Merge b8e983f into 961a7ef

.travis.yml

@@ -1,40 +1,31 @@
 language: python
-sudo: false
+
 python:
-- '2.7'
-- '3.5'
-addons:
-  apt:
-    sources:
-      - ubuntu-toolchain-r-test
-    packages:
-      - g++-4.9
+  - '2.7'
+  - '3.5'
+  - '3.6'
+
+# This section can be removed when Python 3.7 is more cleanly supported in Travis
+matrix:
+  include:
+    - python: '3.7'
+      dist: xenial
+      sudo: true
+
 install:
-- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-    wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-  else
-    wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-  fi
-- bash miniconda.sh -b -p $HOME/miniconda
-- export PATH="$HOME/miniconda/bin:$PATH"
-- hash -r
-- conda config --set always_yes yes --set changeps1 no
-- conda update -q conda
-- conda info -a
-- |
-  conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION basemap matplotlib numpy pandas pip pytables requests cython scikit-learn "pytest<4.0"
-- source activate test-environment
-- pip install pytest-cov coveralls pycodestyle osmnet
-- CC=gcc-4.9 CXX=g++-4.9 python setup.py install
+  - pip install .
+  - pip install -r requirements-dev.txt
+  - pip list
+  - pip show pandana
+
 script:
-- pycodestyle pandana
-- python setup.py test --pytest-args "--cov pandana --cov-report term-missing"
+  - pycodestyle pandana
+  - python setup.py test --pytest-args "--cov pandana --cov-report term-missing"
+
 after_success:
-- coveralls
-- bin/build_docs.sh
-notifications:
-  slack:
-    secure: a6RjANmfIyE0s3iAz4LPy2wS0bOd+ijGlhh7CJf4bRwVnQPuihDTwzQiT92Uje1rHZVUTY0r5A7QzBcg7QcACs/b3hLQ6nYQ0kIm/beC5DfZUqlyHQAuRl6eK76cEg9Le7bX8OXrjWyfTs9jgH7Z2mRGutMieNXVYQG5wMlEKlU=
+  - coveralls
+  - bin/build_docs.sh
+
 env:
   global:
     secure: CMG0rjBgDBNy5FdfXawaaCCJm9ChzHk7e21ywVhIc1jbVS6lMn6bqwKJUnLaJAyjDhhZuxXTcHy+SALJgbzqLrH4GM5hOOL+8Rf4Jf9ESZzTBryvypRecVnUnk63SpJiq2Ki8maNrOcK1IBUAoFhFzptSgE4MDkxZ0LjsDAums8=

MANIFEST.in

@@ -1,3 +1,10 @@
-include ez_setup.py
+# files to include in the source distribution on pypi (setup.py and README.md are included automatically)
+
+include CHANGELOG.md
+include LICENSE.txt
 include README.rst
+include requirements-dev.txt
+include setup.cfg
+
+recursive-include examples *.ipynb *.py
 recursive-include src *.h *.cpp

README.rst

@@ -74,3 +74,41 @@ Related UDST libraries
 .. _forum: http://discussion.urbansim.com/
 .. _OSMnet: https://github.com/udst/osmnet
 .. _UrbanAccess: https://github.com/UDST/urbanaccess
+
+
+Developer notes
+---------------
+
+**Linux installation**
+
+
+1. Make an installation to obtain  file `cyaccess.cpp`. Errors may occur, ignore them:
+
+.. code-block:: 
+
+  git clone git@github.com:UDST/pandana.git
+  git checkout develop
+  virtualenv venv --python=python3.6 numpy brewer2mpl tables
+  source venv/bin/activate
+  cd pandana
+  pip install .
+  CC=gcc CXX=g++ python setup.py develop
+
+This will generate the file `cyaccess.cpp` within `src/`
+
+2. In your final project directory install the `pandana` develop branch
+
+.. code-block::
+
+  git clone git@github.com:UDST/pandana.git
+  virtualenv venv --python=python3.6 numpy brewer2mpl tables
+  source venv/bin/activate
+  cd pandana
+
+
+Copy file `cyaccess.cpp` from previous `pandana` installation into `src/`
+
+.. code-block::
+
+  CC=gcc CXX=g++ python setup.py develop
+

bin/build_docs.sh

@@ -33,10 +33,6 @@ if [ "$TRAVIS_REPO_SLUG" == "UDST/pandana" ] && \
         [ "$TRAVIS_PULL_REQUEST" == "false" ] && \
         [ "$ACTUAL_TRAVIS_JOB_NUMBER" == "1" ]; then
 
-        echo "Installing dependencies"
-        conda install --yes --quiet sphinx numpydoc
-        pip install sphinx_rtd_theme
-
         echo "Building docs"
         cd docs
         make clean

docs/conf.py

@@ -57,9 +57,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.4.1'
+version = '0.4.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.4.1'
+release = '0.4.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/installation.rst

@@ -104,9 +104,18 @@ correctly.  Check the compile output for the gcc compiler you specified
 with :code:`CC` and :code:`CXX` - you might need to change the name slightly depending
 on your platform - for instance :code:`g++-mp-4.9` or :code:`g++-4.8`.
 
+Installation on Windows
+-----------------------
+`Microsoft Visual C++ 2008 SP1 Redistributable Package (x64) 
+<https://www.microsoft.com/en-us/download/details.aspx?id=2092>`_ is required for running 
+Pandana on Windows.  This package enables parallel computations with `OpenMP`_.  Building Pandana 
+from source also requires `Microsoft Visual C++ Compiler for Python 2.7 
+<https://www.microsoft.com/en-us/download/details.aspx?id=44266>`_.
+
+
 .. _Anaconda: http://docs.continuum.io/anaconda/
 .. _pip: https://pip.pypa.io/en/latest/
-.. _OpenMP: http://openmp.org/wp/
+.. _OpenMP: http://openmp.org/
 .. _GNU GCC: https://gcc.gnu.org/
 .. _Homebrew: http://brew.sh/
 .. _MacPorts: https://www.macports.org/
@@ -115,4 +124,4 @@ on your platform - for instance :code:`g++-mp-4.9` or :code:`g++-4.8`.
 .. _numpy: http://www.numpy.org/
 .. _pandas: http://pandas.pydata.org/
 .. _tables: http://www.pytables.org/
-.. _osmnet: http://github.com/udst/osmnet
+.. _osmnet: http://github.com/udst/osmnet

pandana/__init__.py

@@ -1,3 +1,3 @@
 from .network import Network
 
-version = __version__ = '0.4.1'
+version = __version__ = '0.4.2'

pandana/network.py

@@ -10,10 +10,24 @@
 
 from .cyaccess import cyaccess
 from .loaders import pandash5 as ph5
+import warnings
 
 
 def reserve_num_graphs(num):
-    raise Exception("reserve_num_graphs is no longer required - remove from your code")
+    """
+    This function was previously used to reserve memory space for multiple graphs.
+    It is no longer needed in Pandana 0.4+, and will be removed in a future version.
+    Parameters
+    ----------
+    num : int
+        Number of graph to be reserved in memory
+    """
+    warnings.warn(
+        "Function reserve_num_graphs() is no longer needed in Pandana 0.4+\
+         and will be removed in a future version",
+        DeprecationWarning
+    )
+    return None
 
 
 class Network:
@@ -54,7 +68,6 @@ class Network:
 
     def __init__(self, node_x, node_y, edge_from, edge_to, edge_weights,
                  twoway=True):
-
         nodes_df = pd.DataFrame({'x': node_x, 'y': node_y})
         edges_df = pd.DataFrame({'from': edge_from, 'to': edge_to}).\
             join(edge_weights)
@@ -76,19 +89,19 @@ def __init__(self, node_x, node_y, edge_from, edge_to, edge_weights,
                                   index=nodes_df.index)
 
         edges = pd.concat([self._node_indexes(edges_df["from"]),
-                          self._node_indexes(edges_df["to"])], axis=1)
+                           self._node_indexes(edges_df["to"])], axis=1)
 
         self.net = cyaccess(self.node_idx.values,
-                            nodes_df.astype('double').as_matrix(),
-                            edges.as_matrix(),
+                            nodes_df.astype('double').values,
+                            edges.values,
                             edges_df[edge_weights.columns].transpose()
                                                           .astype('double')
-                                                          .as_matrix(),
+                                                          .values,
                             twoway)
 
         self._twoway = twoway
 
-        self.kdtree = KDTree(nodes_df.as_matrix())
+        self.kdtree = KDTree(nodes_df.values)
 
     @classmethod
     def from_hdf5(cls, filename):
@@ -368,7 +381,7 @@ def get_node_ids(self, x_col, y_col, mapping_distance=None):
         """
         xys = pd.DataFrame({'x': x_col, 'y': y_col})
 
-        distances, indexes = self.kdtree.query(xys.as_matrix())
+        distances, indexes = self.kdtree.query(xys.values)
         indexes = np.transpose(indexes)[0]
         distances = np.transpose(distances)[0]
 
@@ -455,7 +468,35 @@ def plot(
 
         return bmap, fig, ax
 
-    def set_pois(self, category, maxdist, maxitems, x_col, y_col):
+    def init_pois(self, num_categories, max_dist, max_pois):
+        """
+        Initialize the point of interest infrastructure.
+        This is no longer needed in Pandana 0.4+ and will be removed in a future version
+
+        Parameters
+        ----------
+        num_categories : int
+            Number of categories of POIs
+        max_dist : float
+            Maximum distance that will be tested to nearest POIs. This will
+            usually be a distance unit in meters however if you have
+            customized the impedance this could be in other
+            units such as utility or time etc.
+        max_pois :
+            Maximum number of POIs to return in the nearest query
+
+        """
+        self.num_categories = num_categories
+        self.max_dist = max_dist
+        self.max_pois = max_pois
+        warnings.warn(
+            "Method init_pois() is no longer needed in Pandana 0.4+ and will be removed in a \
+            future version; maxdist and maxitems should now be passed to set_pois()",
+            DeprecationWarning
+        )
+        return None
+
+    def set_pois(self, category=None, maxdist=None, maxitems=None, x_col=None, y_col=None):
         """
         Set the location of all the pois of this category. The pois are
         connected to the closest node in the Pandana network which assumes
@@ -478,7 +519,26 @@ def set_pois(self, category, maxdist, maxitems, x_col, y_col):
         Returns
         -------
         Nothing
+
         """
+        # condition to check if missing arguments for keyword arguments using set_pois() from v0.3
+        if maxitems is None:
+            print('Reading parameters from init_pois()')
+            maxitems = self.max_pois
+
+        # condition to check for positional arguments in set_pois() from v0.3
+        elif isinstance(maxitems, type(pd.Series())):
+            y_col = maxitems
+            maxitems = self.max_pois
+
+        if maxdist is None:
+            print('Reading parameters from init_pois()')
+            maxdist = self.max_dist
+
+        elif isinstance(maxdist, type(pd.Series())):
+            x_col = maxdist
+            maxdist = self.max_dist
+
         if category not in self.poi_category_names:
             self.poi_category_names.append(category)
 

pandana/tests/test_pandana.py

@@ -76,11 +76,6 @@ def random_x_y(sample_osm, ssize):
     return x, y
 
 
-def test_reserve_num_graphs_raises(sample_osm):
-    with pytest.raises(Exception):
-        pdna.reserve_num_graphs(1)
-
-
 def test_agg_variables_accuracy(sample_osm):
     net = sample_osm
 
@@ -318,7 +313,40 @@ def test_pois2(second_sample_osm):
     net2.nearest_pois(2000, "restaurants", num_pois=10)
 
 
+def test_pois_pandana3(second_sample_osm):
+    net2 = second_sample_osm
+
+    ssize = 50
+    np.random.seed(0)
+    x, y = random_x_y(second_sample_osm, ssize)
+    pdna.reserve_num_graphs(1)
+
+    net2.init_pois(num_categories=1, max_dist=2000, max_pois=10)
+
+    # make sure poi searches work on second graph
+    net2.set_pois(category="restaurants", x_col=x, y_col=y)
+
+    net2.nearest_pois(2000, "restaurants", num_pois=10)
+
+
+def test_pois_pandana3_pos_args(second_sample_osm):
+    net2 = second_sample_osm
+
+    ssize = 50
+    np.random.seed(0)
+    x, y = random_x_y(second_sample_osm, ssize)
+    pdna.reserve_num_graphs(1)
+
+    net2.init_pois(1, 2000, 10)
+
+    # make sure poi searches work on second graph
+    net2.set_pois("restaurants", x, y)
+
+    net2.nearest_pois(2000, "restaurants", num_pois=10)
+
 # test items are sorted
+
+
 def test_sorted_pois(sample_osm):
     net = sample_osm
 

requirements-dev.txt

@@ -0,0 +1,9 @@
+# requirements for development and testing
+
+coveralls
+numpydoc
+pycodestyle
+pytest>=3.6,<4.0
+pytest-cov
+sphinx
+sphinx_rtd_theme