[ENH] Linting, update imports

Dockerfile

@@ -1,8 +1,124 @@
-FROM python:3
+# Generated by Neurodocker v0.2.0-12-g1a1c6f6.
+#
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+#     https://github.com/kaczmarj/neurodocker
+#
+# Timestamp: 2017-08-30 19:05:17
 
-WORKDIR /usr/src/app
+FROM ubuntu:trusty
 
-COPY requirements.txt ./
-RUN pip install --no-cache-dir -r requirements.txt
+ARG DEBIAN_FRONTEND=noninteractive
 
-COPY . .
+#----------------------------------------------------------
+# Install common dependencies and create default entrypoint
+#----------------------------------------------------------
+ENV LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    ND_ENTRYPOINT="/neurodocker/startup.sh"
+RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
+    	bzip2 ca-certificates curl unzip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+    && chmod 777 /opt && chmod a+s /opt \
+    && mkdir -p /neurodocker \
+    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
+         echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
+         && echo 'set +x' >> $ND_ENTRYPOINT \
+         && echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
+       fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+RUN apt-get update -qq && apt-get install -yq --no-install-recommends git vim libxml2-dev libnlopt-dev libxslt-dev\
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+#--------------------
+# Install AFNI latest
+#--------------------
+ENV PATH=/opt/afni:$PATH
+RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa \
+    libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb \
+    && libs_path=/usr/lib/x86_64-linux-gnu \
+    && if [ -f $libs_path/libgsl.so.19 ]; then \
+           ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0; \
+       fi \
+    # Install libxp (not in all ubuntu/debian repositories) \
+    && apt-get install -yq --no-install-recommends libxp6 \
+    || /bin/bash -c " \
+       curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
+       && dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" \
+    # Install libpng12 (not in all ubuntu/debian repositories) \
+    && apt-get install -yq --no-install-recommends libpng12-0 \
+    || /bin/bash -c " \
+       curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
+       && dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" \
+    # Install R \
+    && apt-get install -yq --no-install-recommends \
+    	r-base-dev r-cran-rmpi \
+     || /bin/bash -c " \
+        curl -o /tmp/install_R.sh -sSL https://gist.githubusercontent.com/kaczmarj/8e3792ae1af70b03788163c44f453b43/raw/0577c62e4771236adf0191c826a25249eb69a130/R_installer_debian_ubuntu.sh \
+        && /bin/bash /tmp/install_R.sh" \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+    && echo "Downloading AFNI ..." \
+    && mkdir -p /opt/afni \
+    && curl -sSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
+    | tar zx -C /opt/afni --strip-components=1 \
+    && /opt/afni/rPkgsInstall -pkgs ALL \
+    && rm -rf /tmp/*
+
+# Create new user: neuro
+RUN useradd --no-user-group --create-home --shell /bin/bash neuro
+USER neuro
+
+#------------------
+# Install Miniconda
+#------------------
+ENV CONDA_DIR=/opt/conda \
+    PATH=/opt/conda/bin:$PATH
+RUN echo "Downloading Miniconda installer ..." \
+    && miniconda_installer=/tmp/miniconda.sh \
+    && curl -sSL -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && /bin/bash $miniconda_installer -f -b -p $CONDA_DIR \
+    && rm -f $miniconda_installer \
+    && conda config --system --prepend channels conda-forge \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    && conda update -y -q --all && sync \
+    && conda clean -tipsy && sync
+
+#-----------------------------
+# Create py3 conda environment
+#-----------------------------
+RUN conda create -y -q --name default --channel vida-nyu python=3.6.1 \
+    	numpy pandas reprozip traits \
+    && sync && conda clean -tipsy && sync \
+    && /bin/bash -c "source activate default \
+    	&& pip install -q --no-cache-dir \
+    	nipype ipython scikit-learn scipy ipdb mdp" \
+    && sync
+ENV PATH=/opt/conda/envs/default/bin:$PATH
+
+#------------------------------
+# Create py27 conda environment
+#------------------------------
+RUN conda create -y -q --name py27 python=2.7 \
+    numpy pandas reprozip traits \
+    && sync && conda clean -tipsy && sync \
+    && /bin/bash -c "source activate default \
+        && pip install -q --no-cache-dir \
+        nipype ipython scikit-learn scipy ipdb mdp" \
+    && sync
+
+USER root
+
+# User-defined instruction
+RUN mkdir /home/neuro/code
+
+# User-defined instruction
+RUN mkdir /home/neuro/data
+
+WORKDIR /home/neuro

README.md

@@ -6,9 +6,12 @@ tedana is part of the ME-ICA pipeline, and therefore assumes that you're working
 
 ## About
 
-Multi-echo fMRI data collection entails acquires multiple TEs (commonly called [echo times](http://mriquestions.com/tr-and-te.html)) for each collected fMRI volume. Our signal of interest, Blood Oxygen-Level Dependent or [BOLD signal](http://www.fil.ion.ucl.ac.uk/spm/course/slides10-zurich/Kerstin_BOLD.pdf), is known to decay at a set rate within each fMRI volume. Collecting multiple echos therefore allows us to infer if components of fMRI signal are BOLD-related or driven by acquisition artifacts, like partipant motion. For a review, see [Kundu et al. (2017), _NeuroImage_](https://paperpile.com/shared/eH3PPu).
+Multi-echo fMRI data collection entails acquires multiple TEs (commonly called [echo times](http://mriquestions.com/tr-and-te.html)) for each collected fMRI volume.
+Our signal of interest, Blood Oxygen-Level Dependent or [BOLD signal](http://www.fil.ion.ucl.ac.uk/spm/course/slides10-zurich/Kerstin_BOLD.pdf), is known to decay at a set rate within each fMRI volume.
+Collecting multiple echos therefore allows us to infer if components of fMRI signal are BOLD-related or driven by acquisition artifacts, like participant motion.
+For a review, see [Kundu et al. (2017), _NeuroImage_](https://paperpile.com/shared/eH3PPu).
 
-In tedana, we combine all collected echos, then decompose the resulting timeseries into components that can be classified as BOLD or non-BOLD based. This is performed in a series of steps including:
+In tedana, we combine all collected echos, then decompose the resulting time series into components that can be classified as BOLD or non-BOLD based. This is performed in a series of steps including:
 
 * Principle components analysis
 * Independent components analysis
@@ -40,3 +43,8 @@ We :yellow_heart: new contributors ! To get started, check out [our contributing
 Want to learn more about our plans for developing tedana ? Check out [our roadmap](https://github.com/emdupre/tedana/projects). Have a question, comment, or suggestion ? Open or comment on one of [our issues](https://github.com/emdupre/tedana/issues) !
 
 We ask that all contributions to tedana respect our [code of conduct](https://github.com/emdupre/tedana/blob/master/Code_of_Conduct.md).
+
+### Mozilla Global Sprint (10-11 May, 2018)
+
+This year, tedana will be participating in the [Mozilla Global Sprint](https://foundation.mozilla.org/opportunity/global-sprint/) !
+Look out for issues tagged `global-sprint` for good places to get started during the sprint.

tedana/interfaces/__init__.py

@@ -1,2 +1,7 @@
 # emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
 # ex: set sts=4 ts=4 sw=4 et:
+
+from .t2smap import (t2sadmap, optcom)
+
+__all__ = [
+    't2sadmap', 'optcom']

tedana/interfaces/t2smap.py

@@ -1,7 +1,7 @@
 import numpy as np
 import nibabel as nib
-from tedana.utils.utils import (niwrite, cat2echos,
-                                makeadmask, unmask, fmask)
+from tedana.utils import (niwrite, cat2echos,
+                          makeadmask, unmask, fmask)
 
 
 def t2sadmap(catd, mask, tes, masksum, start_echo):