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Merge branch 'master' into enh/3dtproject
* master: (32 commits) DOC: Use pip-packaged numpydoc FIX: Update pybids data directory sty: spacing enh: improve travis build reliability enh: add test from #2431 fix: set _id property of cloned node too fix: syntax sty: pep8 and better error messages Fix expected CL in doctest Change auto test accordingly enh+sty: autotest and styling enh: add c3d and c4d interface Fix issue #2408 fix: updated custom search to current api fix out_file template bugs FIX: Do not cache grab_exts fix: remove deprecated output from _list_outputs ENH: Reorder traits for better error message ENH: Add info to ImageFile for better error messages ENH: Simplify listifying logic ...
2 parents ae7dc34 + 765b0fc commit 3adfd64

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-1201
lines changed

‎.travis.yml

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cache:
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apt: true
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dist: trusty
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sudo: required
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language: python
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# our build matrix
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python:
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- 2.7
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- 3.4
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- 3.5
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- 3.6
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env:
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- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
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- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
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- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit" CI_SKIP_TEST=1
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- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
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addons:
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apt:
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packages:
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- xvfb
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- fusefat
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- graphviz
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cache:
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directories:
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- ${HOME}/.cache
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before_install:
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- function apt_inst {
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if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
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if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi &&
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bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) &&
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sudo apt-get -y update &&
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sudo apt-get -y install xvfb fusefat graphviz &&
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if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq
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fsl afni elastix fsl-atlases; fi &&
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if $INSTALL_DEB_DEPENDECIES; then
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- if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; sudo ln -s /run/shm /dev/shm; fi
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- travis_retry bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
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- if $INSTALL_DEB_DEPENDECIES; then
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travis_retry sudo apt-get -y update &&
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travis_retry sudo apt-get install -y -qq fsl afni elastix fsl-atlases;
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fi;
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- if $INSTALL_DEB_DEPENDECIES; then
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source /etc/fsl/fsl.sh;
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source /etc/afni/afni.sh;
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export FSLOUTPUTTYPE=NIFTI_GZ; fi }
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- function conda_inst {
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export CONDA_HOME=$HOME/conda &&
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wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
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-O /home/travis/.cache/conda.sh &&
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bash /home/travis/.cache/conda.sh -b -p ${CONDA_HOME} &&
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export PATH=${CONDA_HOME}/bin:$PATH &&
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hash -r &&
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conda config --set always_yes yes --set changeps1 no &&
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conda update -q conda &&
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conda config --add channels conda-forge &&
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conda install python=${TRAVIS_PYTHON_VERSION} &&
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conda install -y icu &&
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pip install -r requirements.txt &&
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pushd $HOME;
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git clone https://github.com/INCF/pybids.git;
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cd pybids;
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pip install -e .;
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popd; }
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# Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
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- travis_retry apt_inst
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- travis_retry conda_inst
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export FSLOUTPUTTYPE=NIFTI_GZ;
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fi;
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# handle python operations separately to reduce timeouts
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- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
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-O /home/travis/.cache/conda.sh
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- bash ${HOME}/.cache/conda.sh -b -p ${HOME}/conda
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- export PATH=${HOME}/conda/bin:$PATH
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- hash -r
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- conda config --set always_yes yes --set changeps1 no
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- travis_retry conda update -q conda
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- conda config --add channels conda-forge
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- travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu
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- travis_retry pip install -r requirements.txt
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- travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids &&
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pip install -e ${HOME}/pybids
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install:
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- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
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script:
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- py.test -v --doctest-modules nipype
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deploy:
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provider: pypi
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user: satra

‎doc/_templates/gse.html

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</style>
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<div class="sidebarblock">
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<div id="cse-search-form">Loading</div>
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<script src="http://www.google.com/jsapi" type="text/javascript"></script>
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<script type="text/javascript">
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google.load('search', '1', {language : 'en'});
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google.setOnLoadCallback(function() {
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var customSearchControl = new google.search.CustomSearchControl(
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'010960497803984932957:u8pmqf7fdoq');
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customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
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var options = new google.search.DrawOptions();
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options.enableSearchboxOnly("{{pathto('searchresults')}}");
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customSearchControl.draw('cse-search-form', options);
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}, true);
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<script>
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(function() {
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var cx = '010960497803984932957:u8pmqf7fdoq';
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var gcse = document.createElement('script');
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gcse.type = 'text/javascript';
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gcse.async = true;
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gcse.src = 'https://cse.google.com/cse.js?cx=' + cx;
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var s = document.getElementsByTagName('script')[0];
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s.parentNode.insertBefore(gcse, s);
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})();
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</script>
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<gcse:search></gcse:search>
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</div>
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{% endblock %}

‎doc/conf.py

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'sphinx.ext.autodoc',
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'sphinx.ext.doctest',
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'sphinx.ext.autosummary',
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'numpy_ext.numpydoc',
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'numpydoc',
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'matplotlib.sphinxext.plot_directive',
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'matplotlib.sphinxext.only_directives',
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'nipype.sphinxext.plot_workflow',
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# General information about the project.
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project = u'nipype'
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copyright = u'2009-17, Neuroimaging in Python team'
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copyright = u'2009-18, Neuroimaging in Python team'
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the

‎doc/searchresults.rst

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.. raw:: html
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<div id="cse" style="width: 100%;">Loading</div>
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<script src="http://www.google.com/jsapi" type="text/javascript"></script>
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<script type="text/javascript">
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function parseQueryFromUrl () {
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var queryParamName = "q";
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var search = window.location.search.substr(1);
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var parts = search.split('&');
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for (var i = 0; i < parts.length; i++) {
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var keyvaluepair = parts[i].split('=');
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if (decodeURIComponent(keyvaluepair[0]) == queryParamName) {
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return decodeURIComponent(keyvaluepair[1].replace(/\+/g, ' '));
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}
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}
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return '';
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}
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google.load('search', '1', {language : 'en', style : google.loader.themes.MINIMALIST});
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google.setOnLoadCallback(function() {
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var customSearchControl = new google.search.CustomSearchControl(
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'010960497803984932957:u8pmqf7fdoq');
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customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
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customSearchControl.draw('cse');
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var queryFromUrl = parseQueryFromUrl();
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if (queryFromUrl) {
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customSearchControl.execute(queryFromUrl);
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}
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}, true);
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</script>
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<link rel="stylesheet" href="http://www.google.com/cse/style/look/default.css" type="text/css" /> <style type="text/css">
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.gsc-control-cse {
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font-family: Arial, sans-serif;
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border-color: #FFFFFF;
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background-color: #FFFFFF;
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}
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input.gsc-input {
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border-color: #BCCDF0;
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}
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input.gsc-search-button {
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border-color: #666666;
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background-color: #CECECE;
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}
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.gsc-tabHeader.gsc-tabhInactive {
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border-color: #E9E9E9;
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background-color: #E9E9E9;
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}
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.gsc-tabHeader.gsc-tabhActive {
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border-top-color: #FF9900;
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border-left-color: #E9E9E9;
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border-right-color: #E9E9E9;
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background-color: #FFFFFF;
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}
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.gsc-tabsArea {
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border-color: #E9E9E9;
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}
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.gsc-webResult.gsc-result,
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.gsc-results .gsc-imageResult {
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border-color: #FFFFFF;
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background-color: #FFFFFF;
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}
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.gsc-webResult.gsc-result:hover,
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.gsc-imageResult:hover {
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border-color: #FFFFFF;
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background-color: #FFFFFF;
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}
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.gs-webResult.gs-result a.gs-title:link,
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.gs-webResult.gs-result a.gs-title:link b,
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.gs-imageResult a.gs-title:link,
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.gs-imageResult a.gs-title:link b {
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color: #0000CC;
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}
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.gs-webResult.gs-result a.gs-title:visited,
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.gs-webResult.gs-result a.gs-title:visited b,
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.gs-imageResult a.gs-title:visited,
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.gs-imageResult a.gs-title:visited b {
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color: #0000CC;
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}
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.gs-webResult.gs-result a.gs-title:hover,
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.gs-webResult.gs-result a.gs-title:hover b,
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.gs-imageResult a.gs-title:hover,
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.gs-imageResult a.gs-title:hover b {
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color: #0000CC;
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}
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.gs-webResult.gs-result a.gs-title:active,
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.gs-webResult.gs-result a.gs-title:active b,
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.gs-imageResult a.gs-title:active,
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.gs-imageResult a.gs-title:active b {
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color: #0000CC;
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}
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.gsc-cursor-page {
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color: #0000CC;
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}
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a.gsc-trailing-more-results:link {
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color: #0000CC;
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}
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.gs-webResult .gs-snippet,
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.gs-imageResult .gs-snippet,
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.gs-fileFormatType {
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color: #000000;
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}
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.gs-webResult div.gs-visibleUrl,
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.gs-imageResult div.gs-visibleUrl {
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color: #008000;
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}
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.gs-webResult div.gs-visibleUrl-short {
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color: #008000;
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}
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.gs-webResult div.gs-visibleUrl-short {
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display: none;
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}
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.gs-webResult div.gs-visibleUrl-long {
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display: block;
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}
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.gsc-cursor-box {
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border-color: #FFFFFF;
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}
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.gsc-results .gsc-cursor-box .gsc-cursor-page {
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border-color: #E9E9E9;
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background-color: #FFFFFF;
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color: #0000CC;
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}
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.gsc-results .gsc-cursor-box .gsc-cursor-current-page {
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border-color: #FF9900;
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background-color: #FFFFFF;
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color: #0000CC;
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}
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.gs-promotion {
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border-color: #336699;
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background-color: #FFFFFF;
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}
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.gs-promotion a.gs-title:link,
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.gs-promotion a.gs-title:link *,
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.gs-promotion .gs-snippet a:link {
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color: #0000CC;
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}
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.gs-promotion a.gs-title:visited,
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.gs-promotion a.gs-title:visited *,
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.gs-promotion .gs-snippet a:visited {
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color: #0000CC;
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}
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.gs-promotion a.gs-title:hover,
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.gs-promotion a.gs-title:hover *,
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.gs-promotion .gs-snippet a:hover {
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color: #0000CC;
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}
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.gs-promotion a.gs-title:active,
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.gs-promotion a.gs-title:active *,
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.gs-promotion .gs-snippet a:active {
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color: #0000CC;
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}
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.gs-promotion .gs-snippet,
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.gs-promotion .gs-title .gs-promotion-title-right,
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.gs-promotion .gs-title .gs-promotion-title-right * {
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color: #000000;
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}
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.gs-promotion .gs-visibleUrl,
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.gs-promotion .gs-visibleUrl-short {
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color: #008000;
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}
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/* Manually added - the layout goes wrong without this */
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.gsc-tabsArea,
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.gsc-webResult:after,
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.gsc-resultsHeader {
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clear: none;
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}
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</style>
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<div id="cse" style="width: 100%;">Loading
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<script>
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(function() {
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var cx = '010960497803984932957:u8pmqf7fdoq';
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var gcse = document.createElement('script');
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gcse.type = 'text/javascript';
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gcse.async = true;
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gcse.src = 'https://cse.google.com/cse.js?cx=' + cx;
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var s = document.getElementsByTagName('script')[0];
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s.parentNode.insertBefore(gcse, s);
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})();
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</script>
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<gcse:search></gcse:search>
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</div>

‎doc/sphinxext/numpy_ext/__init__.py

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