Merge branch 'h5py-compat' into 'master'

Add mode argument to call to h5py.File

Closes #80

See merge request !121

.gitlab-ci.yml

@@ -10,7 +10,7 @@ stages:
 variables:
   PROJECT: xsocs
   EXTRA_SETUP_PY_CMD_OPTIONS: "build --no-cython --no-openmp"
-
+  MANYLINUX_PYTHON_VER: cp27-cp27m cp27-cp27mu cp34-cp34m cp35-cp35m cp36-cp36m cp37-cp37m cp38-cp38
 # Build
 
 

xsocs/gui/project/Hdf5Nodes.py

@@ -201,7 +201,7 @@ class H5Base(Node):
         return newChildren
 
     def _refreshNode(self):
-        with h5py.File(self.h5File) as h5f:
+        with h5py.File(self.h5File, mode="r") as h5f:
             thisItem = h5f[self.h5Path]
             try:
                 keys = set(thisItem.keys())

xsocs/gui/project/ProjectNodes.py

@@ -544,7 +544,7 @@ class QSpaceItemNode(ProjectNode):
                 return os.path.exists(qspaceFile)
 
         try:
-            with h5py.File(projectItem.filename) as h5f:
+            with h5py.File(projectItem.filename, mode="a") as h5f:
                 del h5f[self.h5Path]
         except KeyError:
             pass
@@ -664,7 +664,7 @@ class FitItemNode(ProjectNode):
                 return os.path.exists(fitFile)
 
         try:
-            with h5py.File(projectItem.filename) as h5f:
+            with h5py.File(projectItem.filename, mode="a") as h5f:
                 del h5f[self.h5Path]
         except KeyError:
             pass

xsocs/process/shift/shift.py

@@ -68,7 +68,7 @@ class ScanShift(object):
         self.__init_tmp()
 
     def __init_tmp(self):
-        with h5py.File(self.__tmp_file) as tmp_h5:
+        with h5py.File(self.__tmp_file, mode="a") as tmp_h5:
             ref_p0, ref_p1 = _get_ref_positions(self.__xsocs_h5)
             tmp_h5['ref_p0'] = ref_p0
             tmp_h5['ref_p1'] = ref_p1
@@ -174,7 +174,7 @@ class ScanShift(object):
 
         if not self.__dirtyGrids[entry]:
             dsetPath = '/entries/{0}/grid_indices'.format(entry)
-            with h5py.File(self.__tmp_file) as tmp_h5:
+            with h5py.File(self.__tmp_file, mode="r") as tmp_h5:
                 shifted_idx = tmp_h5.get(dsetPath)[:]
         else:
             with xsocs_h5:
@@ -222,7 +222,7 @@ class ScanShift(object):
                                               + col_idx[valid_idx])
 
             dsetPath = '/entries/{0}/grid_indices'.format(entry)
-            with h5py.File(self.__tmp_file) as tmp_h5:
+            with h5py.File(self.__tmp_file, mode="a") as tmp_h5:
                 if dsetPath not in tmp_h5:
                     tmp_h5.create_dataset(dsetPath, data=shifted_idx)
                 else:
@@ -248,14 +248,14 @@ class ScanShift(object):
 
         dsetPath = '/entries/{0}/free_indices'.format(entry)
         if not self.__dirtyFrees[entry]:
-            with h5py.File(self.__tmp_file) as tmp_h5:
+            with h5py.File(self.__tmp_file, mode="r") as tmp_h5:
                 shifted_idx = tmp_h5.get(dsetPath)[:]
         else:
             shifted_idx = _get_free_shifted_indices(entry,
                                                     self.__xsocs_h5,
                                                     self.__shifts,
                                                     self.__tmp_file)
-            with h5py.File(self.__tmp_file) as tmp_h5:
+            with h5py.File(self.__tmp_file, mode="a") as tmp_h5:
                 if dsetPath not in tmp_h5:
                     tmp_h5.create_dataset(dsetPath, data=shifted_idx)
                 else:
@@ -361,7 +361,7 @@ def _get_free_shifted_indices(entry,
                               ref_p1=None):
 
     if ref_p0 is None or ref_p1 is None:
-        with h5py.File(tmp_file) as tmp_h5:
+        with h5py.File(tmp_file, mode="r") as tmp_h5:
             if ref_p0 is None:
                 ref_p0 = tmp_h5['ref_p0'][:]
             if ref_p1 is None: