Properly close file before next data opened (#360)

* Properly close file before next data opened

* Do not use libver='latest', more compatible hdf5 file

Author: ksunden

CHANGELOG.md

@@ -4,6 +4,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 
 ## [Unreleased]
 
+### Fixed
+- Properly close files prior to new data file creation (fix file inconsistency)
+- Do not use h5py libver="latest" (fix segfault upon copying)
+
 ## [2021.1.0]
 
 ### Added

yaqc_cmds/somatic/_wt5.py

@@ -13,16 +13,21 @@
 
 class DataContainer(object):
     def __init__(self):
-        self.data = None
+        self._data = None
         self.data_filepath = None
         self.last_idx_written = None
         self.lock = threading.RLock()
 
     def __enter__(self):
         self.lock.acquire()
-        return self.data
+        if self.data_filepath:
+            self._data = wt.open(self.data_filepath, edit_local=True)
+        return self._data
 
     def __exit__(self, exc_type, exc_value, traceback):
+        if self._data:
+            self._data.close()
+        self._data = None
         self.lock.release()
 
 
@@ -49,14 +54,9 @@ def create_data(path, headers, destinations, axes, constants, hardware, sensors)
     sensors: list of yaqc_cmds._sensors.Sensor objects
         all active sensors
     """
-    f = h5py.File(path, "w", libver="latest")
+    f = h5py.File(path, "w")
     global data_container
     with data_container as data:
-
-        if data_container.data is not None:
-            data_container.data.close()
-            data_container.data = None
-
         data = wt.Data(f, name=headers["name"], edit_local=True)
         data_container.data_filepath = path
 
@@ -150,7 +150,6 @@ def create_data(path, headers, destinations, axes, constants, hardware, sensors)
             # TODO signed?
             # TODO labels?
 
-        data_container.data = data
         somatic.signals.data_file_created.emit()