Rename classes for clarity, add missing teardown

Author: rly

src/nwb_benchmarks/benchmarks/network_tracking_remote_file_reading.py

@@ -3,6 +3,9 @@
 
 The benchmarks should be consistent with the timing benchmarks - each function should be the same but wrapped in a
 network activity tracker.
+
+Note: even though garbage collection does not affect network activity, we still store the in-memory objects to be
+consistent with timing benchmarks.
 """
 
 import shutil
@@ -47,8 +50,6 @@ class HDF5H5pyFileReadBenchmark(BaseBenchmark):
     Track the network activity during read of remote HDF5 files with h5py using each streaming method.
 
     There is no formal parsing of the `pynwb.NWBFile` object.
-
-    Note: in all cases, store the in-memory objects to be consistent with timing benchmarks.
     """
 
     params = hdf5_redirected_read_params
@@ -122,13 +123,13 @@ def track_network_read_hdf5_h5py_ros3(self, params: dict[str, str]):
 class HDF5PyNWBFileReadBenchmark(BaseBenchmark):
     """
     Track the network activity during read of remote HDF5 NWB files with pynwb using each streaming method.
-
-    Note: in all cases, store the in-memory objects to be consistent with timing benchmarks.
     """
 
     params = hdf5_redirected_read_params
 
     def teardown(self, params: dict[str, str]):
+        if hasattr(self, "io"):
+            self.io.close()
         if hasattr(self, "file"):
             self.file.close()
         if hasattr(self, "bytestream"):
@@ -204,7 +205,7 @@ def track_network_read_hdf5_pynwb_ros3(self, params: dict[str, str]):
 
 class HDF5PyNWBFsspecHttpsPreloadedNoCacheFileReadBenchmark(BaseBenchmark):
     """
-    Time the read of remote HDF5 NWB files using pynwb and fsspec with HTTPS with preloaded data without cache.
+    Track the network activity during read of remote HDF5 NWB files using pynwb and fsspec with HTTPS with preloaded data without cache.
     """
 
     params = hdf5_redirected_read_params
@@ -213,6 +214,14 @@ def setup(self, params: dict[str, str]):
         https_url = params["https_url"]
         self.nwbfile, self.io, self.file, self.bytestream = read_hdf5_pynwb_fsspec_https_no_cache(https_url=https_url)
 
+    def teardown(self, params: dict[str, str]):
+        if hasattr(self, "io"):
+            self.io.close()
+        if hasattr(self, "file"):
+            self.file.close()
+        if hasattr(self, "bytestream"):
+            self.bytestream.close()
+
     @skip_benchmark_if(TSHARK_PATH is None)
     def track_network_read_hdf5_pynwb_fsspec_https_preloaded_no_cache(self, params: dict[str, str]):
         """Read remote NWB file using pynwb and fsspec with HTTPS with preloaded data without cache."""
@@ -226,7 +235,7 @@ def track_network_read_hdf5_pynwb_fsspec_https_preloaded_no_cache(self, params:
 
 class HDF5PyNWBFsspecHttpsPreloadedWithCacheFileReadBenchmark(BaseBenchmark):
     """
-    Time the read of remote HDF5 NWB files using pynwb and fsspec with HTTPS with preloaded cache.
+    Track the network activity during read of remote HDF5 NWB files using pynwb and fsspec with HTTPS with preloaded cache.
     """
 
     params = hdf5_redirected_read_params
@@ -237,6 +246,17 @@ def setup(self, params: dict[str, str]):
             https_url=https_url
         )
 
+    def teardown(self, params: dict[str, str]):
+        if hasattr(self, "io"):
+            self.io.close()
+        if hasattr(self, "file"):
+            self.file.close()
+        if hasattr(self, "bytestream"):
+            self.bytestream.close()
+        if hasattr(self, "tmpdir"):
+            shutil.rmtree(path=self.tmpdir.name, ignore_errors=True)
+            self.tmpdir.cleanup()
+
     @skip_benchmark_if(TSHARK_PATH is None)
     def track_network_read_hdf5_pynwb_fsspec_https_preloaded_with_cache(self, params: dict[str, str]):
         """Read remote NWB file using pynwb and fsspec with HTTPS with preloaded cache."""
@@ -250,7 +270,7 @@ def track_network_read_hdf5_pynwb_fsspec_https_preloaded_with_cache(self, params
 
 class HDF5PyNWBFsspecS3PreloadedNoCacheFileReadBenchmark(BaseBenchmark):
     """
-    Time the read of remote HDF5 NWB files using pynwb and fsspec with S3 with preloaded data without cache.
+    Track the network activity during read of remote HDF5 NWB files using pynwb and fsspec with S3 with preloaded data without cache.
     """
 
     params = hdf5_redirected_read_params
@@ -259,6 +279,14 @@ def setup(self, params: dict[str, str]):
         https_url = params["https_url"]
         self.nwbfile, self.io, self.file, self.bytestream = read_hdf5_pynwb_fsspec_s3_no_cache(https_url=https_url)
 
+    def teardown(self, params: dict[str, str]):
+        if hasattr(self, "io"):
+            self.io.close()
+        if hasattr(self, "file"):
+            self.file.close()
+        if hasattr(self, "bytestream"):
+            self.bytestream.close()
+
     @skip_benchmark_if(TSHARK_PATH is None)
     def track_network_read_hdf5_pynwb_fsspec_s3_preloaded_no_cache(self, params: dict[str, str]):
         """Read remote NWB file using pynwb and fsspec with S3 with preloaded data without cache."""
@@ -270,7 +298,7 @@ def track_network_read_hdf5_pynwb_fsspec_s3_preloaded_no_cache(self, params: dic
 
 class HDF5PyNWBFsspecS3PreloadedWithCacheFileReadBenchmark(BaseBenchmark):
     """
-    Time the read of remote HDF5 NWB files using pynwb and fsspec with S3 with preloaded cache.
+    Track the network activity during read of remote HDF5 NWB files using pynwb and fsspec with S3 with preloaded cache.
     """
 
     params = hdf5_redirected_read_params
@@ -281,6 +309,17 @@ def setup(self, params: dict[str, str]):
             https_url=https_url
         )
 
+    def teardown(self, params: dict[str, str]):
+        if hasattr(self, "io"):
+            self.io.close()
+        if hasattr(self, "file"):
+            self.file.close()
+        if hasattr(self, "bytestream"):
+            self.bytestream.close()
+        if hasattr(self, "tmpdir"):
+            shutil.rmtree(path=self.tmpdir.name, ignore_errors=True)
+            self.tmpdir.cleanup()
+
     @skip_benchmark_if(TSHARK_PATH is None)
     def track_network_read_hdf5_pynwb_fsspec_s3_preloaded_with_cache(self, params: dict[str, str]):
         """Read remote NWB file using pynwb and fsspec with S3 with preloaded cache."""
@@ -294,7 +333,7 @@ def track_network_read_hdf5_pynwb_fsspec_s3_preloaded_with_cache(self, params: d
 
 class HDF5PyNWBRemfilePreloadedNoCacheFileReadBenchmark(BaseBenchmark):
     """
-    Time the read of remote HDF5 NWB files using pynwb and remfile with preloaded data without cache.
+    Track the network activity during read of remote HDF5 NWB files using pynwb and remfile with preloaded data without cache.
     """
 
     params = hdf5_redirected_read_params
@@ -303,6 +342,14 @@ def setup(self, params: dict[str, str]):
         https_url = params["https_url"]
         self.nwbfile, self.io, self.file, self.bytestream = read_hdf5_pynwb_remfile_no_cache(https_url=https_url)
 
+    def teardown(self, params: dict[str, str]):
+        if hasattr(self, "io"):
+            self.io.close()
+        if hasattr(self, "file"):
+            self.file.close()
+        if hasattr(self, "bytestream"):
+            self.bytestream.close()
+
     @skip_benchmark_if(TSHARK_PATH is None)
     def track_network_read_hdf5_pynwb_remfile_preloaded_no_cache(self, params: dict[str, str]):
         """Read remote NWB file using pynwb and remfile with preloaded data without cache."""
@@ -314,7 +361,7 @@ def track_network_read_hdf5_pynwb_remfile_preloaded_no_cache(self, params: dict[
 
 class HDF5PyNWBRemfilePreloadedWithCacheFileReadBenchmark(BaseBenchmark):
     """
-    Time the read of remote HDF5 NWB files using pynwb and remfile with preloaded cache.
+    Track the network activity during read of remote HDF5 NWB files using pynwb and remfile with preloaded cache.
     """
 
     params = hdf5_redirected_read_params
@@ -325,6 +372,17 @@ def setup(self, params: dict[str, str]):
             https_url=https_url
         )
 
+    def teardown(self, params: dict[str, str]):
+        if hasattr(self, "io"):
+            self.io.close()
+        if hasattr(self, "file"):
+            self.file.close()
+        if hasattr(self, "bytestream"):
+            self.bytestream.close()
+        if hasattr(self, "tmpdir"):
+            shutil.rmtree(path=self.tmpdir.name, ignore_errors=True)
+            self.tmpdir.cleanup()
+
     @skip_benchmark_if(TSHARK_PATH is None)
     def track_network_read_hdf5_pynwb_remfile_preloaded_with_cache(self, params: dict[str, str]):
         """Read remote NWB file using pynwb and remfile with preloaded cache."""
@@ -367,8 +425,6 @@ class LindiLocalJSONFileReadBenchmark(BaseBenchmark):
 
     This downloads the remote LINDI JSON file during setup if it does not already exist in the persistent download
     directory.
-
-    Note: in all cases, store the in-memory objects to be consistent with timing benchmarks.
     """
 
     params = lindi_no_redirect_download_params
@@ -402,8 +458,6 @@ def track_network_read_lindi_pynwb(self, params: dict[str, str]):
 class ZarrZarrPythonFileReadBenchmark(BaseBenchmark):
     """
     Track the network activity during read of remote Zarr files with Zarr-Python only (not using PyNWB)
-
-    Note: in all cases, store the in-memory objects to avoid timing garbage collection steps.
     """
 
     params = zarr_direct_read_params
@@ -444,8 +498,6 @@ def track_network_read_zarr_s3_force_no_consolidated(self, params: dict[str, str
 class ZarrPyNWBFileReadBenchmark(BaseBenchmark):
     """
     Track the network activity during read of remote Zarr NWB files with pynwb.
-
-    Note: in all cases, store the in-memory objects to be consistent with timing benchmarks.
     """
 
     params = zarr_direct_read_params