Merge pull request #709 from satra/fix/reporting

few more updates including coveralls support

Author: satra

.coveragerc

@@ -0,0 +1,9 @@
+[run]
+branch = True
+source = nipype
+include = */nipype/*
+omit =
+    */nipype/external/*
+    */nipype/workflows/*
+    */nipype/fixes/*
+    */setup.py

.travis.yml

@@ -1,31 +1,40 @@
 language: python
 python:
-    - "2.7"
+  - 2.7
+# Setup anaconda
 before_install:
-    - deactivate
-    - sudo rmdir /dev/shm
-    - sudo ln -Tsf /{run,dev}/shm
-    - sudo apt-get update -qq
-    - sudo apt-get install lsb-release
-    - source /etc/lsb-release
-    - echo ${DISTRIB_CODENAME}
-    - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-    - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
-    - sudo apt-get update -qq
-    - sudo apt-get install -qq python-scipy python-nose
-    - sudo apt-get install -qq python-networkx python-traits python-setuptools
-    - sudo apt-get install -qq python-nibabel
-    - sudo apt-get install -qq --no-install-recommends fsl afni
-    - sudo apt-get install -qq fsl-atlases
-    - source /etc/fsl/fsl.sh
-    - virtualenv --system-site-packages ~/virtualenv/this
-    - source ~/virtualenv/this/bin/activate
-    - pip install https://github.com/RDFLib/rdflib/archive/master.zip
-    - pip install https://github.com/satra/prov/archive/enh/rdf.zip
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-2.0.3-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-2.0.3-Linux-x86_64.sh -O miniconda.sh; fi
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/anaconda/bin:$PATH
+  # The next couple lines fix a crash with multiprocessing on Travis
+  - sudo rm -rf /dev/shm
+  - sudo ln -s /run/shm /dev/shm
+  - sudo apt-get update -qq
+  - sudo apt-get install lsb-release
+  - source /etc/lsb-release
+  - echo ${DISTRIB_CODENAME}
+  - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+  - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
+  - sudo apt-get update -qq
+  - sudo apt-get install -qq --no-install-recommends fsl afni
+  - sudo apt-get install -qq fsl-atlases
+  - source /etc/fsl/fsl.sh
+
+# Install packages
 install:
-    - source ~/virtualenv/this/bin/activate
-    - python setup.py build_ext --inplace
+  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy nose traits networkx dateutil
+  - pip install nibabel --use-mirrors
+  - pip install python-coveralls --use-mirrors
+  - pip install nose-cov --use-mirrors
+  - pip install https://github.com/RDFLib/rdflib/archive/master.zip
+  - pip install https://github.com/satra/prov/archive/enh/rdf.zip
+  - python setup.py install
+
+# Run test
 script:
-    - source ~/virtualenv/this/bin/activate
-    - make test
+  - nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
 
+# Calculate coverage
+after_success:
+  - coveralls --config_file .coveragerc

Makefile

@@ -57,8 +57,8 @@ test-doc:
 	--doctest-fixtures=_fixture doc/
 
 test-coverage:
-	$(NOSETESTS) -s --with-doctest --with-coverage --cover-erase --cover-html \
-	--cover-html-dir=coverage --cover-package=nipype nipype
+	$(NOSETESTS) -s --with-doctest --with-coverage --cover-package=nipype \
+	--config=.coveragerc
 
 test: clean test-code
 

README.rst

@@ -2,6 +2,12 @@
 NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 ========================================================
 
+.. image:: https://travis-ci.org/nipy/nipype.png?branch=master
+  :target: https://travis-ci.org/nipy/nipype
+
+.. image:: https://coveralls.io/repos/nipy/nipype/badge.png
+  :target: https://coveralls.io/r/nipy/nipype
+
 
 Current neuroimaging software offer users an incredible opportunity to
 analyze data using a variety of different algorithms. However, this has

doc/_templates/indexsidebar.html

@@ -6,6 +6,7 @@ <h3>{{ _('Links') }}</h3>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://groups.google.com/group/nipy-user">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
     <li>Info: <a href="http://nipy.org/software/license/index.html">License</a> · <a href="http://nipy.org/about/funding.html">Funding</a></li>
+    <li><a href="https://travis-ci.org/nipy/nipy"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
 </ul>
 
 {% endblock %}

doc/conf.py

@@ -55,7 +55,7 @@
 
 # General information about the project.
 project = u'nipype'
-copyright = u'2009-12, Neuroimaging in Python team'
+copyright = u'2009-13, Neuroimaging in Python team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the