    with gsd.fl.open(
+        tmp_path / 'test_pending_index_entries.gsd',
+        'w',
+        application='My application',
+        schema='My Schema',
+        schema_version=[1, 0],
+    ) as f:
+        # Frame 0 must be complete to trigger the bug.
+        f.write_chunk(name='0', data=numpy.array([0]))
+        f.end_frame()
+
+        for i in range(16):
+            f.write_chunk(name=str(i), data=numpy.array([i]))
+
+        # Flush with pending chunks in the frame index.
+        f.flush()
+
+        f.end_frame()
+
+        # All test chunks should be present in the file.
+        for i in range(16):
+            assert f.chunk_exists(name=str(i), frame=1)