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Merge pull request #94 from Eric89GXL/travis
ENH: Add Travis
2 parents 9db8414 + 4a9043f commit ca601ac

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+177
-64
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‎.coveragerc

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[run]
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branch = True
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source = surfer
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include = */surfer/*
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omit =
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*/setup.py

‎.gitignore

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pysurfer.egg-info
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*.avi
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.tmp/*.png
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examples/example_data/coord-lh.label

‎.travis.yml

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language: python
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env:
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# Enable python 2 and python 3 builds
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# DEPS=full: build optional dependencies: pandas, nitime, statsmodels,
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# scikit-learn, patsy, nibabel; in the case of Python 2, also
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# nitime
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# DEPS=minimal: don't build optional dependencies; tests that require those
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# dependencies are supposed to be skipped
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- PYTHON=2.7 DEPS=full
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# PYTHON=3.3 DEPS=full # Mayavi doesn't support Py3 :(
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- PYTHON=2.7 DEPS=minimal # mencoder is an optional dependency
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# Setup anaconda
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before_install:
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- wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh
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- chmod +x miniconda.sh
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- ./miniconda.sh -b
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- export PATH=/home/travis/anaconda/bin:$PATH
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- conda update --yes conda
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install:
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- conda create -n testenv --yes pip python=$PYTHON
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- source activate testenv
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# Pillow (or PIL/imaging) is necessary for scipy.misc.imsave to exist
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- conda install --yes --quiet ipython==1.1.0 numpy scipy mayavi matplotlib nose imaging
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- if [ "${DEPS}" == "full" ]; then
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travis_retry sudo apt-get install mencoder;
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fi;
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- pip install -q coverage coveralls nose-timer nibabel flake8
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- python setup.py build
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- python setup.py install
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- SRC_DIR=$(pwd)
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before_script:
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# Let's create a (fake) display on Travis, and let's use a funny resolution
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- export DISPLAY=:99.0
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- /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render
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- cd ~
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- wget --quiet http://faculty.washington.edu/larsoner/fsaverage_min.tar.gz
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- mkdir subjects
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- tar --directory subjects -xzf fsaverage_min.tar.gz
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- export SUBJECTS_DIR="${PWD}/subjects"
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- SURFER_DIR=$(python -c 'import surfer;print(surfer.__path__[0])')
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# Link coverage to src dir, coveralls should be run from there (needs git calls)
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- ln -s ${SURFER_DIR}/../.coverage ${SRC_DIR}/.coverage
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- cd ${SURFER_DIR}/../
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- ln -s ${SRC_DIR}/.coveragerc .coveragerc
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- ln -s ${SRC_DIR}/Makefile Makefile
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- ln -s ${SRC_DIR}/setup.cfg setup.cfg
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- ln -s ${SRC_DIR}/examples examples
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script:
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- # Nose-timer has bugs on 3+ as of Jan 2014
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- if [ "{PYTHON}" == "2.7" ]; then
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nosetests --with-timer --timer-top-n 20;
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else
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nosetests;
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fi
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- cd ${SRC_DIR}
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- make flake
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after_success:
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# Need to run from source dir to exectue "git" commands
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- coveralls

‎Makefile

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# simple makefile to simplify repetetive build env management tasks under posix
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# caution: testing won't work on windows, see README
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PYTHON ?= python
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NOSETESTS ?= nosetests
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CTAGS ?= ctags
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all: clean inplace test
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clean-pyc:
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find . -name "*.pyc" | xargs rm -f
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clean-so:
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find . -name "*.so" | xargs rm -f
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find . -name "*.pyd" | xargs rm -f
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clean-build:
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rm -rf build
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clean-ctags:
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rm -f tags
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clean: clean-build clean-pyc clean-so clean-ctags
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flake:
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if command -v flake8 > /dev/null; then \
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flake8 --count surfer examples; \
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fi
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in: inplace # just a shortcut
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inplace:
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$(PYTHON) setup.py build_ext -i
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nosetests:
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rm -f .coverage
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$(NOSETESTS) surfer
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test: clean nosetests flake
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‎examples/example_data/__init__.py

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‎examples/plot_fmri_activation_volume.py

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anatomy, you can provide project_volume_data with the subject ID, avoiding the
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need to specify a registration file.
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By default, 3mm of smoothing is applied on the surface to clean up the overlay a
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bit, although the extent of smoothing can be controlled.
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By default, 3mm of smoothing is applied on the surface to clean up the overlay
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a bit, although the extent of smoothing can be controlled.
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"""
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zstat = project_volume_data(volume_file, "lh",
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subject_id="fsaverage", smooth_fwhm=0.5)
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It can also be a good idea to plot the inverse of the mask that was used in the
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analysis, so you can be clear about areas that were not included.
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It's good to change some parameters of the sampling to account for the fact that
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you are projecting binary (0, 1) data.
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It's good to change some parameters of the sampling to account for the fact
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that you are projecting binary (0, 1) data.
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"""
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mask_file = "example_data/mask.nii.gz"
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mask = project_volume_data(mask_file, "lh", subject_id="fsaverage",

‎examples/plot_fmri_conjunction.py

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Read both of the activation maps in using
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surfer's io functions.
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"""
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data_dir = op.join("example_data")
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sig1 = io.read_scalar_data(op.join(data_dir, "lh.sig.nii.gz"))
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sig2 = io.read_scalar_data(op.join(data_dir, "lh.alt_sig.nii.gz"))
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sig1 = io.read_scalar_data(op.join('example_data', "lh.sig.nii.gz"))
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sig2 = io.read_scalar_data(op.join('example_data', "lh.alt_sig.nii.gz"))
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"""
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Zero out the vertices that do not meet a threshold.

‎examples/plot_label_foci.py

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coordinate of the point we want to display.
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"""
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brain.add_foci([coord], map_surface="white", coords_as_verts=True,
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color="mediumblue")
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color="mediumblue")
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"""
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Set the camera position to show the extent of the labels.

‎examples/plot_meg_inverse_solution.py

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import os
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import numpy as np
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from surfer import Brain, TimeViewer
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from surfer import Brain
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from surfer.io import read_stc
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"""
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read MNE dSPM inverse solution
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"""
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for hemi in ['lh', 'rh']:
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stc_fname = os.path.join('example_data',
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'meg_source_estimate-' + hemi + '.stc')
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stc_fname = os.path.join('example_data/meg_source_estimate-'
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+ hemi + '.stc')
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stc = read_stc(stc_fname)
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"""
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brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
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"""
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uncomment this line to use the interactive TimeViewer GUI
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uncomment these lines to use the interactive TimeViewer GUI
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"""
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#from surfer import TimeViewer
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#viewer = TimeViewer(brain)

‎examples/plot_resting_correlations.py

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is centered on 0, which is a meaningful transition-point as it marks the change
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from negative correlations to positive correlations.
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We'll also plot the map with some transparency so that we can see through to the
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underlying anatomy.
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We'll also plot the map with some transparency so that we can see through to
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the underlying anatomy.
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"""
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brain.add_data(surf_data_lh, -.7, .7, colormap="coolwarm", alpha=.75, hemi='lh')
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brain.add_data(surf_data_rh, -.7, .7, colormap="coolwarm", alpha=.75, hemi='rh')
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brain.add_data(surf_data_lh, -.7, .7, colormap="coolwarm", alpha=.75,
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hemi='lh')
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brain.add_data(surf_data_rh, -.7, .7, colormap="coolwarm", alpha=.75,
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hemi='rh')
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"""
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This overlay represents resting-state correlations with a

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