nipy · matthew-brett · Mar 15, 2017 · Mar 7, 2017 · Mar 7, 2017 · Mar 7, 2017
diff --git a/.travis.yml b/.travis.yml
@@ -5,18 +5,22 @@
 # - There can't be any leading "-"s - All newlines will be removed, so use
 # ";"s
 sudo: false  # To use travis container infrastructure
+
 language: python
+
 cache:
   directories:
     - $HOME/.cache/pip
+
 env:
-    global:
-        - DEPENDS="numpy scipy sympy matplotlib nibabel"
-        - INSTALL_TYPE="setup"
-        - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
-        - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
-        - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
-        - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+  global:
+    - DEPENDS="numpy scipy sympy matplotlib nibabel"
+    - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+    - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
+    - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
+    - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+    - INSTALL_TYPE="pip"
+
 python:
     - 3.4
     - 3.5
@@ -54,11 +58,28 @@ matrix:
       env:
         - INSTALL_TYPE=requirements
         - DEPENDS=
-    - python: 3.6
     # test 3.5 against pre-release builds of everything
     - python: 3.5
       env:
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
+    # test python setup.py install
+    - python: 3.5
+      env:
+        - INSTALL_TYPE=setup
+    - python: 3.5
+      env:
+        - INSTALL_TYPE="pip_e"
+    - python: 3.5
+      env:
+        - DOC_BUILD=1
+      addons:
+        apt:
+          packages:
+            - graphviz
+            - texlive-latex-base
+            - texlive-latex-extra
+            - texlive-fonts-recommended
+            - texlive-latex-recommended
 
 before_install:
     - source tools/travis_tools.sh
@@ -77,12 +98,17 @@ before_install:
       pip install coverage;
       pip install coveralls codecov;
       fi
+
 # command to install dependencies
 # e.g. pip install -r requirements.txt # --use-mirrors
 install:
     - |
-      if [ "$INSTALL_TYPE" == "setup" ]; then
-          python setup.py install
+      if [ "$INSTALL_TYPE" == "pip" ]; then
+        pip install .
+      elif [ "$INSTALL_TYPE" == "pip_e" ]; then
+        pip install -e .
+      elif [ "$INSTALL_TYPE" == "setup" ]; then
+        python setup.py install
       elif [ "$INSTALL_TYPE" == "sdist" ]; then
         python setup_egg.py egg_info  # check egg_info while we're here
         python setup_egg.py sdist
@@ -96,15 +122,23 @@ install:
         pip install -r requirements.txt
         python setup.py install
       fi
-# command to run tests, e.g. python setup.py test
+
+# command to run tests
 script:
-    # Change into an innocuous directory and find tests from installation
-    - mkdir for_testing
-    - cd for_testing
-    - if [ "${COVERAGE}" == "1" ]; then
-      cp ../.coveragerc .;
-      COVER_ARGS="--with-coverage --cover-package nipy";
+    - |
+      if [ "$DOC_BUILD" ]; then  # doc build
+        pip install -r doc-requirements.txt
+        make html-stamp pdf-stamp
+      else
+        # Change into an innocuous directory and find tests from installation
+        mkdir for_testing
+        cd for_testing
+        if [ "${COVERAGE}" == "1" ]; then
+        cp ../.coveragerc .
+        COVER_ARGS="--with-coverage --cover-package nipy"
+        fi
+        $PYTHON ../tools/nipnost --verbosity=3 $COVER_ARGS nipy
       fi
-    - $PYTHON ../tools/nipnost --verbosity=3 $COVER_ARGS nipy
+
 after_success:
     - if [ "${COVERAGE}" == "1" ]; then coveralls; codecov; fi
diff --git a/Makefile b/Makefile
@@ -43,9 +43,6 @@ dev: cythonize
 test:
 	cd .. && $(PYTHON) -c 'import nipy; nipy.test()'
 
-build:
-	$(PYTHON) setup.py build
-
 install:
 	$(PYTHON) setup.py install
 
@@ -113,11 +110,11 @@ recythonize:
 $(WWW_DIR):
 	if [ ! -d $(WWW_DIR) ]; then mkdir -p $(WWW_DIR); fi
 
-htmldoc: build
-	cd $(DOCSRC_DIR) && PYTHONPATH=$(CURDIR):$(PYTHONPATH) $(MAKE) html
+htmldoc:
+	cd $(DOCSRC_DIR) && $(MAKE) html
 
-pdfdoc: build
-	cd $(DOCSRC_DIR) && PYTHONPATH=$(CURDIR):$(PYTHONPATH) $(MAKE) latex
+pdfdoc:
+	cd $(DOCSRC_DIR) && $(MAKE) latex
 	cd $(LATEX_DIR) && $(MAKE) all-pdf
 
 html: html-stamp

diff --git a/README.rst b/README.rst
@@ -92,36 +92,25 @@ directory of the nipy distribution::
 is part of the nose package.  Try ``nipnost --help`` to see a large number of
 command-line options.
 
-Dependencies
+Installation
 ============
 
-To run NIPY, you will need:
+See the latest `installation instructions`_.
 
-* python_ >= 2.6 (tested with 2.6, 2.7, 3.2 through 3.5)
-* numpy_ >= 1.6.0
-* scipy_ >= 0.9.0
-* sympy_ >= 0.7.0
-* nibabel_ >= 1.2
-
-You will probably also like to have:
+License
+=======
 
-* ipython_ for interactive work
-* matplotlib_ for 2D plotting
-* mayavi_ for 3D plotting
+We use the 3-clause BSD license; the full license is in the file ``LICENSE`` in
+the nipy distribution.
 
+.. links:
 .. _python: http://python.org
 .. _numpy: http://numpy.scipy.org
 .. _scipy: http://www.scipy.org
 .. _sympy: http://sympy.org
 .. _nibabel: http://nipy.org/nibabel
 .. _ipython: http://ipython.org
 .. _matplotlib: http://matplotlib.org
-.. _mayavi: http://code.enthought.com/projects/mayavi/
 .. _nose: http://nose.readthedocs.org/en/latest
 .. _mock: https://pypi.python.org/pypi/mock
-
-License
-=======
-
-We use the 3-clause BSD license; the full license is in the file ``LICENSE``
-in the nipy distribution.
+.. _installation instructions: http://nipy.org/nipy/users/installation.html
diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -0,0 +1,4 @@
+# Requirements for running tests
+-r requirements.txt
+nose
+mock
diff --git a/doc-requirements.txt b/doc-requirements.txt
@@ -0,0 +1,8 @@
+# Requirements for building docs
+# Check these dependencies against doc/conf.py
+-r dev-requirements.txt
+sphinx>=1.0
+numpydoc
+matplotlib
+texext
+ipython
diff --git a/doc/README.txt b/doc/README.txt
@@ -18,6 +18,13 @@ you must have:
 * latex (for the PNG mathematics graphics)
 * graphviz (for the inheritance diagrams)
 
+For the Python dependencies, do::
+
+    pip install -r ../doc-requirements.txt
+
+Files and directories
+=====================
+
 This directory contains:
 
 * Makefile - the build script to build the HTML or PDF docs. Type

diff --git a/doc/conf.py b/doc/conf.py
@@ -13,36 +13,42 @@
 # serve to show the default value.
 
 import sys, os
+from importlib import import_module
+
+import sphinx
+
+# Doc generation depends on being able to import project
+project = 'nipy'
+try:
+    project_module = import_module(project)
+except ImportError:
+    raise RuntimeError('Cannot import {}, please investigate'.format(project))
 
 # If your extensions are in another directory, add it here. If the directory
 # is relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
 sys.path.append(os.path.abspath('sphinxext'))
 
-# Get project related strings.  Please do not change this line to use
-# execfile because execfile is not available in Python 3
-_info_fname = os.path.join('..', 'nipy', 'info.py')
-rel = {}
-exec(open(_info_fname, 'rt').read(), {}, rel)
-
-# Import support for ipython console session syntax highlighting (lives
-# in the sphinxext directory defined above)
-import ipython_console_highlighting
-
 # General configuration
 # ---------------------
 
+# If your documentation needs a minimal Sphinx version, state it here.
+needs_sphinx = '1.0'
+
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.doctest',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.inheritance_diagram',
-              'numpy_ext.numpydoc',
-              'matplotlib.sphinxext.plot_directive',
-              'matplotlib.sphinxext.only_directives', # needed for above
-              ]
+extensions = [
+    'texext.mathcode',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.autosummary',
+    'texext.math_dollar',
+    'numpydoc',
+    'sphinx.ext.inheritance_diagram',
+    'matplotlib.sphinxext.plot_directive',
+    'IPython.sphinxext.ipython_console_highlighting',
+]
 
 # Autosummary on
 autosummary_generate=True
@@ -56,17 +62,15 @@
 # The master toctree document.
 master_doc = 'index'
 
-# General substitutions.
-project = 'nipy'
-
-#copyright = ':ref:`2005-2010, Neuroimaging in Python team. <nipy-software-license>`'
+# copyright = ':ref:`2005-2017, Neuroimaging in Python team.
+# <nipy-software-license>`'
 copyright = '2005-2017, Neuroimaging in Python team'
 
 # The default replacements for |version| and |release|, also used in various
 # other places throughout the built documents.
 #
 # The short X.Y version.
-version = rel['__version__']
+version = project_module.__version__
 # The full version, including alpha/beta/rc tags.
 release = version
 
@@ -164,11 +168,29 @@
 # Options for LaTeX output
 # ------------------------
 
-# The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
+# Additional stuff for the LaTeX preamble.
+_latex_preamble = """
+   \usepackage{amsmath}
+   \usepackage{amssymb}
+   % Uncomment these two if needed
+   %\usepackage{amsfonts}
+   %\usepackage{txfonts}
+"""
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
 
 # The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+
+# Latex figure (float) alignment
+#'figure_align': 'htbp',
+    'preamble': _latex_preamble,
+}
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, document class
@@ -183,21 +205,22 @@
 # the title page.
 #latex_logo = None
 
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-latex_use_parts = True
-
-# Additional stuff for the LaTeX preamble.
-latex_preamble = """
-   \usepackage{amsmath}
-   \usepackage{amssymb}
-   % Uncomment these two if needed
-   %\usepackage{amsfonts}
-   %\usepackage{txfonts}
-"""
+if sphinx.version_info[:2] < (1, 4):
+    # For "manual" documents, if this is true, then toplevel headings are parts,
+    # not chapters.
+    latex_use_parts = True
+else:  # Sphinx >= 1.4
+    latex_toplevel_sectioning = 'part'
 
 # Documents to append as an appendix to all manuals.
 #latex_appendices = []
 
 # If false, no module index is generated.
 latex_use_modindex = True
+
+# Numpy extensions
+# ----------------
+# Worked out by Steven Silvester in
+# https://github.com/scikit-image/scikit-image/pull/1356
+numpydoc_show_class_members = False
+numpydoc_class_members_toctree = False
diff --git a/doc/devel/guidelines/gitwash/branch_dropdown.png b/doc/devel/guidelines/gitwash/branch_dropdown.png
diff --git a/doc/devel/guidelines/gitwash/branch_list.png b/doc/devel/guidelines/gitwash/branch_list.png
diff --git a/doc/devel/guidelines/gitwash/branch_list_compare.png b/doc/devel/guidelines/gitwash/branch_list_compare.png