A few more updates for PyTables 3

dashi/datasets/hdf_datasets.py

@@ -41,12 +41,12 @@ def hdf_toc(h5file):
 
     """
     toc = []
-    for node in h5file.walkNodes(classname="Table"):
+    for node in h5file.walk_nodes(classname="Table"):
         for varname in node.description._v_names:
             toc.append( "%s:%s" % (node._v_pathname, varname) )
 
     for arraytype in ["Array", "EArray"]:
-        for node in h5file.walkNodes(classname=arraytype):
+        for node in h5file.walk_nodes(classname=arraytype):
             toc.append( node._v_pathname ) 
 
     return sorted(toc)
@@ -66,7 +66,7 @@ def store_earray1d(h5file, path, array, complevel=6, **kwargs):
     if complevel > 0:
         filters = tables.Filters(complevel=complevel, complib="zlib")
 
-    earr = h5file.createEArray(parent, arrname,  
+    earr = h5file.create_earray(parent, arrname,  
                                tables.Atom.from_dtype(array.dtype), 
                                (0,),
                                filters=filters,
@@ -101,12 +101,12 @@ def _ds_toc(self):
             if not self.isopen:
                 return toc
 
-            for node in self.walkNodes(classname="Table"):
+            for node in self.walk_nodes(classname="Table"):
                 toc.append( node._v_pathname )
                 for varname in node.description._v_names:
                     toc.append( "%s:%s" % (node._v_pathname, varname) )
 
-            for node in self.walkNodes(classname="Array"):
+            for node in self.walk_nodes(classname="Array"):
                 toc.append( node._v_pathname ) 
 
             self._ds_toc_cache = sorted(toc)
@@ -121,18 +121,18 @@ def _ds_write_variable(self, path, array):
         arrname = os.path.basename(path)
         self._ds_toc_cache = None
         if array.dtype.names is None:
-            earr = self.createEArray(parent, arrname,  
+            earr = self.create_earray(parent, arrname,  
                                      tables.Atom.from_dtype(array.dtype), 
                                      (0,), filters=self.filters, createparents=True)
             earr.append(array)
             earr.flush()
         else:
-            tab = self.createTable(parent, arrname, array, createparents=True, filters=self.filters)
+            tab = self.create_table(parent, arrname, array, createparents=True, filters=self.filters)
             tab.flush()
 
     def _ds_remove_variable(self, path):
         try:
-            self.removeNode(path)
+            self.remove_node(path)
             self.flush()
         except tables.NoSuchNodeError as exc:
             raise ValueError("removing path %s raised a NoSuchNodeError" % path)

dashi/fitting.py

@@ -26,7 +26,7 @@ def __init__(self, callable, integral_callable=None):
         :params integral_callable: a function P(X < x)
         """
         self.dfunc = callable
-        argspec = inspect.getargspec(callable)
+        argspec = inspect.getfullargspec(callable)
         self.func = integral_callable
 
         # initialize params with 1 which is a better starting value than zero for factors

dashi/objbundleutils.py

@@ -68,7 +68,7 @@ def read_hdf(h5file, selection):
                 readorder.insert(0, (varname, [] ))
                 #print "insert", varname
             elif callable(cfg):
-                args = inspect.getargspec(cfg).args
+                args = inspect.getfullargspec(cfg).args
                 if args == ["file"]:
                     # pass h5file, calculation doesn't depend on anything
                     readorder.insert(0, (varname, []) )
@@ -99,7 +99,7 @@ def read_hdf(h5file, selection):
             else:
                 arrays[varname] = h5file.get_node(cfg).read()
         elif callable(cfg):
-            args = inspect.getargspec(cfg).args
+            args = inspect.getfullargspec(cfg).args
             if args == ["file"]:
                 arrays[varname] = cfg(h5file)
             else:

dashi/odict.py

@@ -1,4 +1,2 @@
-
 # Python 3 dictionaries remember insertion order
 OrderedDict = dict
-

dashi/tests/datasets_test.py

@@ -24,8 +24,8 @@
         arr["y"] = n.arange(100, 0, -1, dtype=int)
 
         fname = "%s_%d.h5" % (name,j)
-        f = tables.openFile(fname, "a")
-        f.createTable("/", "test", arr)
+        f = tables.open_file(fname, "a")
+        f.create_table("/", "test", arr)
         f.close()
 
         datafiles[name].append(fname)