From 322e89cf668855bc089bf62dd2c9b92f703a6e38 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Fri, 19 Jan 2024 14:27:11 -0500
Subject: [PATCH 1/4] Add unit test that triggers incorrect behavior with
 pending index entries.

---
 gsd/test/test_fl.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gsd/test/test_fl.py b/gsd/test/test_fl.py
index f3d94294..bdfec68b 100644
--- a/gsd/test/test_fl.py
+++ b/gsd/test/test_fl.py
@@ -1146,3 +1146,24 @@ 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)

From 45b5a4e6e915d05eb2c7729b93cf78ec0bbe5925 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Fri, 19 Jan 2024 14:28:15 -0500
Subject: [PATCH 2/4] Retain all pending index entries.

---
 gsd/gsd.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gsd/gsd.c b/gsd/gsd.c
index 24e70cae..7c254fed 100644
--- a/gsd/gsd.c
+++ b/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];
                 }
             }
 

From 04dd2a9121e865635482a14c8a105a46d54a5ac4 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Fri, 19 Jan 2024 14:33:36 -0500
Subject: [PATCH 3/4] Run pre-commit.

---
 gsd/test/test_fl.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gsd/test/test_fl.py b/gsd/test/test_fl.py
index bdfec68b..ba1185fd 100644
--- a/gsd/test/test_fl.py
+++ b/gsd/test/test_fl.py
@@ -1150,8 +1150,13 @@ def test_file_exists_error():
 
 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:
+    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()

From a32874b8cecd459a4a76ee6f760fbea2ab4f5350 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Mon, 22 Jan 2024 10:10:43 -0500
Subject: [PATCH 4/4] Update change log.

---
 CHANGELOG.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index bea4608b..548397ae 100644
--- a/CHANGELOG.rst
+++ b/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>`__).