More streamlining, fault tolerance, and coverage increasing

pymatbridge/matlab/util/pymat_feval.m

@@ -31,7 +31,14 @@
         arguments = '';
     end
 
-    [resp{1:req.nargout}] = run_dot_m(func_path, arguments, req.nargout);
+    try
+        [resp{1:req.nargout}] = run_dot_m(func_path, arguments, req.nargout);
+    catch ME
+        response.message = ME.message;
+        json_response = json_dump(response);
+        return
+    end
+
     if req.nargout == 1
         response.result = resp{1};
     else

pymatbridge/matlab_magic.py

@@ -22,8 +22,6 @@
 import pymatbridge as pymat
 from .compat import text_type
 
-ipython_version = int(IPython.__version__[0])
-
 
 class MatlabInterperterError(RuntimeError):
     """
@@ -89,16 +87,6 @@ def __init__(self, shell,
         self.Matlab.start()
         self.pyconverter = pyconverter
 
-    def __del__(self):
-        """shut down the Matlab server when the object dies.
-
-        2FIX: this seems to not be called when ipython terminates. bleah.
-        """
-        try:
-            self.Matlab.stop()
-        except:
-            raise
-
     def eval(self, line):
         """
         Parse and evaluate a single line of matlab
@@ -192,29 +180,20 @@ def matlab(self, line, cell=None, local_ns=None):
 
         display_data = []
         if text_output and not args.silent:
-            if ipython_version < 3:
-                display_data.append(('MatlabMagic.matlab',
-                                     {'text/plain':text_output}))
-            else:
-                display_data.append({'text/plain':text_output})
+            display_data.append(('MatlabMagic.matlab',
+                                 {'text/plain': text_output}))
 
         for imgf in imgfiles:
             if len(imgf):
                 # Store the path to the directory so that you can delete it
                 # later on:
                 with open(imgf, 'rb') as fid:
                     image = fid.read()
-                if ipython_version < 3:
-                    display_data.append(('MatlabMagic.matlab',
-                                         {'image/png':image}))
-                else:
-                    display_data.append({'image/png': image})
+                display_data.append(('MatlabMagic.matlab',
+                                     {'image/png': image}))
 
         for disp_d in display_data:
-            if ipython_version < 3:
-                publish_display_data(disp_d[0], disp_d[1])
-            else:
-                publish_display_data(disp_d)
+            publish_display_data(source=disp_d[0], data=disp_d[1])
 
         # Delete the temporary data files created by matlab:
         if len(data_dir):
@@ -237,5 +216,6 @@ def unload_ipython_extension(ip):
     global _loaded
     if _loaded:
         magic = ip.magics_manager.registry.pop('MatlabMagics')
+        magic.Matlab.stop()
         _loaded = False
 

pymatbridge/publish.py

@@ -48,10 +48,9 @@ def mfile_to_lines(mfile):
         Full path to an m file
     """
     # We should only be able to read this file:
-    f = file(mfile, 'r')
-    lines = f.readlines()
-    f.close()
-    return lines
+    with open(mfile) as fid:
+        return fid.readlines()
+
 
 def lines_to_notebook(lines, name=None):
     """
@@ -122,13 +121,9 @@ def convert_mfile(mfile, outfile=None):
         Full path to the output ipynb file
 
     """
-    f = file(mfile, 'r')
-    lines = f.readlines()
-    f.close()
+    lines = mfile_to_lines(mfile)
     nb = lines_to_notebook(lines)
     if outfile is None:
         outfile = mfile.split('.m')[0] + '.ipynb'
-    nbfile = file(outfile, 'w')
-    nbformat.write(nb, nbfile, format='ipynb')
-    nbfile.close()
-
+    with open(outfile, 'w') as fid:
+        nbformat.write(nb, fid, format='ipynb')

pymatbridge/pymatbridge.py

@@ -21,6 +21,7 @@
 
 """
 
+import atexit
 import os
 import time
 import base64
@@ -30,12 +31,7 @@
 import json
 from uuid import uuid4
 
-try:
-    from numpy import ndarray, generic, float64, frombuffer, asfortranarray
-except ImportError:
-    class ndarray:
-        pass
-    generic = ndarray
+from numpy import ndarray, generic, float64, frombuffer, asfortranarray
 
 try:
     from scipy.sparse import spmatrix
@@ -52,7 +48,7 @@ def encode_ndarray(obj):
     if obj.flags.c_contiguous:
         obj = obj.T
     elif not obj.flags.f_contiguous:
-        obj = asfortranarray(obj)
+        obj = asfortranarray(obj.T)
     else:
         obj = obj.T
     try:
@@ -169,8 +165,9 @@ def __init__(self, executable, socket_addr=None,
 
         self.context = None
         self.socket = None
+        atexit.register(self.stop)
 
-    def _program_name(self):
+    def _program_name(self):  # pragma: no cover
         raise NotImplemented
 
     def _preamble_code(self):
@@ -182,7 +179,7 @@ def _preamble_code(self):
                 "warning(old_warning_state)",
                 "clear old_warning_state"]
 
-    def _execute_flag(self):
+    def _execute_flag(self):  # pragma: no cover
         raise NotImplemented
 
     def _run_server(self):
@@ -227,6 +224,9 @@ def _response(self, **kwargs):
 
     # Stop the Matlab server
     def stop(self):
+        if not self.started:
+            return True
+
         # Matlab should respond with "exit" if successful
         if self._response(cmd='exit') == "exit":
             print("%s closed" % self._program_name())

pymatbridge/tests/test_magic.py

@@ -1,6 +1,7 @@
 import os
 
 import pymatbridge as pymat
+from pymatbridge.matlab_magic import MatlabInterperterError
 from IPython.testing.globalipapp import get_ipython
 
 import numpy.testing as npt
@@ -96,3 +97,7 @@ def test_struct(self):
         npt.assert_equal(self.ip.user_ns['obj']['num'], self.ip.user_ns['num'])
         npt.assert_equal(self.ip.user_ns['obj']['num_array'].squeeze(), self.ip.user_ns['num_array'])
         npt.assert_equal(self.ip.user_ns['obj']['str'], self.ip.user_ns['str'])
+
+    def test_faulty(self):
+        npt.assert_raises(MatlabInterperterError,
+                          lambda: self.ip.run_line_magic('matlab', '1 = 2'))

pymatbridge/tests/test_publish.py

@@ -1,5 +1,11 @@
 import numpy.testing as npt
 import pymatbridge.publish as publish
+import json
+import os
+
+
+MFILE = os.path.join(os.path.dirname(__file__), 'test_publish.m')
+
 
 def test_format_line():
     """
@@ -32,3 +38,22 @@ def test_lines_to_notebook():
 
     npt.assert_equal(nb['worksheets'][0]['cells'][1]['source'][0],
                      ' This is a first line\n\n')
+
+
+def test_convert_mfile():
+    publish.convert_mfile(MFILE)
+    nb_file = MFILE.replace('.m', '.ipynb')
+    with open(nb_file) as fid:
+        nb = json.load(fid)
+    npt.assert_equal(nb['worksheets'][0]['cells'][1]['source'][0],
+                     ' Experimenting with conversion from matlab to ipynb\n\n')
+    os.remove(nb_file)
+
+
+def test_mfile_to_lines():
+    lines = publish.mfile_to_lines(MFILE)
+
+    nb = publish.lines_to_notebook(lines)
+
+    npt.assert_equal(nb['worksheets'][0]['cells'][1]['source'][0],
+                     ' Experimenting with conversion from matlab to ipynb\n\n')

pymatbridge/tests/test_array.py → pymatbridge/tests/test_set_variable.py

@@ -31,4 +31,19 @@ def test_array_content(self):
         test_array = np.asfortranarray(test_array)
         self.mlab.set_variable('test', test_array)
         npt.assert_equal(self.mlab.get_variable('test'), test_array)
-
+        # force non-contiguous
+        test_array = test_array[::-1]
+        self.mlab.set_variable('test', test_array)
+        npt.assert_equal(self.mlab.get_variable('test'), test_array)
+
+    def test_object_array(self):
+        test_array = np.array(['hello', 1])
+        self.mlab.set_variable('test', test_array)
+        npt.assert_equal(self.mlab.get_variable('test'), test_array)
+
+    def test_others(self):
+        self.mlab.set_variable('test', np.float(1.5))
+        npt.assert_equal(self.mlab.get_variable('test'), 1.5)
+        self.mlab.set_variable('test', 'hello')
+        npt.assert_equal(self.mlab.get_variable('test'), 'hello')
+

pymatbridge/tests/test_utils.py

@@ -6,7 +6,7 @@ def on_octave():
     return bool(os.environ.get('USE_OCTAVE', False))
 
 def connect_to_matlab():
-    mlab = pymat.Octave() if on_octave() else pymat.Matlab()
+    mlab = pymat.Octave() if on_octave() else pymat.Matlab(log=True)
     mlab.start()
     npt.assert_(mlab.is_connected(), msg = "connect_to_matlab(): Connection failed")