From 5533b1ccbf90514981e426fa8ddc92c617611039 Mon Sep 17 00:00:00 2001
From: Billy Charlton <bcharlton@psrc.org>
Date: Thu, 31 Oct 2013 15:06:38 -0700
Subject: [PATCH 01/17] Create structure for multiple language APIs

---
 README.md              |   0
 omx/Exceptions.py      |   3 +
 omx/File.py            | 228 +++++++++++++++++++++++++++++++++++++++++
 omx/__init__.py        |  42 ++++++++
 omx/tests/test_file.py |  78 ++++++++++++++
 5 files changed, 351 insertions(+)
 create mode 100644 README.md
 create mode 100644 omx/Exceptions.py
 create mode 100644 omx/File.py
 create mode 100644 omx/__init__.py
 create mode 100644 omx/tests/test_file.py

diff --git a/README.md b/README.md
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/omx/Exceptions.py b/omx/Exceptions.py
new file mode 100644
index 0000000000..4688e2ebdd
--- /dev/null
+++ b/omx/Exceptions.py
@@ -0,0 +1,3 @@
+class ShapeError(Exception):
+    pass
+
diff --git a/omx/File.py b/omx/File.py
new file mode 100644
index 0000000000..1ee80e47c4
--- /dev/null
+++ b/omx/File.py
@@ -0,0 +1,228 @@
+# OMX package
+# release 1
+
+import tables  # requires pytables >= 2.4
+
+from Exceptions import *
+
+
+class File(tables.File):
+
+    def __init__(self, f,m,t,r,f1, **kwargs):
+        tables.File.__init__(self,f,m,t,r,f1,**kwargs)
+        self._shape = None
+
+    def version(self):
+        if 'OMX_VERSION' in self.root._v_attrs:
+            return self.root._v_attrs['OMX_VERSION']
+        else:
+            return None
+
+
+    def createMatrix(self, name, atom=None, shape=None, title='', filters=None,
+                     chunkshape=None, byteorder=None, createparents=False, obj=None,
+                     attrs=None):
+        """Create OMX Matrix (CArray) at root level. User must pass in either
+           an existing numpy matrix, or a shape and an atom type."""
+
+        # If object was passed in, make sure its shape is correct
+        if self.shape() != None and obj != None and obj.shape != self.shape():
+            raise ShapeError('%s has shape %s but this file requires shape %s' %
+                (name, obj.shape, self.shape()))
+
+        if tables.__version__.startswith('3'):
+            matrix = self.createCArray(self.root.data, name, atom, shape, title, filters,
+                                       chunkshape, byteorder, createparents, obj)
+        else:
+            # this version is tables 2.4-compatible:
+            matrix = self.createCArray(self.root.data, name, atom, shape, title, filters,
+                                       chunkshape, byteorder, createparents)
+            if (obj != None):
+                matrix[:] = obj
+
+        # attributes
+        if attrs:
+            for key in attrs:
+                matrix.attrs[key] = attrs[key]
+
+        return matrix
+
+    def shape(self):
+        """Return the one and only shape of all matrices in this File"""
+
+        # If we already have the shape, just return it
+        if self._shape:
+            return self._shape
+
+        # If shape is already set in root node attributes, grab it
+        if 'SHAPE' in self.root._v_attrs:
+            self._shape = self.root._v_attrs['SHAPE']
+            return self._shape
+
+        # Inspect the first CArray object to determine its shape
+        if len(self) > 0:
+            self._shape = self.iterNodes(self.root.data,'CArray').next().shape
+
+            # Store it if we can
+            if self._isWritable():
+                self.root._v_attrs['SHAPE'] = self._shape
+
+            return self._shape
+
+        else:
+            return None
+
+
+    def listMatrices(self):
+        """Return list of Matrix names in this File"""
+        return [node.name for node in self.listNodes(self.root.data,'CArray')]
+
+
+    def listAllAttributes(self):
+        """Return combined list of all attributes used for any Matrix in this File"""
+        all_tags = set()
+        for m in self.listNodes(self.root,'CArray'):
+            if m.attrs != None:
+                all_tags.update(m.attrs._v_attrnames)
+        return sorted(list(all_tags))
+
+
+    # MAPPINGS -----------------------------------------------
+    def listMappings(self):
+        try:
+            return [m.name for m in self.listNodes(self.root.lookup)]
+        except:
+            return []
+
+
+    def deleteMapping(self, title):
+        try:
+            self.removeNode(self.root.lookup, title)
+        except:
+            raise LookupError('No such mapping: '+title)
+
+
+    def mapping(self, title):
+        """Return dict containing key:value pairs for specified mapping. Keys
+           represent the map item and value represents the array offset."""
+        try:
+            # fetch entries
+            entries = []
+            entries.extend(self.getNode(self.root.lookup, title)[:])
+
+            # build reverse key-lookup
+            keymap = {}
+            for i in range(len(entries)):
+                keymap[entries[i]] = i
+
+            return keymap
+
+        except:
+            raise LookupError('No such mapping: '+title)
+
+    def mapentries(self, title):
+        """Return entries[] with key for each array offset."""
+        try:
+            # fetch entries
+            entries = []
+            entries.extend(self.getNode(self.root.lookup, title)[:])
+
+            return (keymap,entries)
+
+        except:
+            raise LookupError('No such mapping: '+title)
+
+
+    def createMapping(self, title, entries, overwrite=False):
+        """Create an equivalency index, which maps a raw data dimension to
+           another integer value. Once created, mappings can be referenced by
+           offset or by key."""
+
+        # Enforce shape-checking
+        if self.shape():
+            if not len(entries) in self._shape:
+                raise ShapeError('Mapping must match one data dimension')
+
+        # Handle case where mapping already exists:
+        if title in self.listMappings():
+            if overwrite:
+                self.deleteMapping(title)
+            else:
+                raise LookupError(title+' mapping already exists.')
+
+        # Create lookup group under root if it doesn't already exist.
+        if 'lookup' not in self.root:
+            self.createGroup(self.root, 'lookup')
+
+        # Write the mapping!
+        mymap = self.createArray(self.root.lookup, title, atom=tables.UInt16Atom(),
+                                 shape=(len(entries)) )
+        mymap[:] = entries
+
+        return mymap
+
+
+    # The following functions implement Python list/dictionary lookups. ----
+    def __getitem__(self,key):
+        """Return a matrix by name, or a list of matrices by attributes"""
+
+        if isinstance(key, str):
+            return self.getNode(self.root.data, key)
+
+        if 'keys' not in dir(key):
+            raise LookupError('Key %s not found' % key)
+
+        # Loop through key/value pairs
+        mats = self.listNodes(self.root.data, 'CArray')
+        for a in key.keys():
+            mats = self._getMatricesByAttribute(a, key[a], mats)
+
+        return mats
+
+
+    def _getMatricesByAttribute(self, key, value, matrices=None):
+
+        answer = []
+
+        if matrices==None:
+            matrices = self.listNodes(self.root.data,'CArray')
+
+        for m in matrices:
+            if m.attrs == None: continue
+
+            # Only test if key is present in matrix attributes
+            if key in m.attrs._v_attrnames and m.attrs[key] == value:
+                answer.append(m)
+
+        return answer
+
+
+    def __len__(self):
+        return len(self.listNodes(self.root.data, 'CArray'))
+
+
+    def __setitem__(self, key, dataset):
+        # We need to determine atom and shape from the object that's been passed in.
+        # This assumes 'dataset' is a numpy object.
+        atom = tables.Atom.from_dtype(dataset.dtype)
+        shape = dataset.shape
+
+        #checks to see if it is already a tables instance, and if so, just copies it
+        if dataset.__class__.__name__ == 'CArray':
+            return dataset.copy(self.root.data, key)
+        else:
+            return self.createMatrix(key, atom, shape, obj=dataset)
+
+
+    def __delitem__(self, key):
+        self.removeNode(self.root.data, key)
+
+
+    def __iter__(self):
+        """Iterate over the keys in this container"""
+        return self.iterNodes(self.root.data, 'CArray')
+
+
+    def __contains__(self, item):
+        return item in self.root.data._v_children
+
diff --git a/omx/__init__.py b/omx/__init__.py
new file mode 100644
index 0000000000..ed3eb59568
--- /dev/null
+++ b/omx/__init__.py
@@ -0,0 +1,42 @@
+# OMX package
+# release 1
+
+import tables
+from File import *
+from Exceptions import *
+
+# GLOBAL VARIABLES -----------
+__version__ = '0.2'
+
+# GLOBAL FUNCTIONS -----------
+def openFile(filename, mode='r', title='', root_uep='/',
+             filters=tables.Filters(complevel=1,shuffle=True,fletcher32=False,complib='zlib'),
+             shape=None, **kwargs):
+    """Open or create a new OMX file. New files will be created with default
+       zlib compression enabled."""
+
+    f = File(filename, mode, title, root_uep, filters, **kwargs);
+
+    # add omx structure if file is writable
+    if mode != 'r':
+        # version number
+        if 'OMX_VERSION' not in f.root._v_attrs:
+            f.root._v_attrs['OMX_VERSION'] = __version__
+
+        # shape
+        if shape:
+            f.root._v_attrs['SHAPE'] = shape
+
+        # /data and /lookup folders
+        if 'data' not in f.root:
+            f.createGroup(f.root,"data")
+        if 'lookup' not in f.root:
+            f.createGroup(f.root,"lookup")
+
+    return f
+
+
+if __name__ == "__main__":
+    print 'OMX!'
+
+
diff --git a/omx/tests/test_file.py b/omx/tests/test_file.py
new file mode 100644
index 0000000000..d0101a1e09
--- /dev/null
+++ b/omx/tests/test_file.py
@@ -0,0 +1,78 @@
+import tables,omx,numpy,os
+from nose.tools import *
+
+def setup_clean():
+    try:
+        os.remove('test1.omx')
+    except:
+        pass
+
+
+def setup_empty_file():
+    try:
+        os.remove('test1.omx')
+        f = omx.openFile('test.omx','w')
+        f.close()
+    except:
+        pass
+
+
+def teardown_clean():
+    try:
+        os.remove('test2.omx')
+    except:
+        pass
+
+
+@with_setup(setup_clean,teardown_clean)
+def test_create_file():
+    f = omx.openFile('test1.omx','w')
+    f.close()
+    assert(os.path.exists('test1.omx'))
+
+def test_open_readonly_hdf5_file():
+    f = tables.openFile('test2.omx','w')
+    f.close()
+    f = omx.openFile('test2.omx','r')
+    f.close() 
+
+def test_add_numpy_matrix_using_brackets():
+    f = omx.openFile('test3.omx','w')
+    f['m1'] = numpy.ones((5,5))
+    f.close()
+
+def test_add_numpy_matrix_using_create_matrix():
+    f = omx.openFile('test4.omx','w')
+    f.createMatrix('m1', obj=numpy.ones((5,5)))
+    f.close()
+
+def test_add_matrix_to_readonly_file():
+    f = omx.openFile('test6.omx','w')
+    f['m2'] = numpy.ones((5,5))
+    f.close()
+    f = omx.openFile('test6.omx','r')
+    assert_raises(tables.FileModeError, add_m1_node, f)
+    f.close() 
+
+def test_add_matrix_with_same_name():
+    f = omx.openFile('test5.omx','w')
+    add_m1_node(f)
+    # now add m1 again:
+    assert_raises(tables.NodeError, add_m1_node, f)
+    f.close()
+
+@with_setup(setup_clean,teardown_clean)
+def test_get_length_of_file():
+    f = omx.openFile('test7.omx','w')
+    f['m1'] = numpy.ones((5,5))
+    f['m2'] = numpy.ones((5,5))
+    f['m3'] = numpy.ones((5,5))
+    f['m4'] = numpy.ones((5,5))
+    f['m5'] = numpy.ones((5,5))
+    assert(len(f)==5)
+    assert(len(f.listMatrices())==5)
+    f.close()
+
+def add_m1_node(f):
+    f.createMatrix('m1', obj=numpy.ones((7,7)))
+

From 30142ba7991d4224525d68829b42e9e35252193c Mon Sep 17 00:00:00 2001
From: Billy Charlton <billy@worldofbilly.com>
Date: Wed, 7 May 2014 20:42:31 -0700
Subject: [PATCH 02/17] Fix SHAPE attribute to be compatible with R and C++ OMX
 formats

---
 omx/File.py     | 21 ++++++++++++++++++---
 omx/__init__.py |  5 ++++-
 2 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/omx/File.py b/omx/File.py
index 1ee80e47c4..50e27632ec 100644
--- a/omx/File.py
+++ b/omx/File.py
@@ -1,6 +1,7 @@
 # OMX package
 # release 1
 
+import numpy as np
 import tables  # requires pytables >= 2.4
 
 from Exceptions import *
@@ -29,7 +30,8 @@ def createMatrix(self, name, atom=None, shape=None, title='', filters=None,
         if self.shape() != None and obj != None and obj.shape != self.shape():
             raise ShapeError('%s has shape %s but this file requires shape %s' %
                 (name, obj.shape, self.shape()))
-
+                
+        # Create the HDF5 array
         if tables.__version__.startswith('3'):
             matrix = self.createCArray(self.root.data, name, atom, shape, title, filters,
                                        chunkshape, byteorder, createparents, obj)
@@ -40,6 +42,12 @@ def createMatrix(self, name, atom=None, shape=None, title='', filters=None,
             if (obj != None):
                 matrix[:] = obj
 
+        # Store shape if we don't have one yet
+        if self._shape == None:
+            storeshape = np.array([matrix.shape[0],matrix.shape[1]], dtype='int32')
+            self.root._v_attrs['SHAPE'] = storeshape
+            self._shape = matrix.shape
+
         # attributes
         if attrs:
             for key in attrs:
@@ -56,7 +64,11 @@ def shape(self):
 
         # If shape is already set in root node attributes, grab it
         if 'SHAPE' in self.root._v_attrs:
-            self._shape = self.root._v_attrs['SHAPE']
+            # Shape is stored as a numpy.array:
+            arrayshape = self.root._v_attrs['SHAPE']
+            # which must be converted to a tuple:
+            realshape = (array[0],array[1])
+            self._shape = realshape
             return self._shape
 
         # Inspect the first CArray object to determine its shape
@@ -65,7 +77,10 @@ def shape(self):
 
             # Store it if we can
             if self._isWritable():
-                self.root._v_attrs['SHAPE'] = self._shape
+                storeshape = np.array(
+                    [self._shape[0],self._shape[1]],
+                    dtype='int32')
+                self.root._v_attrs['SHAPE'] = storeshape
 
             return self._shape
 
diff --git a/omx/__init__.py b/omx/__init__.py
index ed3eb59568..7dd7504c33 100644
--- a/omx/__init__.py
+++ b/omx/__init__.py
@@ -2,6 +2,8 @@
 # release 1
 
 import tables
+import numpy as np
+
 from File import *
 from Exceptions import *
 
@@ -25,7 +27,8 @@ def openFile(filename, mode='r', title='', root_uep='/',
 
         # shape
         if shape:
-            f.root._v_attrs['SHAPE'] = shape
+            storeshape = numpy.array([shape[0],shape[1]], dtype='int32')
+            f.root._v_attrs['SHAPE'] = storeshape
 
         # /data and /lookup folders
         if 'data' not in f.root:

From a1171a6750d439ad6a14adf0a5b4c8834b6e83ae Mon Sep 17 00:00:00 2001
From: Billy Charlton <billy@worldofbilly.com>
Date: Wed, 7 May 2014 20:47:36 -0700
Subject: [PATCH 03/17] Ensure shape of mapping is a one-tuple, not a scalar

---
 omx/File.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/omx/File.py b/omx/File.py
index 50e27632ec..ef351aab43 100644
--- a/omx/File.py
+++ b/omx/File.py
@@ -171,7 +171,7 @@ def createMapping(self, title, entries, overwrite=False):
 
         # Write the mapping!
         mymap = self.createArray(self.root.lookup, title, atom=tables.UInt16Atom(),
-                                 shape=(len(entries)) )
+                                 shape=(len(entries),) )
         mymap[:] = entries
 
         return mymap

From 70aabb2c0cb91b9478531e9b2b3462981e7410c4 Mon Sep 17 00:00:00 2001
From: Billy Charlton <billy@worldofbilly.com>
Date: Wed, 7 May 2014 22:07:01 -0700
Subject: [PATCH 04/17] fix typo in shape()

---
 omx/File.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/omx/File.py b/omx/File.py
index ef351aab43..82e3e91478 100644
--- a/omx/File.py
+++ b/omx/File.py
@@ -67,7 +67,7 @@ def shape(self):
             # Shape is stored as a numpy.array:
             arrayshape = self.root._v_attrs['SHAPE']
             # which must be converted to a tuple:
-            realshape = (array[0],array[1])
+            realshape = (arrayshape[0],arrayshape[1])
             self._shape = realshape
             return self._shape
 

From 4d077c8685b58949dc5ce142ac953a7c9cd884c6 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Wed, 10 Dec 2014 15:09:01 -0800
Subject: [PATCH 05/17] move files to match activitysim structure

---
 README.md                                   | 0
 {omx => activitysim/omx}/Exceptions.py      | 0
 {omx => activitysim/omx}/File.py            | 0
 {omx => activitysim/omx}/__init__.py        | 0
 {omx => activitysim/omx}/tests/test_file.py | 0
 5 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 README.md
 rename {omx => activitysim/omx}/Exceptions.py (100%)
 rename {omx => activitysim/omx}/File.py (100%)
 rename {omx => activitysim/omx}/__init__.py (100%)
 rename {omx => activitysim/omx}/tests/test_file.py (100%)

diff --git a/README.md b/README.md
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/omx/Exceptions.py b/activitysim/omx/Exceptions.py
similarity index 100%
rename from omx/Exceptions.py
rename to activitysim/omx/Exceptions.py
diff --git a/omx/File.py b/activitysim/omx/File.py
similarity index 100%
rename from omx/File.py
rename to activitysim/omx/File.py
diff --git a/omx/__init__.py b/activitysim/omx/__init__.py
similarity index 100%
rename from omx/__init__.py
rename to activitysim/omx/__init__.py
diff --git a/omx/tests/test_file.py b/activitysim/omx/tests/test_file.py
similarity index 100%
rename from omx/tests/test_file.py
rename to activitysim/omx/tests/test_file.py

From 9e4b7d0fd2526cce29deae6145d538bff7737889 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 11:32:19 -0800
Subject: [PATCH 06/17] omx module renames

---
 activitysim/omx/{Exceptions.py => exceptions.py}        | 0
 activitysim/omx/{File.py => omxfile.py}                 | 0
 activitysim/omx/tests/{test_file.py => test_omxfile.py} | 0
 3 files changed, 0 insertions(+), 0 deletions(-)
 rename activitysim/omx/{Exceptions.py => exceptions.py} (100%)
 rename activitysim/omx/{File.py => omxfile.py} (100%)
 rename activitysim/omx/tests/{test_file.py => test_omxfile.py} (100%)

diff --git a/activitysim/omx/Exceptions.py b/activitysim/omx/exceptions.py
similarity index 100%
rename from activitysim/omx/Exceptions.py
rename to activitysim/omx/exceptions.py
diff --git a/activitysim/omx/File.py b/activitysim/omx/omxfile.py
similarity index 100%
rename from activitysim/omx/File.py
rename to activitysim/omx/omxfile.py
diff --git a/activitysim/omx/tests/test_file.py b/activitysim/omx/tests/test_omxfile.py
similarity index 100%
rename from activitysim/omx/tests/test_file.py
rename to activitysim/omx/tests/test_omxfile.py

From 43fdcc53b073f4027b32d08cc28595ad11aa3b18 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 12:09:00 -0800
Subject: [PATCH 07/17] pep8 fixes for omx

---
 activitysim/omx/__init__.py           | 33 +++++----
 activitysim/omx/exceptions.py         |  1 -
 activitysim/omx/omxfile.py            | 97 +++++++++++++--------------
 activitysim/omx/tests/test_omxfile.py | 74 +++++++++++---------
 4 files changed, 106 insertions(+), 99 deletions(-)

diff --git a/activitysim/omx/__init__.py b/activitysim/omx/__init__.py
index 7dd7504c33..f2902e3e92 100644
--- a/activitysim/omx/__init__.py
+++ b/activitysim/omx/__init__.py
@@ -1,45 +1,42 @@
 # OMX package
 # release 1
 
+import numpy
 import tables
-import numpy as np
 
-from File import *
-from Exceptions import *
+from .omxile import File
+from .exceptions import ShapeError
 
 # GLOBAL VARIABLES -----------
-__version__ = '0.2'
+OMX_VERSION = '0.2'
+
 
 # GLOBAL FUNCTIONS -----------
-def openFile(filename, mode='r', title='', root_uep='/',
-             filters=tables.Filters(complevel=1,shuffle=True,fletcher32=False,complib='zlib'),
-             shape=None, **kwargs):
+def open_omxfile(
+        filename, mode='r', title='', root_uep='/',
+        filters=tables.Filters(
+            complevel=1, shuffle=True, fletcher32=False, complib='zlib'),
+        shape=None, **kwargs):
     """Open or create a new OMX file. New files will be created with default
        zlib compression enabled."""
 
-    f = File(filename, mode, title, root_uep, filters, **kwargs);
+    f = File(filename, mode, title, root_uep, filters, **kwargs)
 
     # add omx structure if file is writable
     if mode != 'r':
         # version number
         if 'OMX_VERSION' not in f.root._v_attrs:
-            f.root._v_attrs['OMX_VERSION'] = __version__
+            f.root._v_attrs['OMX_VERSION'] = OMX_VERSION
 
         # shape
         if shape:
-            storeshape = numpy.array([shape[0],shape[1]], dtype='int32')
+            storeshape = numpy.array([shape[0], shape[1]], dtype='int32')
             f.root._v_attrs['SHAPE'] = storeshape
 
         # /data and /lookup folders
         if 'data' not in f.root:
-            f.createGroup(f.root,"data")
+            f.createGroup(f.root, "data")
         if 'lookup' not in f.root:
-            f.createGroup(f.root,"lookup")
+            f.createGroup(f.root, "lookup")
 
     return f
-
-
-if __name__ == "__main__":
-    print 'OMX!'
-
-
diff --git a/activitysim/omx/exceptions.py b/activitysim/omx/exceptions.py
index 4688e2ebdd..6f82cdb605 100644
--- a/activitysim/omx/exceptions.py
+++ b/activitysim/omx/exceptions.py
@@ -1,3 +1,2 @@
 class ShapeError(Exception):
     pass
-
diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index 82e3e91478..569cc4fe46 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -4,13 +4,12 @@
 import numpy as np
 import tables  # requires pytables >= 2.4
 
-from Exceptions import *
+from .exceptions import ShapeError
 
 
 class File(tables.File):
-
-    def __init__(self, f,m,t,r,f1, **kwargs):
-        tables.File.__init__(self,f,m,t,r,f1,**kwargs)
+    def __init__(self, f, m, t, r, f1, **kwargs):
+        tables.File.__init__(self, f, m, t, r, f1, **kwargs)
         self._shape = None
 
     def version(self):
@@ -19,32 +18,38 @@ def version(self):
         else:
             return None
 
-
-    def createMatrix(self, name, atom=None, shape=None, title='', filters=None,
-                     chunkshape=None, byteorder=None, createparents=False, obj=None,
-                     attrs=None):
+    def createMatrix(
+            self, name, atom=None, shape=None, title='', filters=None,
+            chunkshape=None, byteorder=None, createparents=False, obj=None,
+            attrs=None):
         """Create OMX Matrix (CArray) at root level. User must pass in either
            an existing numpy matrix, or a shape and an atom type."""
 
         # If object was passed in, make sure its shape is correct
-        if self.shape() != None and obj != None and obj.shape != self.shape():
-            raise ShapeError('%s has shape %s but this file requires shape %s' %
+        if (self.shape() is not None and
+                obj is not None and
+                obj.shape != self.shape()):
+            raise ShapeError(
+                '%s has shape %s but this file requires shape %s' %
                 (name, obj.shape, self.shape()))
-                
+
         # Create the HDF5 array
         if tables.__version__.startswith('3'):
-            matrix = self.createCArray(self.root.data, name, atom, shape, title, filters,
-                                       chunkshape, byteorder, createparents, obj)
+            matrix = self.createCArray(
+                self.root.data, name, atom, shape, title, filters,
+                chunkshape, byteorder, createparents, obj)
         else:
             # this version is tables 2.4-compatible:
-            matrix = self.createCArray(self.root.data, name, atom, shape, title, filters,
-                                       chunkshape, byteorder, createparents)
-            if (obj != None):
+            matrix = self.createCArray(
+                self.root.data, name, atom, shape, title, filters,
+                chunkshape, byteorder, createparents)
+            if (obj is not None):
                 matrix[:] = obj
 
         # Store shape if we don't have one yet
-        if self._shape == None:
-            storeshape = np.array([matrix.shape[0],matrix.shape[1]], dtype='int32')
+        if self._shape is None:
+            storeshape = np.array(
+                [matrix.shape[0], matrix.shape[1]], dtype='int32')
             self.root._v_attrs['SHAPE'] = storeshape
             self._shape = matrix.shape
 
@@ -67,18 +72,18 @@ def shape(self):
             # Shape is stored as a numpy.array:
             arrayshape = self.root._v_attrs['SHAPE']
             # which must be converted to a tuple:
-            realshape = (arrayshape[0],arrayshape[1])
+            realshape = (arrayshape[0], arrayshape[1])
             self._shape = realshape
             return self._shape
 
         # Inspect the first CArray object to determine its shape
         if len(self) > 0:
-            self._shape = self.iterNodes(self.root.data,'CArray').next().shape
+            self._shape = self.iterNodes(self.root.data, 'CArray').next().shape
 
             # Store it if we can
             if self._isWritable():
                 storeshape = np.array(
-                    [self._shape[0],self._shape[1]],
+                    [self._shape[0], self._shape[1]],
                     dtype='int32')
                 self.root._v_attrs['SHAPE'] = storeshape
 
@@ -87,21 +92,22 @@ def shape(self):
         else:
             return None
 
-
     def listMatrices(self):
         """Return list of Matrix names in this File"""
-        return [node.name for node in self.listNodes(self.root.data,'CArray')]
-
+        return [node.name for node in self.listNodes(self.root.data, 'CArray')]
 
     def listAllAttributes(self):
-        """Return combined list of all attributes used for any Matrix in this File"""
+        """
+        Return combined list of all attributes used for
+        any Matrix in this File
+
+        """
         all_tags = set()
-        for m in self.listNodes(self.root,'CArray'):
-            if m.attrs != None:
+        for m in self.listNodes(self.root, 'CArray'):
+            if m.attrs is not None:
                 all_tags.update(m.attrs._v_attrnames)
         return sorted(list(all_tags))
 
-
     # MAPPINGS -----------------------------------------------
     def listMappings(self):
         try:
@@ -109,13 +115,11 @@ def listMappings(self):
         except:
             return []
 
-
     def deleteMapping(self, title):
         try:
             self.removeNode(self.root.lookup, title)
         except:
-            raise LookupError('No such mapping: '+title)
-
+            raise LookupError('No such mapping: ' + title)
 
     def mapping(self, title):
         """Return dict containing key:value pairs for specified mapping. Keys
@@ -142,12 +146,11 @@ def mapentries(self, title):
             entries = []
             entries.extend(self.getNode(self.root.lookup, title)[:])
 
-            return (keymap,entries)
+            return (keymap, entries)
 
         except:
             raise LookupError('No such mapping: '+title)
 
-
     def createMapping(self, title, entries, overwrite=False):
         """Create an equivalency index, which maps a raw data dimension to
            another integer value. Once created, mappings can be referenced by
@@ -170,15 +173,15 @@ def createMapping(self, title, entries, overwrite=False):
             self.createGroup(self.root, 'lookup')
 
         # Write the mapping!
-        mymap = self.createArray(self.root.lookup, title, atom=tables.UInt16Atom(),
-                                 shape=(len(entries),) )
+        mymap = self.createArray(
+            self.root.lookup, title, atom=tables.UInt16Atom(),
+            shape=(len(entries),))
         mymap[:] = entries
 
         return mymap
 
-
     # The following functions implement Python list/dictionary lookups. ----
-    def __getitem__(self,key):
+    def __getitem__(self, key):
         """Return a matrix by name, or a list of matrices by attributes"""
 
         if isinstance(key, str):
@@ -194,16 +197,16 @@ def __getitem__(self,key):
 
         return mats
 
-
     def _getMatricesByAttribute(self, key, value, matrices=None):
 
         answer = []
 
-        if matrices==None:
-            matrices = self.listNodes(self.root.data,'CArray')
+        if matrices is None:
+            matrices = self.listNodes(self.root.data, 'CArray')
 
         for m in matrices:
-            if m.attrs == None: continue
+            if m.attrs is None:
+                continue
 
             # Only test if key is present in matrix attributes
             if key in m.attrs._v_attrnames and m.attrs[key] == value:
@@ -211,33 +214,29 @@ def _getMatricesByAttribute(self, key, value, matrices=None):
 
         return answer
 
-
     def __len__(self):
         return len(self.listNodes(self.root.data, 'CArray'))
 
-
     def __setitem__(self, key, dataset):
-        # We need to determine atom and shape from the object that's been passed in.
+        # We need to determine atom and shape from the object that's
+        # been passed in.
         # This assumes 'dataset' is a numpy object.
         atom = tables.Atom.from_dtype(dataset.dtype)
         shape = dataset.shape
 
-        #checks to see if it is already a tables instance, and if so, just copies it
+        # checks to see if it is already a tables instance, and if so,
+        # copies it
         if dataset.__class__.__name__ == 'CArray':
             return dataset.copy(self.root.data, key)
         else:
             return self.createMatrix(key, atom, shape, obj=dataset)
 
-
     def __delitem__(self, key):
         self.removeNode(self.root.data, key)
 
-
     def __iter__(self):
         """Iterate over the keys in this container"""
         return self.iterNodes(self.root.data, 'CArray')
 
-
     def __contains__(self, item):
         return item in self.root.data._v_children
-
diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index d0101a1e09..c1e713902f 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -1,5 +1,11 @@
-import tables,omx,numpy,os
-from nose.tools import *
+import os
+
+import nose.tools as nt
+import numpy
+import tables
+
+from .. import open_omxfile
+
 
 def setup_clean():
     try:
@@ -11,7 +17,7 @@ def setup_clean():
 def setup_empty_file():
     try:
         os.remove('test1.omx')
-        f = omx.openFile('test.omx','w')
+        f = open_omxfile('test.omx', 'w')
         f.close()
     except:
         pass
@@ -24,55 +30,61 @@ def teardown_clean():
         pass
 
 
-@with_setup(setup_clean,teardown_clean)
+@nt.with_setup(setup_clean, teardown_clean)
 def test_create_file():
-    f = omx.openFile('test1.omx','w')
+    f = open_omxfile('test1.omx', 'w')
     f.close()
-    assert(os.path.exists('test1.omx'))
+    nt.assert(os.path.exists('test1.omx'))
+
 
 def test_open_readonly_hdf5_file():
-    f = tables.openFile('test2.omx','w')
+    f = tables.openFile('test2.omx', 'w')
     f.close()
-    f = omx.openFile('test2.omx','r')
-    f.close() 
+    f = open_omxfile('test2.omx', 'r')
+    f.close()
+
 
 def test_add_numpy_matrix_using_brackets():
-    f = omx.openFile('test3.omx','w')
-    f['m1'] = numpy.ones((5,5))
+    f = open_omxfile('test3.omx', 'w')
+    f['m1'] = numpy.ones((5, 5))
     f.close()
 
+
 def test_add_numpy_matrix_using_create_matrix():
-    f = omx.openFile('test4.omx','w')
-    f.createMatrix('m1', obj=numpy.ones((5,5)))
+    f = open_omxfile('test4.omx', 'w')
+    f.createMatrix('m1', obj=numpy.ones((5, 5)))
     f.close()
 
+
 def test_add_matrix_to_readonly_file():
-    f = omx.openFile('test6.omx','w')
-    f['m2'] = numpy.ones((5,5))
+    f = open_omxfile('test6.omx', 'w')
+    f['m2'] = numpy.ones((5, 5))
+    f.close()
+    f = open_omxfile('test6.omx', 'r')
+    nt.assert_raises(tables.FileModeError, add_m1_node, f)
     f.close()
-    f = omx.openFile('test6.omx','r')
-    assert_raises(tables.FileModeError, add_m1_node, f)
-    f.close() 
+
 
 def test_add_matrix_with_same_name():
-    f = omx.openFile('test5.omx','w')
+    f = open_omxfile('test5.omx', 'w')
     add_m1_node(f)
     # now add m1 again:
-    assert_raises(tables.NodeError, add_m1_node, f)
+    nt.assert_raises(tables.NodeError, add_m1_node, f)
     f.close()
 
-@with_setup(setup_clean,teardown_clean)
+
+@nt.with_setup(setup_clean, teardown_clean)
 def test_get_length_of_file():
-    f = omx.openFile('test7.omx','w')
-    f['m1'] = numpy.ones((5,5))
-    f['m2'] = numpy.ones((5,5))
-    f['m3'] = numpy.ones((5,5))
-    f['m4'] = numpy.ones((5,5))
-    f['m5'] = numpy.ones((5,5))
-    assert(len(f)==5)
-    assert(len(f.listMatrices())==5)
+    f = open_omxfile('test7.omx', 'w')
+    f['m1'] = numpy.ones((5, 5))
+    f['m2'] = numpy.ones((5, 5))
+    f['m3'] = numpy.ones((5, 5))
+    f['m4'] = numpy.ones((5, 5))
+    f['m5'] = numpy.ones((5, 5))
+    nt.assert(len(f) == 5)
+    nt.assert(len(f.listMatrices()) == 5)
     f.close()
 
-def add_m1_node(f):
-    f.createMatrix('m1', obj=numpy.ones((7,7)))
 
+def add_m1_node(f):
+    f.createMatrix('m1', obj=numpy.ones((7, 7)))

From 25606a7046ea233640d2a00f84e8473f442fa69c Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 12:42:29 -0800
Subject: [PATCH 08/17] get omx tests running under pytest

---
 activitysim/omx/__init__.py           |   2 +-
 activitysim/omx/tests/__init__.py     |   0
 activitysim/omx/tests/test_omxfile.py | 107 +++++++++++++-------------
 3 files changed, 55 insertions(+), 54 deletions(-)
 create mode 100644 activitysim/omx/tests/__init__.py

diff --git a/activitysim/omx/__init__.py b/activitysim/omx/__init__.py
index f2902e3e92..19df77cf8c 100644
--- a/activitysim/omx/__init__.py
+++ b/activitysim/omx/__init__.py
@@ -4,7 +4,7 @@
 import numpy
 import tables
 
-from .omxile import File
+from .omxfile import File
 from .exceptions import ShapeError
 
 # GLOBAL VARIABLES -----------
diff --git a/activitysim/omx/tests/__init__.py b/activitysim/omx/tests/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index c1e713902f..5f8f5052ab 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -1,90 +1,91 @@
 import os
+import tempfile
 
-import nose.tools as nt
-import numpy
+import numpy as np
+import pytest
 import tables
 
 from .. import open_omxfile
+from ..exceptions import ShapeError
 
 
-def setup_clean():
-    try:
-        os.remove('test1.omx')
-    except:
-        pass
+@pytest.fixture
+def tmpomx(request):
+    with tempfile.NamedTemporaryFile() as f:
+        fname = f.name
 
+    def cleanup():
+        if os.path.exists(fname):
+            os.remove(fname)
+    request.addfinalizer(cleanup)
 
-def setup_empty_file():
-    try:
-        os.remove('test1.omx')
-        f = open_omxfile('test.omx', 'w')
-        f.close()
-    except:
-        pass
+    return fname
 
 
-def teardown_clean():
-    try:
-        os.remove('test2.omx')
-    except:
-        pass
-
-
-@nt.with_setup(setup_clean, teardown_clean)
-def test_create_file():
-    f = open_omxfile('test1.omx', 'w')
+def test_create_file(tmpomx):
+    f = open_omxfile(tmpomx, 'w')
     f.close()
-    nt.assert(os.path.exists('test1.omx'))
+    assert os.path.exists(tmpomx)
 
 
-def test_open_readonly_hdf5_file():
-    f = tables.openFile('test2.omx', 'w')
+def test_open_readonly_hdf5_file(tmpomx):
+    f = tables.openFile(tmpomx, 'w')
     f.close()
-    f = open_omxfile('test2.omx', 'r')
+    f = open_omxfile(tmpomx, 'r')
     f.close()
 
 
-def test_add_numpy_matrix_using_brackets():
-    f = open_omxfile('test3.omx', 'w')
-    f['m1'] = numpy.ones((5, 5))
+def test_add_numpy_matrix_using_brackets(tmpomx):
+    f = open_omxfile(tmpomx, 'w')
+    f['m1'] = np.ones((5, 5))
     f.close()
 
 
-def test_add_numpy_matrix_using_create_matrix():
-    f = open_omxfile('test4.omx', 'w')
-    f.createMatrix('m1', obj=numpy.ones((5, 5)))
+def test_add_np_matrix_using_create_matrix(tmpomx):
+    f = open_omxfile(tmpomx, 'w')
+    f.createMatrix('m1', obj=np.ones((5, 5)))
+
+    # test check for shape matching
+    with pytest.raises(ShapeError):
+        f.createMatrix('m2', obj=np.ones((8, 8)))
+
     f.close()
 
 
-def test_add_matrix_to_readonly_file():
-    f = open_omxfile('test6.omx', 'w')
-    f['m2'] = numpy.ones((5, 5))
+def test_add_matrix_to_readonly_file(tmpomx):
+    f = open_omxfile(tmpomx, 'w')
+    f['m2'] = np.ones((7, 7))
     f.close()
-    f = open_omxfile('test6.omx', 'r')
-    nt.assert_raises(tables.FileModeError, add_m1_node, f)
+    f = open_omxfile(tmpomx, 'r')
+
+    with pytest.raises(tables.FileModeError):
+        add_m1_node(f)
+
     f.close()
 
 
-def test_add_matrix_with_same_name():
-    f = open_omxfile('test5.omx', 'w')
+def test_add_matrix_with_same_name(tmpomx):
+    f = open_omxfile(tmpomx, 'w')
     add_m1_node(f)
     # now add m1 again:
-    nt.assert_raises(tables.NodeError, add_m1_node, f)
+
+    with pytest.raises(tables.NodeError):
+        add_m1_node(f)
+
     f.close()
 
 
-@nt.with_setup(setup_clean, teardown_clean)
-def test_get_length_of_file():
-    f = open_omxfile('test7.omx', 'w')
-    f['m1'] = numpy.ones((5, 5))
-    f['m2'] = numpy.ones((5, 5))
-    f['m3'] = numpy.ones((5, 5))
-    f['m4'] = numpy.ones((5, 5))
-    f['m5'] = numpy.ones((5, 5))
-    nt.assert(len(f) == 5)
-    nt.assert(len(f.listMatrices()) == 5)
+def test_get_length_of_file(tmpomx):
+    f = open_omxfile(tmpomx, 'w')
+    f['m1'] = np.ones((5, 5))
+    f['m2'] = np.ones((5, 5))
+    f['m3'] = np.ones((5, 5))
+    f['m4'] = np.ones((5, 5))
+    f['m5'] = np.ones((5, 5))
+    assert len(f) == 5
+    assert len(f.listMatrices()) == 5
     f.close()
 
 
 def add_m1_node(f):
-    f.createMatrix('m1', obj=numpy.ones((7, 7)))
+    f.createMatrix('m1', obj=np.ones((7, 7)))

From 72e1a4eab1f07768a7b0128115bd4f09fe72fef0 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 13:39:28 -0800
Subject: [PATCH 09/17] more pep8 fixes and general cleanup

---
 activitysim/omx/__init__.py           |  42 +----------
 activitysim/omx/omxfile.py            | 102 +++++++++++++++++---------
 activitysim/omx/tests/test_omxfile.py |  13 ++--
 3 files changed, 74 insertions(+), 83 deletions(-)

diff --git a/activitysim/omx/__init__.py b/activitysim/omx/__init__.py
index 19df77cf8c..4608c44aa8 100644
--- a/activitysim/omx/__init__.py
+++ b/activitysim/omx/__init__.py
@@ -1,42 +1,2 @@
-# OMX package
-# release 1
-
-import numpy
-import tables
-
-from .omxfile import File
+from .omxfile import OMXFile, open_omxfile, OMX_VERSION
 from .exceptions import ShapeError
-
-# GLOBAL VARIABLES -----------
-OMX_VERSION = '0.2'
-
-
-# GLOBAL FUNCTIONS -----------
-def open_omxfile(
-        filename, mode='r', title='', root_uep='/',
-        filters=tables.Filters(
-            complevel=1, shuffle=True, fletcher32=False, complib='zlib'),
-        shape=None, **kwargs):
-    """Open or create a new OMX file. New files will be created with default
-       zlib compression enabled."""
-
-    f = File(filename, mode, title, root_uep, filters, **kwargs)
-
-    # add omx structure if file is writable
-    if mode != 'r':
-        # version number
-        if 'OMX_VERSION' not in f.root._v_attrs:
-            f.root._v_attrs['OMX_VERSION'] = OMX_VERSION
-
-        # shape
-        if shape:
-            storeshape = numpy.array([shape[0], shape[1]], dtype='int32')
-            f.root._v_attrs['SHAPE'] = storeshape
-
-        # /data and /lookup folders
-        if 'data' not in f.root:
-            f.createGroup(f.root, "data")
-        if 'lookup' not in f.root:
-            f.createGroup(f.root, "lookup")
-
-    return f
diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index 569cc4fe46..b88a8942eb 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -6,10 +6,12 @@
 
 from .exceptions import ShapeError
 
+OMX_VERSION = '0.2'
 
-class File(tables.File):
-    def __init__(self, f, m, t, r, f1, **kwargs):
-        tables.File.__init__(self, f, m, t, r, f1, **kwargs)
+
+class OMXFile(tables.File):
+    def __init__(self, *args, **kwargs):
+        super(OMXFile, self).__init__(*args, **kwargs)
         self._shape = None
 
     def version(self):
@@ -18,7 +20,7 @@ def version(self):
         else:
             return None
 
-    def createMatrix(
+    def create_matrix(
             self, name, atom=None, shape=None, title='', filters=None,
             chunkshape=None, byteorder=None, createparents=False, obj=None,
             attrs=None):
@@ -35,12 +37,12 @@ def createMatrix(
 
         # Create the HDF5 array
         if tables.__version__.startswith('3'):
-            matrix = self.createCArray(
+            matrix = self.create_carray(
                 self.root.data, name, atom, shape, title, filters,
                 chunkshape, byteorder, createparents, obj)
         else:
             # this version is tables 2.4-compatible:
-            matrix = self.createCArray(
+            matrix = self.create_carray(
                 self.root.data, name, atom, shape, title, filters,
                 chunkshape, byteorder, createparents)
             if (obj is not None):
@@ -78,13 +80,12 @@ def shape(self):
 
         # Inspect the first CArray object to determine its shape
         if len(self) > 0:
-            self._shape = self.iterNodes(self.root.data, 'CArray').next().shape
+            self._shape = self.iter_nodes(
+                self.root.data, 'CArray').next().shape
 
             # Store it if we can
-            if self._isWritable():
-                storeshape = np.array(
-                    [self._shape[0], self._shape[1]],
-                    dtype='int32')
+            if self._iswritable():
+                storeshape = np.array(self._shape, dtype='int32')
                 self.root._v_attrs['SHAPE'] = storeshape
 
             return self._shape
@@ -92,32 +93,33 @@ def shape(self):
         else:
             return None
 
-    def listMatrices(self):
+    def list_matrices(self):
         """Return list of Matrix names in this File"""
-        return [node.name for node in self.listNodes(self.root.data, 'CArray')]
+        return [
+            node.name for node in self.list_nodes(self.root.data, 'CArray')]
 
-    def listAllAttributes(self):
+    def list_all_attributes(self):
         """
         Return combined list of all attributes used for
         any Matrix in this File
 
         """
         all_tags = set()
-        for m in self.listNodes(self.root, 'CArray'):
+        for m in self.list_nodes(self.root, 'CArray'):
             if m.attrs is not None:
                 all_tags.update(m.attrs._v_attrnames)
         return sorted(list(all_tags))
 
     # MAPPINGS -----------------------------------------------
-    def listMappings(self):
+    def list_mappings(self):
         try:
-            return [m.name for m in self.listNodes(self.root.lookup)]
+            return [m.name for m in self.list_nodes(self.root.lookup)]
         except:
             return []
 
-    def deleteMapping(self, title):
+    def delete_mapping(self, title):
         try:
-            self.removeNode(self.root.lookup, title)
+            self.remove_node(self.root.lookup, title)
         except:
             raise LookupError('No such mapping: ' + title)
 
@@ -127,7 +129,7 @@ def mapping(self, title):
         try:
             # fetch entries
             entries = []
-            entries.extend(self.getNode(self.root.lookup, title)[:])
+            entries.extend(self.get_node(self.root.lookup, title)[:])
 
             # build reverse key-lookup
             keymap = {}
@@ -144,14 +146,14 @@ def mapentries(self, title):
         try:
             # fetch entries
             entries = []
-            entries.extend(self.getNode(self.root.lookup, title)[:])
+            entries.extend(self.get_node(self.root.lookup, title)[:])
 
             return (keymap, entries)
 
         except:
             raise LookupError('No such mapping: '+title)
 
-    def createMapping(self, title, entries, overwrite=False):
+    def create_mapping(self, title, entries, overwrite=False):
         """Create an equivalency index, which maps a raw data dimension to
            another integer value. Once created, mappings can be referenced by
            offset or by key."""
@@ -162,18 +164,18 @@ def createMapping(self, title, entries, overwrite=False):
                 raise ShapeError('Mapping must match one data dimension')
 
         # Handle case where mapping already exists:
-        if title in self.listMappings():
+        if title in self.list_mappings():
             if overwrite:
-                self.deleteMapping(title)
+                self.delete_mapping(title)
             else:
                 raise LookupError(title+' mapping already exists.')
 
         # Create lookup group under root if it doesn't already exist.
         if 'lookup' not in self.root:
-            self.createGroup(self.root, 'lookup')
+            self.create_group(self.root, 'lookup')
 
         # Write the mapping!
-        mymap = self.createArray(
+        mymap = self.create_array(
             self.root.lookup, title, atom=tables.UInt16Atom(),
             shape=(len(entries),))
         mymap[:] = entries
@@ -185,24 +187,24 @@ def __getitem__(self, key):
         """Return a matrix by name, or a list of matrices by attributes"""
 
         if isinstance(key, str):
-            return self.getNode(self.root.data, key)
+            return self.get_node(self.root.data, key)
 
         if 'keys' not in dir(key):
             raise LookupError('Key %s not found' % key)
 
         # Loop through key/value pairs
-        mats = self.listNodes(self.root.data, 'CArray')
+        mats = self.list_nodes(self.root.data, 'CArray')
         for a in key.keys():
-            mats = self._getMatricesByAttribute(a, key[a], mats)
+            mats = self._get_matrices_by_attribute(a, key[a], mats)
 
         return mats
 
-    def _getMatricesByAttribute(self, key, value, matrices=None):
+    def _get_matrices_by_attribute(self, key, value, matrices=None):
 
         answer = []
 
         if matrices is None:
-            matrices = self.listNodes(self.root.data, 'CArray')
+            matrices = self.list_nodes(self.root.data, 'CArray')
 
         for m in matrices:
             if m.attrs is None:
@@ -215,7 +217,7 @@ def _getMatricesByAttribute(self, key, value, matrices=None):
         return answer
 
     def __len__(self):
-        return len(self.listNodes(self.root.data, 'CArray'))
+        return len(self.list_nodes(self.root.data, 'CArray'))
 
     def __setitem__(self, key, dataset):
         # We need to determine atom and shape from the object that's
@@ -229,14 +231,44 @@ def __setitem__(self, key, dataset):
         if dataset.__class__.__name__ == 'CArray':
             return dataset.copy(self.root.data, key)
         else:
-            return self.createMatrix(key, atom, shape, obj=dataset)
+            return self.create_matrix(key, atom, shape, obj=dataset)
 
     def __delitem__(self, key):
-        self.removeNode(self.root.data, key)
+        self.remove_node(self.root.data, key)
 
     def __iter__(self):
         """Iterate over the keys in this container"""
-        return self.iterNodes(self.root.data, 'CArray')
+        return self.iter_nodes(self.root.data, 'CArray')
 
     def __contains__(self, item):
         return item in self.root.data._v_children
+
+
+def open_omxfile(
+        filename, mode='r', title='', root_uep='/',
+        filters=tables.Filters(
+            complevel=1, shuffle=True, fletcher32=False, complib='zlib'),
+        shape=None, **kwargs):
+    """Open or create a new OMX file. New files will be created with default
+       zlib compression enabled."""
+
+    f = OMXFile(filename, mode, title, root_uep, filters, **kwargs)
+
+    # add omx structure if file is writable
+    if mode != 'r':
+        # version number
+        if 'OMX_VERSION' not in f.root._v_attrs:
+            f.root._v_attrs['OMX_VERSION'] = OMX_VERSION
+
+        # shape
+        if shape:
+            storeshape = np.array([shape[0], shape[1]], dtype='int32')
+            f.root._v_attrs['SHAPE'] = storeshape
+
+        # /data and /lookup folders
+        if 'data' not in f.root:
+            f.create_group(f.root, "data")
+        if 'lookup' not in f.root:
+            f.create_group(f.root, "lookup")
+
+    return f
diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index 5f8f5052ab..758e132b34 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -5,8 +5,7 @@
 import pytest
 import tables
 
-from .. import open_omxfile
-from ..exceptions import ShapeError
+from .. import open_omxfile, ShapeError
 
 
 @pytest.fixture
@@ -29,7 +28,7 @@ def test_create_file(tmpomx):
 
 
 def test_open_readonly_hdf5_file(tmpomx):
-    f = tables.openFile(tmpomx, 'w')
+    f = tables.open_file(tmpomx, 'w')
     f.close()
     f = open_omxfile(tmpomx, 'r')
     f.close()
@@ -43,11 +42,11 @@ def test_add_numpy_matrix_using_brackets(tmpomx):
 
 def test_add_np_matrix_using_create_matrix(tmpomx):
     f = open_omxfile(tmpomx, 'w')
-    f.createMatrix('m1', obj=np.ones((5, 5)))
+    f.create_matrix('m1', obj=np.ones((5, 5)))
 
     # test check for shape matching
     with pytest.raises(ShapeError):
-        f.createMatrix('m2', obj=np.ones((8, 8)))
+        f.create_matrix('m2', obj=np.ones((8, 8)))
 
     f.close()
 
@@ -83,9 +82,9 @@ def test_get_length_of_file(tmpomx):
     f['m4'] = np.ones((5, 5))
     f['m5'] = np.ones((5, 5))
     assert len(f) == 5
-    assert len(f.listMatrices()) == 5
+    assert len(f.list_matrices()) == 5
     f.close()
 
 
 def add_m1_node(f):
-    f.createMatrix('m1', obj=np.ones((7, 7)))
+    f.create_matrix('m1', obj=np.ones((7, 7)))

From 097f0ac628d4d22686d51e37011af42c44e8bde9 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 13:42:10 -0800
Subject: [PATCH 10/17] remove tables 2 compatibility

---
 activitysim/omx/omxfile.py | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index b88a8942eb..6c70d9a3de 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -2,7 +2,7 @@
 # release 1
 
 import numpy as np
-import tables  # requires pytables >= 2.4
+import tables
 
 from .exceptions import ShapeError
 
@@ -40,13 +40,6 @@ def create_matrix(
             matrix = self.create_carray(
                 self.root.data, name, atom, shape, title, filters,
                 chunkshape, byteorder, createparents, obj)
-        else:
-            # this version is tables 2.4-compatible:
-            matrix = self.create_carray(
-                self.root.data, name, atom, shape, title, filters,
-                chunkshape, byteorder, createparents)
-            if (obj is not None):
-                matrix[:] = obj
 
         # Store shape if we don't have one yet
         if self._shape is None:

From 67227841b80f2fec8471a3caf34ae13497f57052 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 13:48:31 -0800
Subject: [PATCH 11/17] remove unused mapentries method

---
 activitysim/omx/omxfile.py | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index 6c70d9a3de..ba5be68474 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -132,19 +132,7 @@ def mapping(self, title):
             return keymap
 
         except:
-            raise LookupError('No such mapping: '+title)
-
-    def mapentries(self, title):
-        """Return entries[] with key for each array offset."""
-        try:
-            # fetch entries
-            entries = []
-            entries.extend(self.get_node(self.root.lookup, title)[:])
-
-            return (keymap, entries)
-
-        except:
-            raise LookupError('No such mapping: '+title)
+            raise LookupError('No such mapping: ' + title)
 
     def create_mapping(self, title, entries, overwrite=False):
         """Create an equivalency index, which maps a raw data dimension to
@@ -255,7 +243,7 @@ def open_omxfile(
 
         # shape
         if shape:
-            storeshape = np.array([shape[0], shape[1]], dtype='int32')
+            storeshape = np.array(shape, dtype='int32')
             f.root._v_attrs['SHAPE'] = storeshape
 
         # /data and /lookup folders

From 7c0bff899fe4254f0be93c91c80283585770f932 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 16:18:21 -0800
Subject: [PATCH 12/17] use context managers in tests

---
 activitysim/omx/omxfile.py            |  2 +-
 activitysim/omx/tests/test_omxfile.py | 65 +++++++++++++--------------
 2 files changed, 31 insertions(+), 36 deletions(-)

diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index ba5be68474..d75e5a8358 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -67,7 +67,7 @@ def shape(self):
             # Shape is stored as a numpy.array:
             arrayshape = self.root._v_attrs['SHAPE']
             # which must be converted to a tuple:
-            realshape = (arrayshape[0], arrayshape[1])
+            realshape = tuple(arrayshape)
             self._shape = realshape
             return self._shape
 
diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index 758e132b34..6c9f9613e5 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -8,6 +8,10 @@
 from .. import open_omxfile, ShapeError
 
 
+def add_m1_node(f):
+    f.create_matrix('m1', obj=np.ones((7, 7)))
+
+
 @pytest.fixture
 def tmpomx(request):
     with tempfile.NamedTemporaryFile() as f:
@@ -35,56 +39,47 @@ def test_open_readonly_hdf5_file(tmpomx):
 
 
 def test_add_numpy_matrix_using_brackets(tmpomx):
-    f = open_omxfile(tmpomx, 'w')
-    f['m1'] = np.ones((5, 5))
-    f.close()
+    with open_omxfile(tmpomx, 'w') as f:
+        f['m1'] = np.ones((5, 5))
 
 
 def test_add_np_matrix_using_create_matrix(tmpomx):
-    f = open_omxfile(tmpomx, 'w')
-    f.create_matrix('m1', obj=np.ones((5, 5)))
-
-    # test check for shape matching
-    with pytest.raises(ShapeError):
-        f.create_matrix('m2', obj=np.ones((8, 8)))
+    with open_omxfile(tmpomx, 'w') as f:
+        f.create_matrix('m1', obj=np.ones((5, 5)))
 
-    f.close()
+        # test check for shape matching
+        with pytest.raises(ShapeError):
+            f.create_matrix('m2', obj=np.ones((8, 8)))
 
 
 def test_add_matrix_to_readonly_file(tmpomx):
-    f = open_omxfile(tmpomx, 'w')
-    f['m2'] = np.ones((7, 7))
-    f.close()
-    f = open_omxfile(tmpomx, 'r')
+    with open_omxfile(tmpomx, 'w') as f:
+        f['m2'] = np.ones((7, 7))
 
-    with pytest.raises(tables.FileModeError):
-        add_m1_node(f)
-
-    f.close()
+    with open_omxfile(tmpomx, 'r') as f:
+        with pytest.raises(tables.FileModeError):
+            add_m1_node(f)
 
 
 def test_add_matrix_with_same_name(tmpomx):
-    f = open_omxfile(tmpomx, 'w')
-    add_m1_node(f)
-    # now add m1 again:
-
-    with pytest.raises(tables.NodeError):
+    with open_omxfile(tmpomx, 'w') as f:
         add_m1_node(f)
 
-    f.close()
+        # now add m1 again:
+        with pytest.raises(tables.NodeError):
+            add_m1_node(f)
 
 
 def test_get_length_of_file(tmpomx):
-    f = open_omxfile(tmpomx, 'w')
-    f['m1'] = np.ones((5, 5))
-    f['m2'] = np.ones((5, 5))
-    f['m3'] = np.ones((5, 5))
-    f['m4'] = np.ones((5, 5))
-    f['m5'] = np.ones((5, 5))
-    assert len(f) == 5
-    assert len(f.list_matrices()) == 5
-    f.close()
+    mats = ['m{}'.format(x) for x in range(5)]
+    with open_omxfile(tmpomx, 'w') as f:
+        for m in mats:
+            f[m] = np.ones((5, 5))
 
+        assert f.list_matrices() == mats
 
-def add_m1_node(f):
-    f.create_matrix('m1', obj=np.ones((7, 7)))
+
+def test_shapeerror(tmpomx):
+    with open_omxfile(tmpomx, mode='w', shape=(5, 5)) as f:
+        with pytest.raises(ShapeError):
+            f['test'] = np.ones(10)

From 219303805f21b64cad6f961466e45b96a8f81393 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 16:38:30 -0800
Subject: [PATCH 13/17] add a test array fixture

---
 activitysim/omx/tests/test_omxfile.py | 45 ++++++++++++++-------------
 1 file changed, 24 insertions(+), 21 deletions(-)

diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index 6c9f9613e5..83f3f25ecb 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -2,16 +2,13 @@
 import tempfile
 
 import numpy as np
+import numpy.testing as npt
 import pytest
 import tables
 
 from .. import open_omxfile, ShapeError
 
 
-def add_m1_node(f):
-    f.create_matrix('m1', obj=np.ones((7, 7)))
-
-
 @pytest.fixture
 def tmpomx(request):
     with tempfile.NamedTemporaryFile() as f:
@@ -25,61 +22,67 @@ def cleanup():
     return fname
 
 
-def test_create_file(tmpomx):
-    f = open_omxfile(tmpomx, 'w')
-    f.close()
-    assert os.path.exists(tmpomx)
+@pytest.fixture
+def ones5x5():
+    return np.ones((5, 5))
 
 
 def test_open_readonly_hdf5_file(tmpomx):
     f = tables.open_file(tmpomx, 'w')
     f.close()
+    assert os.path.exists(tmpomx)
     f = open_omxfile(tmpomx, 'r')
     f.close()
 
 
-def test_add_numpy_matrix_using_brackets(tmpomx):
+def test_setitem_getitem(tmpomx, ones5x5):
     with open_omxfile(tmpomx, 'w') as f:
-        f['m1'] = np.ones((5, 5))
+        f['m1'] = ones5x5
+        npt.assert_array_equal(f['m1'], ones5x5)
+        assert f.shape() == (5, 5)
 
 
-def test_add_np_matrix_using_create_matrix(tmpomx):
+def test_create_matrix(tmpomx, ones5x5):
     with open_omxfile(tmpomx, 'w') as f:
-        f.create_matrix('m1', obj=np.ones((5, 5)))
+        f.create_matrix('m1', obj=ones5x5)
+        npt.assert_array_equal(f['m1'], ones5x5)
+        assert f.shape() == (5, 5)
 
         # test check for shape matching
         with pytest.raises(ShapeError):
             f.create_matrix('m2', obj=np.ones((8, 8)))
 
 
-def test_add_matrix_to_readonly_file(tmpomx):
+def test_add_matrix_to_readonly_file(tmpomx, ones5x5):
     with open_omxfile(tmpomx, 'w') as f:
-        f['m2'] = np.ones((7, 7))
+        f['m2'] = ones5x5
 
     with open_omxfile(tmpomx, 'r') as f:
         with pytest.raises(tables.FileModeError):
-            add_m1_node(f)
+            f['m1'] = ones5x5
 
 
-def test_add_matrix_with_same_name(tmpomx):
+def test_add_matrix_with_same_name(tmpomx, ones5x5):
     with open_omxfile(tmpomx, 'w') as f:
-        add_m1_node(f)
+        f['m1'] = ones5x5
 
         # now add m1 again:
         with pytest.raises(tables.NodeError):
-            add_m1_node(f)
+            f['m1'] = ones5x5
 
 
-def test_get_length_of_file(tmpomx):
+def test_get_length_of_file(tmpomx, ones5x5):
     mats = ['m{}'.format(x) for x in range(5)]
     with open_omxfile(tmpomx, 'w') as f:
         for m in mats:
-            f[m] = np.ones((5, 5))
+            f[m] = ones5x5
 
         assert f.list_matrices() == mats
 
 
-def test_shapeerror(tmpomx):
+def test_shape(tmpomx):
     with open_omxfile(tmpomx, mode='w', shape=(5, 5)) as f:
+        assert f.shape() == (5, 5)
+
         with pytest.raises(ShapeError):
             f['test'] = np.ones(10)

From a1a0760a22fa332bbf4441a09d9a91e91563c493 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 21:37:02 -0800
Subject: [PATCH 14/17] test coverage, cleanup, and bug fixes

---
 activitysim/omx/omxfile.py            | 34 ++++++++----------
 activitysim/omx/tests/test_omxfile.py | 50 ++++++++++++++++++++++++---
 2 files changed, 59 insertions(+), 25 deletions(-)

diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index d75e5a8358..86e9078832 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -1,6 +1,3 @@
-# OMX package
-# release 1
-
 import numpy as np
 import tables
 
@@ -43,8 +40,7 @@ def create_matrix(
 
         # Store shape if we don't have one yet
         if self._shape is None:
-            storeshape = np.array(
-                [matrix.shape[0], matrix.shape[1]], dtype='int32')
+            storeshape = np.array(matrix.shape, dtype='int32')
             self.root._v_attrs['SHAPE'] = storeshape
             self._shape = matrix.shape
 
@@ -98,10 +94,9 @@ def list_all_attributes(self):
 
         """
         all_tags = set()
-        for m in self.list_nodes(self.root, 'CArray'):
-            if m.attrs is not None:
-                all_tags.update(m.attrs._v_attrnames)
-        return sorted(list(all_tags))
+        for m in self.iter_nodes(self.root.data, 'CArray'):
+            all_tags.update(m.attrs._v_attrnamesuser)
+        return sorted(all_tags)
 
     # MAPPINGS -----------------------------------------------
     def list_mappings(self):
@@ -149,7 +144,7 @@ def create_mapping(self, title, entries, overwrite=False):
             if overwrite:
                 self.delete_mapping(title)
             else:
-                raise LookupError(title+' mapping already exists.')
+                raise LookupError(title + ' mapping already exists.')
 
         # Create lookup group under root if it doesn't already exist.
         if 'lookup' not in self.root:
@@ -181,7 +176,6 @@ def __getitem__(self, key):
         return mats
 
     def _get_matrices_by_attribute(self, key, value, matrices=None):
-
         answer = []
 
         if matrices is None:
@@ -192,7 +186,7 @@ def _get_matrices_by_attribute(self, key, value, matrices=None):
                 continue
 
             # Only test if key is present in matrix attributes
-            if key in m.attrs._v_attrnames and m.attrs[key] == value:
+            if key in m.attrs and m.attrs[key] == value:
                 answer.append(m)
 
         return answer
@@ -201,17 +195,17 @@ def __len__(self):
         return len(self.list_nodes(self.root.data, 'CArray'))
 
     def __setitem__(self, key, dataset):
-        # We need to determine atom and shape from the object that's
-        # been passed in.
-        # This assumes 'dataset' is a numpy object.
-        atom = tables.Atom.from_dtype(dataset.dtype)
-        shape = dataset.shape
-
         # checks to see if it is already a tables instance, and if so,
         # copies it
-        if dataset.__class__.__name__ == 'CArray':
+        if isinstance(dataset, tables.CArray):
             return dataset.copy(self.root.data, key)
         else:
+            # We need to determine atom and shape from the object that's
+            # been passed in.
+            # This assumes 'dataset' is a numpy object.
+            atom = tables.Atom.from_dtype(dataset.dtype)
+            shape = dataset.shape
+
             return self.create_matrix(key, atom, shape, obj=dataset)
 
     def __delitem__(self, key):
@@ -222,7 +216,7 @@ def __iter__(self):
         return self.iter_nodes(self.root.data, 'CArray')
 
     def __contains__(self, item):
-        return item in self.root.data._v_children
+        return item in self.root.data
 
 
 def open_omxfile(
diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index 83f3f25ecb..f54f247ba1 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -27,6 +27,18 @@ def ones5x5():
     return np.ones((5, 5))
 
 
+@pytest.fixture
+def basic_omx(request, tmpomx, ones5x5):
+    f = open_omxfile(tmpomx, mode='w')
+    f['m1'] = ones5x5
+
+    def fin():
+        f.close()
+    request.addfinalizer(fin)
+
+    return f
+
+
 def test_open_readonly_hdf5_file(tmpomx):
     f = tables.open_file(tmpomx, 'w')
     f.close()
@@ -35,11 +47,13 @@ def test_open_readonly_hdf5_file(tmpomx):
     f.close()
 
 
-def test_setitem_getitem(tmpomx, ones5x5):
+def test_set_get_del(tmpomx, ones5x5):
     with open_omxfile(tmpomx, 'w') as f:
         f['m1'] = ones5x5
         npt.assert_array_equal(f['m1'], ones5x5)
         assert f.shape() == (5, 5)
+        del f['m1']
+        assert 'm1' not in f
 
 
 def test_create_matrix(tmpomx, ones5x5):
@@ -71,13 +85,17 @@ def test_add_matrix_with_same_name(tmpomx, ones5x5):
             f['m1'] = ones5x5
 
 
-def test_get_length_of_file(tmpomx, ones5x5):
-    mats = ['m{}'.format(x) for x in range(5)]
+def test_len_list_iter(tmpomx, ones5x5):
+    names = ['m{}'.format(x) for x in range(5)]
     with open_omxfile(tmpomx, 'w') as f:
-        for m in mats:
+        for m in names:
             f[m] = ones5x5
 
-        assert f.list_matrices() == mats
+        for mat in f:
+            npt.assert_array_equal(mat, ones5x5)
+
+        assert len(f) == len(names)
+        assert f.list_matrices() == names
 
 
 def test_shape(tmpomx):
@@ -86,3 +104,25 @@ def test_shape(tmpomx):
 
         with pytest.raises(ShapeError):
             f['test'] = np.ones(10)
+
+
+def test_contains(basic_omx):
+    assert 'm1' in basic_omx
+
+
+def test_list_all_attrs(basic_omx, ones5x5):
+    basic_omx['m2'] = ones5x5
+
+    assert basic_omx.list_all_attributes() == []
+
+    basic_omx['m1'].attrs['a1'] = 'a1'
+    basic_omx['m1'].attrs['a2'] = 'a2'
+    basic_omx['m2'].attrs['a2'] = 'a2'
+    basic_omx['m2'].attrs['a3'] = 'a3'
+
+    assert basic_omx.list_all_attributes() == ['a1', 'a2', 'a3']
+
+
+def test_set_with_carray(basic_omx):
+    basic_omx['m2'] = basic_omx['m1']
+    npt.assert_array_equal(basic_omx['m2'], basic_omx['m1'])

From 1febc8458c8271d8ee8989f9489a0e1184b7f6fb Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 21:51:24 -0800
Subject: [PATCH 15/17] Split getitem and get_matrices_by_attr

Instead of having a dual-purpose __getitem__, only
have it return matrices by name.
To get matrices matching a key/value attribute pair use
the method get_matrices_by_attr.
---
 activitysim/omx/omxfile.py            | 44 +++++++++++----------------
 activitysim/omx/tests/test_omxfile.py | 20 ++++++++++++
 2 files changed, 38 insertions(+), 26 deletions(-)

diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index 86e9078832..46cbef579b 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -158,38 +158,30 @@ def create_mapping(self, title, entries, overwrite=False):
 
         return mymap
 
-    # The following functions implement Python list/dictionary lookups. ----
     def __getitem__(self, key):
         """Return a matrix by name, or a list of matrices by attributes"""
+        return self.get_node(self.root.data, key)
 
-        if isinstance(key, str):
-            return self.get_node(self.root.data, key)
-
-        if 'keys' not in dir(key):
-            raise LookupError('Key %s not found' % key)
-
-        # Loop through key/value pairs
-        mats = self.list_nodes(self.root.data, 'CArray')
-        for a in key.keys():
-            mats = self._get_matrices_by_attribute(a, key[a], mats)
-
-        return mats
-
-    def _get_matrices_by_attribute(self, key, value, matrices=None):
-        answer = []
-
-        if matrices is None:
-            matrices = self.list_nodes(self.root.data, 'CArray')
+    def get_matrices_by_attr(self, key, value):
+        """
+        Returns a list of matrices that have an attribute matching
+        a certain value.
 
-        for m in matrices:
-            if m.attrs is None:
-                continue
+        Parameters
+        ----------
+        key : str
+            Attribute name to match.
+        value : object
+            Attribute value to match.
 
-            # Only test if key is present in matrix attributes
-            if key in m.attrs and m.attrs[key] == value:
-                answer.append(m)
+        Returns
+        -------
+        matrices : list
 
-        return answer
+        """
+        return [
+            m for m in self
+            if key in m.attrs and m.attrs[key] == value]
 
     def __len__(self):
         return len(self.list_nodes(self.root.data, 'CArray'))
diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index f54f247ba1..9b5bb6d239 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -123,6 +123,26 @@ def test_list_all_attrs(basic_omx, ones5x5):
     assert basic_omx.list_all_attributes() == ['a1', 'a2', 'a3']
 
 
+def test_matrices_by_attr(basic_omx, ones5x5):
+    bo = basic_omx
+    bo['m2'] = ones5x5
+    bo['m3'] = ones5x5
+
+    for m in bo:
+        m.attrs['a1'] = 'a1'
+        m.attrs['a2'] = 'a2'
+    bo['m3'].attrs['a2'] = 'a22'
+    bo['m3'].attrs['a3'] = 'a3'
+
+    gmba = bo.get_matrices_by_attr
+
+    assert gmba('zz', 'zz') == []
+    assert gmba('a1', 'a1') == [bo['m1'], bo['m2'], bo['m3']]
+    assert gmba('a2', 'a2') == [bo['m1'], bo['m2']]
+    assert gmba('a2', 'a22') == [bo['m3']]
+    assert gmba('a3', 'a3') == [bo['m3']]
+
+
 def test_set_with_carray(basic_omx):
     basic_omx['m2'] = basic_omx['m1']
     npt.assert_array_equal(basic_omx['m2'], basic_omx['m1'])

From 64db23b57efe25a1354b499d766c0a70dd4701e8 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Thu, 11 Dec 2014 22:03:28 -0800
Subject: [PATCH 16/17] Add Apache v2 license and license notices to OMX files

---
 activitysim/omx/LICENSE.TXT           | 202 ++++++++++++++++++++++++++
 activitysim/omx/__init__.py           |   5 +
 activitysim/omx/exceptions.py         |   6 +
 activitysim/omx/omxfile.py            |   5 +
 activitysim/omx/tests/test_omxfile.py |   5 +
 5 files changed, 223 insertions(+)
 create mode 100644 activitysim/omx/LICENSE.TXT

diff --git a/activitysim/omx/LICENSE.TXT b/activitysim/omx/LICENSE.TXT
new file mode 100644
index 0000000000..d645695673
--- /dev/null
+++ b/activitysim/omx/LICENSE.TXT
@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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+
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+
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diff --git a/activitysim/omx/__init__.py b/activitysim/omx/__init__.py
index 4608c44aa8..ab6663217f 100644
--- a/activitysim/omx/__init__.py
+++ b/activitysim/omx/__init__.py
@@ -1,2 +1,7 @@
+# Licensed under the Apache License, v2.0
+# See activitysim/omx/LICENSE.txt
+# Modified from the original OMX library available at
+# https://github.com/osPlanning/omx/tree/dev/api/python/omx
+
 from .omxfile import OMXFile, open_omxfile, OMX_VERSION
 from .exceptions import ShapeError
diff --git a/activitysim/omx/exceptions.py b/activitysim/omx/exceptions.py
index 6f82cdb605..f7220e21bb 100644
--- a/activitysim/omx/exceptions.py
+++ b/activitysim/omx/exceptions.py
@@ -1,2 +1,8 @@
+# Licensed under the Apache License, v2.0
+# See activitysim/omx/LICENSE.txt
+# Modified from the original OMX library available at
+# https://github.com/osPlanning/omx/tree/dev/api/python/omx
+
+
 class ShapeError(Exception):
     pass
diff --git a/activitysim/omx/omxfile.py b/activitysim/omx/omxfile.py
index 46cbef579b..182d0d5362 100644
--- a/activitysim/omx/omxfile.py
+++ b/activitysim/omx/omxfile.py
@@ -1,3 +1,8 @@
+# Licensed under the Apache License, v2.0
+# See activitysim/omx/LICENSE.txt
+# Modified from the original OMX library available at
+# https://github.com/osPlanning/omx/tree/dev/api/python/omx
+
 import numpy as np
 import tables
 
diff --git a/activitysim/omx/tests/test_omxfile.py b/activitysim/omx/tests/test_omxfile.py
index 9b5bb6d239..7f8b6ac23a 100644
--- a/activitysim/omx/tests/test_omxfile.py
+++ b/activitysim/omx/tests/test_omxfile.py
@@ -1,3 +1,8 @@
+# Licensed under the Apache License, v2.0
+# See activitysim/omx/LICENSE.txt
+# Modified from the original OMX library available at
+# https://github.com/osPlanning/omx/tree/dev/api/python/omx
+
 import os
 import tempfile
 

From e1398aeeaff3375fc0a3b8a7517c6de9a5123711 Mon Sep 17 00:00:00 2001
From: Matt Davis <jiffyclub@gmail.com>
Date: Fri, 12 Dec 2014 10:44:14 -0800
Subject: [PATCH 17/17] explicitly add tables and urbansim as dependencies

---
 .travis.yml | 2 +-
 setup.py    | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 4af264e0bc..94539674f1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -18,7 +18,7 @@ install:
 - >
   conda create -q -c synthicity -n test-environment
   python=$TRAVIS_PYTHON_VERSION
-  numpy pandas pip pytest urbansim
+  numpy pandas pip pytables pytest urbansim
 - source activate test-environment
 - pip install pytest-cov coveralls pep8
 - pip install .
diff --git a/setup.py b/setup.py
index 2bbe07261e..d88ecdb149 100644
--- a/setup.py
+++ b/setup.py
@@ -20,5 +20,7 @@
     install_requires=[
         'numpy>=1.8.0',
         'pandas>=0.13.1',
+        'tables>=3.1.0',
+        'urbansim>=1.3'
     ]
 )