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Merge branch 'master' into debug_permission
2 parents 1359b0b + 85990a9 commit 3c2fda2

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‎Dockerfile

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@@ -136,13 +136,13 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
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&& sync && conda clean --all && sync \
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&& bash -c "source activate neuro \
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&& pip install --no-cache-dir \
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'https://github.com/nipy/nipype/tarball/master' \
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'https://github.com/INCF/pybids/tarball/0.6.5' \
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'nilearn' \
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'datalad[full]' \
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'nipy' \
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'duecredit' \
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'nbval'" \
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https://github.com/nipy/nipype/tarball/master \
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https://github.com/INCF/pybids/tarball/0.7.1 \
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nilearn \
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datalad[full] \
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nipy \
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duecredit \
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nbval" \
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&& rm -rf ~/.cache/pip/* \
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&& sync \
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&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
@@ -249,7 +249,7 @@ RUN echo '{ \
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\n ], \
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\n "pip_install": [ \
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\n "https://github.com/nipy/nipype/tarball/master", \
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\n "https://github.com/INCF/pybids/tarball/0.%3Cspan%20class="x x-first x-last">6.5", \
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\n "https://github.com/INCF/pybids/tarball/0.%3Cspan%20class="x x-first x-last">7.1", \
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\n "nilearn", \
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\n "datalad[full]", \
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\n "nipy", \

‎Singularity

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@@ -126,13 +126,13 @@ conda install -y -q --name neuro \
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sync && conda clean --all && sync
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bash -c "source activate neuro
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pip install --no-cache-dir \
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'https://github.com/nipy/nipype/tarball/master' \
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'https://github.com/INCF/pybids/tarball/0.6.5' \
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'nilearn' \
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'datalad[full]' \
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'nipy' \
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'duecredit' \
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'nbval'"
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https://github.com/nipy/nipype/tarball/master \
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https://github.com/INCF/pybids/tarball/0.7.1 \
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nilearn \
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datalad[full] \
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nipy \
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duecredit \
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nbval"
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rm -rf ~/.cache/pip/*
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sync
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sed -i '$isource activate neuro' $ND_ENTRYPOINT
@@ -241,7 +241,7 @@ echo '{
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\n ],
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\n "pip_install": [
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\n "https://github.com/nipy/nipype/tarball/master",
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\n "https://github.com/INCF/pybids/tarball/0.%3Cspan%20class="x x-first x-last">6.5",
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\n "https://github.com/INCF/pybids/tarball/0.%3Cspan%20class="x x-first x-last">7.1",
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\n "nilearn",
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\n "datalad[full]",
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\n "nipy",

‎docs/index.html

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@@ -11891,7 +11891,7 @@
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<div class="pure-g domain-table-container color04">
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_create_interfaces.html">Create Interfaces</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_interfaces_caching.html">Interfaces Caching</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_command_line_interface.html">Nipype Command Line Interface</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_nipypecli.html">Nipype Command Line Interface</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_aws.html">Amazon Web Services (AWS)</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_sphinx_ext.html">Sphinx extensions</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_spmmcr.html">SPM with MATLAB Common Runtime (MCR)</a>
@@ -12062,7 +12062,7 @@ <h2 class="domain-header color04"><a class="domain-title">Advanced Concepts</a><
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<div class="pure-g domain-table-container color04">
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_create_interfaces.html">Create Interfaces</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_interfaces_caching.html">Interfaces Caching</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_command_line_interface.html">Nipype Command Line Interface</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_nipypecli.html">Nipype Command Line Interface</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_aws.html">Amazon Web Services (AWS)</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_sphinx_ext.html">Sphinx extensions</a>
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<a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_spmmcr.html">SPM with MATLAB Common Runtime (MCR)</a>

‎docs/notebooks/advanced_command_line_interface.html

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<!DOCTYPE html>
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<html>
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<head><meta charset="utf-8" />
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<title>advanced_command_line_interface</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
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<title>advanced_nipypecli</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.0.3/jquery.min.js"></script>
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<style type="text/css">

‎generate.sh

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@@ -18,7 +18,7 @@ generate_docker() {
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
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traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
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pip_install="https://github.com/nipy/nipype/tarball/master
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https://github.com/INCF/pybids/tarball/0.6.5
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https://github.com/INCF/pybids/tarball/0.7.1
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nilearn datalad[full] nipy duecredit nbval" \
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create_env="neuro" \
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activate=True \
@@ -57,7 +57,7 @@ generate_singularity() {
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
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traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
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pip_install="https://github.com/nipy/nipype/tarball/master
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https://github.com/INCF/pybids/tarball/0.6.5
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https://github.com/INCF/pybids/tarball/0.7.1
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nilearn datalad[full] nipy duecredit nbval" \
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create_env="neuro" \
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activate=True \

‎index.ipynb

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@@ -111,7 +111,7 @@
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" <div class=\"pure-g domain-table-container color04\">\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_create_interfaces.ipynb\">Create Interfaces</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_interfaces_caching.ipynb\">Interfaces Caching</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_command_line_interface.ipynb\">Nipype Command Line Interface</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_nipypecli.ipynb\">Nipype Command Line Interface</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_aws.ipynb\">Amazon Web Services (AWS)</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_sphinx_ext.ipynb\">Sphinx extensions</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_spmmcr.ipynb\">SPM with MATLAB Common Runtime (MCR)</a>\n",
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" <div class=\"pure-g domain-table-container color04\">\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_create_interfaces.ipynb\">Create Interfaces</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_interfaces_caching.ipynb\">Interfaces Caching</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_command_line_interface.ipynb\">Nipype Command Line Interface</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_nipypecli.ipynb\">Nipype Command Line Interface</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_aws.ipynb\">Amazon Web Services (AWS)</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_sphinx_ext.ipynb\">Sphinx extensions</a>\n",
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" <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_spmmcr.ipynb\">SPM with MATLAB Common Runtime (MCR)</a>\n",

‎notebooks/advanced_command_line_interface.ipynb renamed to ‎notebooks/advanced_nipypecli.ipynb

File renamed without changes.

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