Merge pull request #169 from amueller/ci_no_sudo

Ci no sudo

.travis.yml

@@ -1,4 +1,23 @@
+sudo: false
 language: python
+addons:
+  apt:
+    sources:
+    - boost-latest
+    packages:
+    - python-scipy
+    - python-nose
+    - python-pip
+    - cython
+    - cmake
+    - time
+    - libatlas-dev
+    - libatlas3gf-base
+    - liblapack-dev
+    - liblapack3gf
+    - libhdf5-serial-dev
+    - libboost1.55-dev
+    - libboost-python1.55-dev
 virtualenv:
   system_site_packages: true
 env:
@@ -11,10 +30,10 @@ env:
       NUMPY_VERSION="1.6.2" SCIPY_VERSION="0.11.0"
     ## This environment tests the newest supported anaconda env
     - DISTRIB="conda" PYTHON_VERSION="2.7"
-      NUMPY_VERSION="1.8.1" SCIPY_VERSION="0.14.0"
+      NUMPY_VERSION="1.10.1" SCIPY_VERSION="0.16.0"
     # python3 only on ubuntu because of cvxopt
     - DISTRIB="conda" PYTHON_VERSION="3.4" OPENGM="false"
-      NUMPY_VERSION="1.8.1" SCIPY_VERSION="0.14.0"
+      NUMPY_VERSION="1.10.1" SCIPY_VERSION="0.16.0"
 install: source continuous_integration/install.sh
 script: bash continuous_integration/test_script.sh
 after_success:

continuous_integration/install.sh

@@ -15,18 +15,15 @@ export CXX=g++
 export PIP=pip
 
 # add cython repository
-sudo add-apt-repository ppa:cython-dev/master-ppa -y
-sudo apt-get update -qq
+#sudo add-apt-repository ppa:cython-dev/master-ppa -y
+#sudo apt-get update -qq
 
 if [[ "$OPENGM" == "true" ]]; then
-    sudo add-apt-repository ppa:ukplc-team/testing -y
-    sudo apt-get update -qq
-    sudo apt-get install libhdf5-serial-dev libboost1.49-dev libboost-python1.49-dev
     git clone https://github.com/opengm/opengm.git
     cd opengm
-    cmake . -DWITH_BOOST=TRUE -DWITH_HDF5=TRUE -DBUILD_PYTHON_WRAPPER=TRUE -DBUILD_EXAMPLES=FALSE -DBUILD_TESTING=FALSE
+    cmake . -DCMAKE_INSTALL_PREFIX=/home/travis/.local -DWITH_BOOST=TRUE -DWITH_HDF5=TRUE -DBUILD_PYTHON_WRAPPER=TRUE -DBUILD_EXAMPLES=FALSE -DBUILD_TESTING=FALSE
     make -j2 --quiet
-    sudo make install
+    make install
     cd ..
 fi
 
@@ -46,17 +43,8 @@ if [[ "$DISTRIB" == "conda" ]]; then
     # Configure the conda environment and put it in the path using the
     # provided versions
 
-    if [[ "$PYTHON_VERSION" == "3.4" ]]; then
-        apt-cache search liblapack
-        sudo apt-get install build-essential python-dev python-setuptools \
-             python-numpy python-scipy libatlas-dev libatlas3gf-base liblapack-dev liblapack3gf
-        conda create -n testenv --yes python=$PYTHON_VERSION pip nose cython scikit-learn\
-            numpy=$NUMPY_VERSION scipy=$SCIPY_VERSION
-    else
-        conda create -n testenv --yes python=$PYTHON_VERSION pip nose cython scikit-learn cvxopt\
-            numpy=$NUMPY_VERSION scipy=$SCIPY_VERSION
-    fi
-
+    conda create -n testenv --yes python=$PYTHON_VERSION pip nose cython scikit-learn cvxopt\
+        numpy=$NUMPY_VERSION scipy=$SCIPY_VERSION
 
     source activate testenv
 
@@ -71,15 +59,15 @@ if [[ "$DISTRIB" == "conda" ]]; then
 elif [[ "$DISTRIB" == "ubuntu" ]]; then
     # Use standard ubuntu packages in their default version
     # except for cython :-/
-    sudo apt-get install -qq python-scipy python-nose python-pip python-cvxopt cython
+    $PIP install --user cvxopt
 fi
 
 if [[ "$COVERAGE" == "true" ]]; then
     $PIP install coverage coveralls
 fi
 
 # install our favorite inference packages 
-$PIP install pyqpbo ad3 scikit-learn cvxopt
+$PIP install pyqpbo ad3 scikit-learn
 
 # Build scikit-learn in the install.sh script to collapse the verbose
 # build output in the travis output when it succeeds.

doc/conf.py

@@ -15,7 +15,8 @@
 import sys
 import os
 import sphinx_bootstrap_theme
-import sphinxgallery
+import pystruct
+#import sphinx_gallery
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -32,7 +33,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
               'sphinx.ext.doctest', 'sphinx.ext.pngmath',
-              'sphinx.ext.viewcode', 'numpy_ext.numpydoc', 'sphinxgallery.gen_gallery']
+              'sphinx.ext.viewcode', 'numpy_ext.numpydoc', 'sphinx_gallery.gen_gallery']
 
 autosummary_generate = True
 
@@ -61,12 +62,21 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-import pystruct
 # The short X.Y version.
 version = pystruct.__version__
 # The full version, including alpha/beta/rc tags.
 release = pystruct.__version__
 
+sphinx_gallery_conf = {
+    'reference_url': {
+        # The module you locally document uses a None
+        'pystruct': None,
+
+        # External python modules use their documentation websites
+        'sklearn': 'http://scikit-learn.org/stable',
+        'matplotlib': 'http://matplotlib.org',
+        'numpy': 'http://docs.scipy.org/doc/numpy-1.9.1'}}
+
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #language = None
@@ -134,7 +144,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static', sphinxgallery.path_static()]
+html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.

doc/sphinxext/numpy_ext/docscrape.py

@@ -6,8 +6,12 @@
 import textwrap
 import re
 import pydoc
-from StringIO import StringIO
 from warnings import warn
+# Try Python 2 first, otherwise load from Python 3
+try:
+    from StringIO import StringIO
+except:
+    from io import StringIO
 
 
 class Reader(object):
@@ -115,7 +119,7 @@ def __getitem__(self, key):
         return self._parsed_data[key]
 
     def __setitem__(self, key, val):
-        if not self._parsed_data.has_key(key):
+        if key not in self._parsed_data:
             warn("Unknown section %s" % key)
         else:
             self._parsed_data[key] = val
@@ -435,7 +439,7 @@ def __init__(self, func, role='func', doc=None, config={}):
                 argspec = inspect.formatargspec(*argspec)
                 argspec = argspec.replace('*', '\*')
                 signature = '%s%s' % (func_name, argspec)
-            except TypeError, e:
+            except TypeError as e:
                 signature = '%s()' % func_name
             self['Signature'] = signature
 
@@ -457,8 +461,8 @@ def __str__(self):
                  'meth': 'method'}
 
         if self._role:
-            if not roles.has_key(self._role):
-                print "Warning: invalid role %s" % self._role
+            if self._role not in roles:
+                print("Warning: invalid role %s" % self._role)
             out += '.. %s:: %s\n    \n\n' % (roles.get(self._role, ''),
                                              func_name)
 

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -2,10 +2,9 @@
 import inspect
 import textwrap
 import pydoc
-import sphinx
-from docscrape import NumpyDocString
-from docscrape import FunctionDoc
-from docscrape import ClassDoc
+from .docscrape import NumpyDocString
+from .docscrape import FunctionDoc
+from .docscrape import ClassDoc
 
 
 class SphinxDocString(NumpyDocString):
@@ -156,6 +155,7 @@ def _str_references(self):
             out += ['']
             # Latex collects all references to a separate bibliography,
             # so we need to insert links to it
+            import sphinx  # local import to avoid test dependency
             if sphinx.__version__ >= "0.6":
                 out += ['.. only:: latex', '']
             else:
@@ -188,14 +188,14 @@ def __str__(self, indent=0, func_role="obj"):
         out += self._str_index() + ['']
         out += self._str_summary()
         out += self._str_extended_summary()
-        for param_list in ('Parameters', 'Returns', 'Raises'):
+        for param_list in ('Parameters', 'Returns', 'Raises', 'Attributes'):
             out += self._str_param_list(param_list)
         out += self._str_warnings()
         out += self._str_see_also(func_role)
         out += self._str_section('Notes')
         out += self._str_references()
         out += self._str_examples()
-        for param_list in ('Attributes', 'Methods'):
+        for param_list in ('Methods',):
             out += self._str_member_list(param_list)
         out = self._str_indent(out, indent)
         return '\n'.join(out)

doc/sphinxext/numpy_ext/numpydoc.py

@@ -17,12 +17,14 @@
 
 """
 
+from __future__ import unicode_literals
+
+import sys # Only needed to check Python version
 import os
 import re
 import pydoc
-from docscrape_sphinx import get_doc_object
-from docscrape_sphinx import SphinxDocString
-from sphinx.util.compat import Directive
+from .docscrape_sphinx import get_doc_object
+from .docscrape_sphinx import SphinxDocString
 import inspect
 
 
@@ -34,17 +36,20 @@ def mangle_docstrings(app, what, name, obj, options, lines,
 
     if what == 'module':
         # Strip top title
-        title_re = re.compile(ur'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
+        title_re = re.compile(r'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
                               re.I | re.S)
-        lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n")
+        lines[:] = title_re.sub('', "\n".join(lines)).split("\n")
     else:
-        doc = get_doc_object(obj, what, u"\n".join(lines), config=cfg)
-        lines[:] = unicode(doc).split(u"\n")
+        doc = get_doc_object(obj, what, "\n".join(lines), config=cfg)
+        if sys.version_info[0] < 3:
+            lines[:] = unicode(doc).splitlines()
+        else:
+            lines[:] = str(doc).splitlines()
 
     if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \
            obj.__name__:
         if hasattr(obj, '__module__'):
-            v = dict(full_name=u"%s.%s" % (obj.__module__, obj.__name__))
+            v = dict(full_name="%s.%s" % (obj.__module__, obj.__name__))
         else:
             v = dict(full_name=obj.__name__)
         lines += [u'', u'.. htmlonly::', '']
@@ -55,7 +60,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
     references = []
     for line in lines:
         line = line.strip()
-        m = re.match(ur'^.. \[([a-z0-9_.-])\]', line, re.I)
+        m = re.match(r'^.. \[([a-z0-9_.-])\]', line, re.I)
         if m:
             references.append(m.group(1))
 
@@ -64,8 +69,8 @@ def mangle_docstrings(app, what, name, obj, options, lines,
     if references:
         for i, line in enumerate(lines):
             for r in references:
-                if re.match(ur'^\d+$', r):
-                    new_r = u"R%d" % (reference_offset[0] + int(r))
+                if re.match(r'^\d+$', r):
+                    new_r = "R%d" % (reference_offset[0] + int(r))
                 else:
                     new_r = u"%s%d" % (r, reference_offset[0])
                 lines[i] = lines[i].replace(u'[%s]_' % r,
@@ -91,16 +96,20 @@ def mangle_signature(app, what, name, obj,
 
     doc = SphinxDocString(pydoc.getdoc(obj))
     if doc['Signature']:
-        sig = re.sub(u"^[^(]*", u"", doc['Signature'])
-        return sig, u''
+        sig = re.sub("^[^(]*", "", doc['Signature'])
+        return sig, ''
 
 
 def setup(app, get_doc_object_=get_doc_object):
     global get_doc_object
     get_doc_object = get_doc_object_
 
-    app.connect('autodoc-process-docstring', mangle_docstrings)
-    app.connect('autodoc-process-signature', mangle_signature)
+    if sys.version_info[0] < 3:
+        app.connect(b'autodoc-process-docstring', mangle_docstrings)
+        app.connect(b'autodoc-process-signature', mangle_signature)
+    else:
+        app.connect('autodoc-process-docstring', mangle_docstrings)
+        app.connect('autodoc-process-signature', mangle_signature)
     app.add_config_value('numpydoc_edit_link', None, False)
     app.add_config_value('numpydoc_use_plots', None, False)
     app.add_config_value('numpydoc_show_class_members', True, True)
@@ -113,9 +122,13 @@ def setup(app, get_doc_object_=get_doc_object):
 # Docstring-mangling domains
 #-----------------------------------------------------------------------------
 
-from docutils.statemachine import ViewList
-from sphinx.domains.c import CDomain
-from sphinx.domains.python import PythonDomain
+try:
+    import sphinx  # lazy to avoid test dependency
+except ImportError:
+    CDomain = PythonDomain = object
+else:
+    from sphinx.domains.c import CDomain
+    from sphinx.domains.python import PythonDomain
 
 
 class ManglingDomainBase(object):
@@ -170,6 +183,8 @@ def run(self):
 
             lines = list(self.content)
             mangle_docstrings(env.app, objtype, name, None, None, lines)
+            # local import to avoid testing dependency
+            from docutils.statemachine import ViewList
             self.content = ViewList(lines, self.content.parent)
 
             return base_directive.run(self)

examples/plot_latent_node.py

@@ -54,10 +54,10 @@ def plot_boxes(boxes, size=4, title=""):
 
 G = [make_grid_edges(x) for x in X]
 
-asdf = zip(X_flat, G)
-svm.fit(asdf, Y_flat)
-plot_boxes(svm.predict(asdf), title="Non-latent SSVM predictions")
-print("Training score binary grid CRF: %f" % svm.score(asdf, Y_flat))
+X_grid_edges = list(zip(X_flat, G))
+svm.fit(X_grid_edges, Y_flat)
+plot_boxes(svm.predict(X_grid_edges), title="Non-latent SSVM predictions")
+print("Training score binary grid CRF: %f" % svm.score(X_grid_edges, Y_flat))
 
 # using one latent variable for each 2x2 rectangle
 latent_crf = LatentNodeCRF(n_labels=2, n_features=1, n_hidden_states=2,
@@ -83,7 +83,7 @@ def plot_boxes(boxes, size=4, title=""):
 plot_boxes(H_init, title="Top: Random initial hidden states. Bottom: Ground"
            "truth labeling.")
 
-X_ = zip(X_flat, G, [2 * 2 for x in X_flat])
+X_ = list(zip(X_flat, G, [2 * 2 for x in X_flat]))
 
 latent_svm.fit(X_, Y_flat, H_init)
 

pystruct/datasets/synthetic_grids.py

@@ -304,8 +304,6 @@ def generate_crosses_explicit(n_samples=5, noise=30, size=9, n_crosses=2):
     ix, iy, iz = np.ogrid[:X.shape[0], :X.shape[1], :X.shape[2]]
     X[ix, iy, iz, Y_flips] = 1
     X[ix, iy, iz, 2 * Y_flips] = 1
-    #Y = (Y != 0).astype(np.int)
-    #X = X[:, :, :, :2]
     return X, Y
 
 

pystruct/models/graph_crf.py

@@ -66,7 +66,8 @@ class GraphCRF(CRF):
         Possible values are:
 
             - 'max-product' for max-product belief propagation.
-                Recommended for chains an trees. Loopy belief propagatin in case of a general graph.
+                Recommended for chains an trees. Loopy belief propagation in
+                case of a general graph.
             - 'lp' for Linear Programming relaxation using cvxopt.
             - 'ad3' for AD3 dual decomposition.
             - 'qpbo' for QPBO + alpha expansion.