Merge remote-tracking branch 'upstream/master' into enh/circleci-neurodocker

Author: jakubk

.circleci/tests.sh

@@ -17,8 +17,8 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_pytests.sh && \
-    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
+    docker run --rm=false -it -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_pytests.sh && \
+    docker run --rm=false -it -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
     docker run --rm=false -it -v $WORKDIR:/work -w /src/nipype/doc --entrypoint=/usr/bin/run_builddocs.sh nipype/nipype:py36 /usr/bin/run_builddocs.sh && \
     docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
     docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
@@ -30,8 +30,8 @@ case ${CIRCLE_NODE_INDEX} in
     exitcode=$?
     ;;
   2)
-    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
-    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
+    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
+    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
     exitcode=$?
     ;;
   3)

.travis.yml

@@ -8,10 +8,10 @@ python:
 - 3.5
 - 3.6
 env:
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
-- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
+- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit" CI_SKIP_TEST=1
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
 before_install:
 - function apt_inst {
   if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
@@ -34,10 +34,10 @@ before_install:
   hash -r &&
   conda config --set always_yes yes --set changeps1 no &&
   conda update -q conda &&
-  conda install python=${TRAVIS_PYTHON_VERSION} &&
   conda config --add channels conda-forge &&
-  conda install -y nipype icu &&
-  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*;
+  conda install python=${TRAVIS_PYTHON_VERSION} &&
+  conda install -y icu &&
+  pip install -r requirements.txt &&
   pushd $HOME;
   git clone https://github.com/INCF/pybids.git;
   cd pybids;

CHANGES

@@ -1,6 +1,46 @@
-Upcoming release
+Upcoming release (0.14.0)
 ================
 
+* ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
+* ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
+* ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
+* ENH: Centralize virtual/physical $DISPLAYs (https://github.com/nipy/nipype/pull/2203, https://github.com/nipy/nipype/pull/2211)
+* ENH: New ResourceMonitor - replaces resource profiler (https://github.com/nipy/nipype/pull/2200)
+* ENH: Quickshear interface (https://github.com/nipy/nipype/pull/2047)
+* MAINT: updated deprecated HasTraits method (https://github.com/nipy/nipype/pull/2048)
+* ENH: CLI versioning (https://github.com/nipy/nipype/pull/2054)
+* ENH: Dual Regression interface (https://github.com/nipy/nipype/pull/2057)
+* ENH: Additional args to ANTs registration (https://github.com/nipy/nipype/pull/2062, https://github.com/nipy/nipype/pull/2078)
+* FIX: Mp2rage interfaces updated for new parameter names in cbstools 3 (https://github.com/nipy/nipype/pull/2065)
+* MAINT: Removed automatic nipype folder creation in HOME (https://github.com/nipy/nipype/pull/2076)
+* MAINT: Additional Windows support (https://github.com/nipy/nipype/pull/2085)
+* ENH: Output realignment matrices from TOPUP (https://github.com/nipy/nipype/pull/2084)
+* ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize,
+       3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, 
+       https://github.com/nipy/nipype/pull/2095, https://github.com/nipy/nipype/pull/2099, https://github.com/nipy/nipype/pull/2103,
+       https://github.com/nipy/nipype/pull/2114, https://github.com/nipy/nipype/pull/2135, https://github.com/nipy/nipype/pull/2186,
+       https://github.com/nipy/nipype/pull/2201, https://github.com/nipy/nipype/pull/2210)
+* MAINT: cleanup and update AFNI's Allineate (https://github.com/nipy/nipype/pull/2098)
+* ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)
+* FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)
+* FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)
+* ENH: ANTs MeasureImageSimilarity Inteface (https://github.com/nipy/nipype/pull/2128)
+* FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)
+* ENH: FreeSurfer lta_convert and mri_coreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)
+* ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)
+* FIX: Allow S3DataGrabber to grab single file (https://github.com/nipy/nipype/pull/2147)
+* FIX: Allow 4D images as inputs to buildtemplateparallel.sh and N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/2151)
+* MAINT: Detect and warn unconnected duplicate nodes (https://github.com/nipy/nipype/pull/2163)
+* ENH: Calcmedian Interface (https://github.com/nipy/nipype/pull/2167)
+* FIX: probtrackx2 outputs (https://github.com/nipy/nipype/pull/2169)
+* ENH: Improve FreeSurfer registration (https://github.com/nipy/nipype/pull/2172)
+* ENH: BIDSDataGrabber interface (https://github.com/nipy/nipype/pull/2174)
+* MAINT: Set minimum numpy version to 1.9.0 (https://github.com/nipy/nipype/pull/2182)
+* ENH: Support for multiple intial-moving-transforms (https://github.com/nipy/nipype/pull/2187)
+* MAINT: Fixes for networkx and afni (https://github.com/nipy/nipype/pull/2196, https://github.com/nipy/nipype/pull/2171)
+* TST: Update C3D version in Docker build (https://github.com/nipy/nipype/pull/2199)
+* ENH: SimpleInterface interface (https://github.com/nipy/nipype/pull/2220)
+* ENH: Add LTA to Tkregister2 (https://github.com/nipy/nipype/pull/2217)
 
 0.13.1 (May 20, 2017)
 =====================

CODE_OF_CONDUCT.md

@@ -0,0 +1,73 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting project leaders Satrajit Ghosh <<[email protected]>> or Chris Gorgolewski <<[email protected]>>. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project leaders is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org

CONTRIBUTING.md

@@ -1,3 +1,5 @@
+**Are you new to open source and GitHub?** If so reading the "[How to submit a contribution](https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution)" guide will provide a great introduction to contributing to Nipype and other Open Source projects. All the Nipype specific contributing instructions listed below will make much more sense after reading this guide.
+
 ## Contributing pull-requests (PRs)
 
 * All work is submitted via Pull Requests.
@@ -20,7 +22,7 @@
   * adding more information about what may have caused the error.
     Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.
     Do not log this, as it creates redundant/confusing logs.
-* If you are new to the project don't forget to add your name and affiliation to the `.zenodo.json` file.
+* **If you are new to the project don't forget to add your name and affiliation to the `.zenodo.json` file.**
 
 ## Contributing issues
 

README.rst

@@ -90,33 +90,8 @@ To participate in the Nipype development related discussions please use the foll
 
 Please add *[nipype]* to the subject line when posting on the mailing list.
 
+Contributing to the project
+---------------------------
 
-Nipype structure
-----------------
-
-Currently Nipype consists of the following files and directories:
-
-  INSTALL
-    NIPYPE prerequisites, installation, development, testing, and
-    troubleshooting.
-
-  README
-    This document.
-
-  THANKS
-    NIPYPE developers and contributors. Please keep it up to date!!
-
-  LICENSE
-    NIPYPE license terms.
-
-  doc/
-    Sphinx/reST documentation
-
-  examples/
-
-  nipype/
-    Contains the source code.
-
-  setup.py
-    Script for building and installing NIPYPE.
+If you'd like to contribute to the project please read our `guidelines <https://github.com/nipy/nipype/blob/master/CONTRIBUTING.md>`_. Please also read through our `code of conduct <https://github.com/nipy/nipype/blob/master/CODE_OF_CONDUCT.md>`_.
 

doc/devel/interface_specs.rst

@@ -159,6 +159,70 @@ generated depending on inputs, by the tool.  OutputSpecs inherit from
 ``interfaces.base.TraitedSpec`` directly.
 
 
+Controlling outputs to terminal
+-------------------------------
+
+It is very likely that the software wrapped within the interface writes
+to the standard output or the standard error of the terminal.
+Interfaces provide a means to access and retrieve these outputs, by
+using the ``terminal_output`` attribute: ::
+
+  import nipype.interfaces.fsl as fsl
+  mybet = fsl.BET(from_file='bet-settings.json')
+  mybet.terminal_output = 'file_split'
+
+In the example, the ``terminal_output = 'file_split'`` will redirect the
+standard output and the standard error to split files (called
+``stdout.nipype`` and ``stderr.nipype`` respectively).
+The possible values for ``terminal_output`` are:
+
+*file*
+    Redirects both standard output and standard error to the same file
+    called ``output.nipype``.
+    Messages from both streams will be overlapped as they arrive to
+    the file.
+
+*file_split*
+    Redirects the output streams separately, to ``stdout.nipype``
+    and ``stderr.nipype`` respectively, as described in the example.
+
+*file_stdout*
+    Only the standard output will be redirected to ``stdout.nipype``
+    and the standard error will be discarded.
+
+*file_stderr*
+    Only the standard error will be redirected to ``stderr.nipype``
+    and the standard output will be discarded.
+
+*stream*
+    Both output streams are redirected to the current logger printing
+    their messages interleaved and immediately to the terminal.
+
+*allatonce*
+    Both output streams will be forwarded to a buffer and stored
+    separately in the `runtime` object that the `run()` method returns.
+    No files are written nor streams printed out to terminal.
+
+*none*
+    Both outputs are discarded
+
+In all cases, except for the ``'none'`` setting of ``terminal_output``,
+the ``run()`` method will return a "runtime" object that will contain
+the streams in the corresponding properties (``runtime.stdout``
+for the standard output, ``runtime.stderr`` for the standard error, and
+``runtime.merged`` for both when streams are mixed, eg. when using the
+*file* option). ::
+
+  import nipype.interfaces.fsl as fsl
+  mybet = fsl.BET(from_file='bet-settings.json')
+  mybet.terminal_output = 'file_split'
+  ...
+  result = mybet.run()
+  result.runtime.stdout
+  ' ... captured standard output ...'
+
+
+
 Traited Attributes
 ------------------