Merge pull request #139 from blink1073/travis-nose

isbadawi · isbadawi · commit 211ab13d2e20 · 2015-02-15T10:54:30.000-05:00
Add Travis Testing against Octave
diff --git a/.travis.yml b/.travis.yml
@@ -1,5 +1,4 @@
 language: python
-sudo: false
 deploy:
   provider: pypi
   user: arokem
@@ -10,5 +9,35 @@ deploy:
     repo: arokem/python-matlab-bridge
     # until this is fixed: https://github.com/travis-ci/travis-ci/issues/1675
     all_branches: true
+env:
+    - CONDA="python=2.7 numpy=1.7"
+    - CONDA="python=3.3 numpy"
+before_install:
+  - sudo apt-add-repository -y ppa:octave/stable;
+  - sudo apt-get update -qq;
+  - sudo apt-get install -qq octave liboctave-dev default-jdk;
+  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes
+  - conda update conda
+  - conda info -a
+  - travis_retry conda create -n test $CONDA IPython pip nose pyzmq
+  - source activate test
+  - travis_retry pip install coveralls
+
+install:
+  - export USE_OCTAVE=True
+  - python setup.py install
+
 script:
-  - true
+    # run coverage on py2.7, regular on others
+  - if [[ $CONDA == python=2.7* ]]; then
+      nosetests --exe -v --with-cov --cover-package pymatbridge;
+    else
+      nosetests --exe -v pymatbridge;
+    fi
+
+after_success:
+    - coveralls
diff --git a/README.md b/README.md
@@ -115,17 +115,7 @@ Rather than looking for `matlab` at the shell, this will look for `octave`.
 As with `pymatbridge.Matlab`, you can override this by specifying the
 `executable` keyword argument.
 
-There are a few caveats to note about Octave support:
-
-* The zmq messenger used to communicate with the Octave session is written in C
-and needs to be compiled. For MATLAB various prebuilt binaries are provided
-and added to MATLAB's runtime path, but as of this writing the same isn't
-true for Octave. You'll need to compile the messenger (in
-`messenger/src/messenger.c`) using an incantation like
-`mkoctfile --mex -lzmq messenger.c` and place the resulting `messenger.mex`
-file somewhere in Octave's runtime path.
-
-Finally, rather than `~/startup.m`, Octave looks for an `~/.octaverc` file for
+Rather than `~/startup.m`, Octave looks for an `~/.octaverc` file for
 commands to execute before every session. (This is a good place to manipulate
 the runtime path, for example).
 
@@ -154,11 +144,11 @@ More examples are provided in the `examples` directory
 The installation of `pymatbridge` includes a binary of a mex function to communicate between 
 Python and Matlab using the [0MQ](http://zeromq.org/) messaging library. This should work 
 without any need for compilation on most computers. However, in some cases, you might want
-to build the pymatbridge messenger from source. To do so, you will need to follow the 
+to build the pymatbridge messenger from source. To do so, you will need to follow the instructions below:
 
 ### Install zmq library
 Please refer to the [official guide](http://zeromq.org/intro:get-the-software) on how to
-build and install zmq. After zmq is installed, make sure you can find the location where
+build and install zmq. On Ubuntu, it is as simple as `sudo apt-get install libzmq3-dev`.  After zmq is installed, make sure you can find the location where
 libzmq is installed. The library extension name and default location on different systems
 are listed below.
 
@@ -215,12 +205,23 @@ be supported. If you have an old version of pyzmq, please update it.
 
 ### Install pymatbridge
 After the steps above are done, you can install pymatbridge. Download the zip file of the 
-latest release. Unzip it somewhere on your machine and then issue:
+latest release. Unzip it somewhere on your machine.
+
+For Matlab:
 
 	cd messenger
 	python make.py 
 	cd ..
 	python setup.py install
+
+
+For Octave:
+
+    cd messenger/octave
+    # edit make.py if not using Ubuntu-derivative
+    python make.py
+    cd ..
+    python setup.py
 	
 This should make the python-matlab-bridge import-able.
 
diff --git a/messenger/octave/make.py b/messenger/octave/make.py
@@ -0,0 +1,7 @@
+
+import os
+
+os.system('sudo apt-get install libzmq3-dev liboctave-dev')
+os.system('cd ../src; mkoctfile --mex -lzmq messenger.c')
+os.system('mv ../src/messenger.mex .')
+os.system('cp messenger.mex ../pymatbridge/matlab')
diff --git a/messenger/octave/messenger.mex b/messenger/octave/messenger.mex
diff --git a/pymatbridge/matlab/util/isrow.m b/pymatbridge/matlab/util/isrow.m
@@ -7,8 +7,8 @@
 %
 %
 
-if ndims(X)==2 & size(X,1)==1 & size(X,2)>=1
+if ndims(X)==2 && size(X,1)==1 && size(X,2)>=1
    Y = logical(1);
 else
    Y = logical(0);
-end
+end
diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/json_dump.m b/pymatbridge/matlab/util/json_v0.2.2/json/json_dump.m
@@ -143,7 +143,7 @@
     end
   elseif isnumeric(value)
     if isreal(value)
-      obj = javaObject('java.lang.Double', value);
+      obj = value;
     % Encode complex number as a struct
     else
       complex_struct = struct;
diff --git a/pymatbridge/matlab/util/pymat_get_variable.m b/pymatbridge/matlab/util/pymat_get_variable.m
@@ -34,6 +34,7 @@
 else
     response.exists = true;
     response.var = evalin('base', varname);
+    response.success = 'true';
 end
 
 json_response = json_dump(response);
diff --git a/pymatbridge/matlab_magic.py b/pymatbridge/matlab_magic.py
@@ -7,36 +7,23 @@
 
 """
 
-import sys, os
-import tempfile
-from glob import glob
 from shutil import rmtree
-from getopt import getopt
 
 import numpy as np
-try:
-    import scipy.io as sio
-    has_io = True
-except ImportError:
-    has_io = False
-    no_io_str = "Must have scipy.io to perform i/o"
-    no_io_str += "operations with the Matlab session"
-
 import IPython
 
-ipython_version = int(IPython.__version__[0])
-
 from IPython.core.displaypub import publish_display_data
-from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic,
+from IPython.core.magic import (Magics, magics_class,
                                 line_cell_magic, needs_local_scope)
-from IPython.testing.skipdoctest import skip_doctest
 from IPython.core.magic_arguments import (argument, magic_arguments,
                                           parse_argstring)
-from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3
+from IPython.utils.py3compat import unicode_to_str, PY3
 
 import pymatbridge as pymat
 from .compat import text_type
 
+ipython_version = int(IPython.__version__[0])
+
 
 class MatlabInterperterError(RuntimeError):
     """
@@ -95,7 +82,10 @@ def __init__(self, shell,
         super(MatlabMagics, self).__init__(shell)
         self.cache_display_data = cache_display_data
 
-        self.Matlab = pymat.Matlab(matlab, maxtime=maxtime)
+        if 'octave' in matlab.lower():
+            self.Matlab = pymat.Octave(matlab, maxtime=maxtime)
+        else:
+            self.Matlab = pymat.Matlab(matlab, maxtime=maxtime)
         self.Matlab.start()
         self.pyconverter = pyconverter
 
@@ -173,19 +163,15 @@ def matlab(self, line, cell=None, local_ns=None):
         self.Matlab.set_default_plot_size(width, height)
 
         if args.input:
-            if has_io:
-                for input in ','.join(args.input).split(','):
-                    try:
-                        val = local_ns[input]
-                    except KeyError:
-                        val = self.shell.user_ns[input]
-                    # The _Session.set_variable function which this calls
-                    # should correctly detect numpy arrays and serialize them
-                    # as json correctly.
-                    self.set_matlab_var(input, val)
-
-            else:
-                raise RuntimeError(no_io_str)
+            for input in ','.join(args.input).split(','):
+                try:
+                    val = local_ns[input]
+                except KeyError:
+                    val = self.shell.user_ns[input]
+                # The _Session.set_variable function which this calls
+                # should correctly detect numpy arrays and serialize them
+                # as json correctly.
+                self.set_matlab_var(input, val)
 
         try:
             result_dict = self.eval(code)
@@ -216,7 +202,8 @@ def matlab(self, line, cell=None, local_ns=None):
             if len(imgf):
                 # Store the path to the directory so that you can delete it
                 # later on:
-                image = open(imgf, 'rb').read()
+                with open(imgf, 'rb') as fid:
+                    image = fid.read()
                 if ipython_version < 3:
                     display_data.append(('MatlabMagic.matlab',
                                          {'image/png':image}))
@@ -234,11 +221,8 @@ def matlab(self, line, cell=None, local_ns=None):
             rmtree(data_dir)
 
         if args.output:
-            if has_io:
-                for output in ','.join(args.output).split(','):
-                    self.shell.push({output:self.Matlab.get_variable(output)})
-            else:
-                raise RuntimeError(no_io_str)
+            for output in ','.join(args.output).split(','):
+                self.shell.push({output:self.Matlab.get_variable(output)})
 
 
 _loaded = False
@@ -253,6 +237,5 @@ def unload_ipython_extension(ip):
     global _loaded
     if _loaded:
         magic = ip.magics_manager.registry.pop('MatlabMagics')
-        magic.Matlab.stop()
         _loaded = False
 
diff --git a/pymatbridge/pymatbridge.py b/pymatbridge/pymatbridge.py
@@ -23,7 +23,7 @@
 
 import os
 import time
-import codecs
+import base64
 import zmq
 import subprocess
 import sys
@@ -60,7 +60,7 @@ def encode_ndarray(obj):
     except AttributeError:
         data = obj.astype(float64).tostring()
 
-    data = codecs.encode(data, 'base64').decode('utf-8')
+    data = base64.b64encode(data).decode('utf-8')
     return data, shape
 
 
@@ -89,19 +89,19 @@ def default(self, obj):
 def decode_arr(data):
     """Extract a numpy array from a base64 buffer"""
     data = data.encode('utf-8')
-    return frombuffer(codecs.decode(data, 'base64'), float64)
+    return frombuffer(base64.b64decode(data), float64)
 
 
 # JSON decoder for arrays and complex numbers
 def decode_pymat(dct):
     if 'ndarray' in dct and 'data' in dct:
         value = decode_arr(dct['data'])
-        shape = decode_arr(dct['shape'])
+        shape = decode_arr(dct['shape']).astype(int)
         return value.reshape(shape, order='F')
     elif 'ndarray' in dct and 'imag' in dct:
         real = decode_arr(dct['real'])
         imag = decode_arr(dct['imag'])
-        shape = decode_arr(dct['shape'])
+        shape = decode_arr(dct['shape']).astype(int)
         data = real + 1j * imag
         return data.reshape(shape, order='F')
     elif 'real' in dct and 'imag' in dct:
@@ -428,6 +428,7 @@ def _preamble_code(self):
         if self.log:
             code.append("diary('./pymatbridge/logs/octavelog_%s.txt')" % self.id)
         code.append("set(0, 'defaultfigurevisible', 'off');")
+        code.append("graphics_toolkit('gnuplot')")
         return code
 
     def _execute_flag(self):
diff --git a/pymatbridge/tests/test_magic.py b/pymatbridge/tests/test_magic.py
@@ -1,24 +1,30 @@
+import os
+
 import pymatbridge as pymat
-import IPython
+from IPython.testing.globalipapp import get_ipython
 
 import numpy.testing as npt
 
+
 class TestMagic:
 
     # Create an IPython shell and load Matlab magic
     @classmethod
     def setup_class(cls):
-        cls.ip = IPython.InteractiveShell()
+        cls.ip = get_ipython()
         cls.ip.run_cell('import random')
         cls.ip.run_cell('import numpy as np')
-        pymat.load_ipython_extension(cls.ip)
+        if 'USE_OCTAVE' in os.environ:
+            matlab = 'octave'
+        else:
+            matlab = 'matlab'
+        pymat.load_ipython_extension(cls.ip, matlab=matlab)
 
-    # Unload the magic, shut down Matlab
+    # Unload the magic
     @classmethod
     def teardown_class(cls):
         pymat.unload_ipython_extension(cls.ip)
 
-
     # Test single operation on different data structures
     def test_cell_magic_number(self):
         # A double precision real number
diff --git a/setup.py b/setup.py
@@ -30,7 +30,8 @@ def copy_bin(bin_path):
 
 for copy_this in ["./messenger/mexmaci64/messenger.mexmaci64",
                   "./messenger/mexa64/messenger.mexa64",
-                  "./messenger/mexw64/messenger.mexw64"]:
+                  "./messenger/mexw64/messenger.mexw64",
+                  "./messenger/octave/messenger.mex"]:
     copy_bin(copy_this)
         
 # Get version and release info, which is all stored in pymatbridge/version.py

Original file line number	Diff line number	Diff line change
`@@ -7,8 +7,8 @@`
`7`	`7`	`%`
`8`	`8`	`%`
`9`	`9`
`10`		`-if ndims(X)==2 & size(X,1)==1 & size(X,2)>=1`
	`10`	`+if ndims(X)==2 && size(X,1)==1 && size(X,2)>=1`
`11`	`11`	`Y = logical(1);`
`12`	`12`	`else`
`13`	`13`	`Y = logical(0);`
`14`		`-end`
	`14`	`+end`