Merge tag 'v0.5.4' into debian

heudiconv 0.5.4

* tag 'v0.5.4': (56 commits)
  rel: 0.5.4
  bump: dcm2niix to latest release
  fix: avoid relative import in nipype node
  fix: remove print statement
  fix: minimize processing before batch submission
  fix: imports, outdated argument help
  fix: revert to explicit relative imports, use heudiconv executable for queue submissions
  fix: better support for queue args
  rf: move to absolute import
  ENH: manually fixed up already existing MD links to contain empty trailing []
  Updated link_issues_CHANGELOG with new version from datalad 0.12.0rc2-125-gc350b96e
  fix: utils api link
  fix: batch example
  doc: finalize rtd
  doc: install all project dependencies on rtd
  fix: extension name
  doc: doc-building dependencies
  sty: whitespace + sphinx argparser
  sty+enh: try new style, add more content
  update dcm2niix to v1.0.20181125
  ...

Author: yarikoptic

.github/ISSUE_TEMPLATE.md

@@ -1,3 +1,8 @@
+<!-- DO NOT DELETE THIS! 
+This template is used to facilitate issue resolution.
+All text in <!-> tags will not be displayed.
+-->
+
 ### Summary
 <!-- If you are having conversion troubles, please share as much
 relevant information as possible. This includes, but is not limited to:
@@ -16,4 +21,4 @@ Choose one:
 <!-- If selected, please provide container name and tag"-->
 
 - Heudiconv version: 
-<!-- Command: heudiconv --version -->
+<!-- To check: run heudiconv with just the --version flag -->

.gitignore

@@ -3,3 +3,5 @@
 .coverage
 *.egg-info/
 .idea/
+venvs/
+_build/

CHANGELOG.md

@@ -4,6 +4,43 @@ All notable changes to this project will be documented (for humans) in this file
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [0.5.4] - 2019-04-29
+
+This release includes fixes to BIDS multi-echo conversions, the
+ re-implementation of queuing support (currently just SLURM), as well as
+ some bugfixes.
+
+ Starting today, we will (finally) push versioned releases to DockerHub.
+ Finally, to more accurately reflect on-going development, the `latest`
+ tag has been renamed to `unstable`.
+
+### Added
+- Readthedocs documentation ([#327][])
+
+### Changed
+- Update Docker dcm2niix to v.1.0.20190410 ([#334][])
+- Allow usage of `--files` with basic heuristics. This requires
+  use of `--subject` flag, and is limited to one subject. ([#293][])
+
+### Deprecated
+
+### Fixed
+- Improve support for multiple `--queue-args` ([#328][])
+- Fixed an issue where generated BIDS sidecar files were missing additional
+  information - treating all conversions as if the `--minmeta` flag was
+  used ([#306][])
+- Re-enable SLURM queuing support ([#304][])
+- BIDS multi-echo support for EPI + T1 images ([#293][])
+- Correctly handle the case when `outtype` of heuristic has "dicom"
+  before '.nii.gz'. Previously would have lead to absent additional metadata
+  extraction etc ([#310][])
+
+### Removed
+- `--sbargs` argument was renamed to `--queue-args` ([#304][])
+
+### Security
+
+
 ## [0.5.3] - 2019-01-12
 
 Minor hot bugfix release
@@ -101,28 +138,28 @@ The first release after major refactoring:
 - Many other various issues
 
 ## [0.4] - 2017-10-15
-A usable release to support [DBIC] use-case
+A usable release to support [DBIC][] use-case
 ### Added
 - more testing
 ### Changes
-- Dockerfile updates (added pigz, progressed forward [dcm2niix])
+- Dockerfile updates (added pigz, progressed forward [dcm2niix][])
 ### Fixed
 - correct date/time in BIDS `_scans` files
 - sort entries in `_scans` by date and then filename
 
 ## [0.3] - 2017-07-10
-A somewhat working release on the way to support [DBIC] use-case
+A somewhat working release on the way to support [DBIC][] use-case
 ### Added
 - more tests
 - groupping of dicoms by series if provided
 - many more features and fixes
 
 ## [0.2] - 2016-10-20
-An initial release on the way to support [DBIC] use-case
+An initial release on the way to support [DBIC][] use-case
 ### Added
 - basic Python project assets (`setup.py`, etc)
 - basic tests
-- [datalad] support
+- [datalad][] support
 - dbic_bids heuristic
 - `--dbg` command line flag to enter `pdb` environment upon failure
 ## Fixed
@@ -152,3 +189,8 @@ TODO Summary
 [DBIC]: http://dbic.dartmouth.edu
 [datalad]: http://datalad.org
 [dcm2niix]: https://github.com/rordenlab/dcm2niix
+[#293]: https://github.com/nipy/heudiconv/issues/293
+[#301]: https://github.com/nipy/heudiconv/issues/301
+[#304]: https://github.com/nipy/heudiconv/issues/304
+[#306]: https://github.com/nipy/heudiconv/issues/306
+[#310]: https://github.com/nipy/heudiconv/issues/310

Dockerfile

@@ -39,7 +39,7 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
 
 ENTRYPOINT ["/neurodocker/startup.sh"]
 
-ENV PATH="/opt/dcm2niix-v1.0.20180622/bin:$PATH"
+ENV PATH="/opt/dcm2niix-v1.0.20190410/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            cmake \
@@ -54,10 +54,10 @@ RUN apt-get update -qq \
     && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
     && cd /tmp/dcm2niix \
     && git fetch --tags \
-    && git checkout v1.0.20180622 \
+    && git checkout v1.0.20190410 \
     && mkdir /tmp/dcm2niix/build \
     && cd /tmp/dcm2niix/build \
-    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180622 .. \
+    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20190410 .. \
     && make \
     && make install \
     && rm -rf /tmp/dcm2niix
@@ -115,7 +115,7 @@ RUN echo '{ \
     \n    [ \
     \n      "dcm2niix", \
     \n      { \
-    \n        "version": "v1.0.20180622", \
+    \n        "version": "v1.0.20190410", \
     \n        "method": "source" \
     \n      } \
     \n    ], \

README.md

@@ -76,6 +76,8 @@ dicomstack.
 
 - YouTube:
     - ["Heudiconv Example"](https://www.youtube.com/watch?v=O1kZAuR7E00) by [James Kent](https://github.com/jdkent)
+- Blog post:
+    - ["BIDS Tutorial Series: HeuDiConv Walkthrough"](http://reproducibility.stanford.edu/bids-tutorial-series-part-2a/) by the [Stanford Center for Reproducible Neuroscience](http://reproducibility.stanford.edu/)
 
 ## How it works (in some more detail)
 

README.rst

@@ -0,0 +1,35 @@
+=============
+**HeuDiConv**
+=============
+
+`a heuristic-centric DICOM converter`
+
+.. image:: https://img.shields.io/badge/docker-nipy/heudiconv:unstable-brightgreen.svg?logo=docker&style=flat
+  :target: https://hub.docker.com/r/nipy/heudiconv/tags/
+  :alt: Our Docker image
+
+.. image:: https://travis-ci.org/nipy/heudiconv.svg?branch=master
+  :target: https://travis-ci.org/nipy/heudiconv
+  :alt: TravisCI
+
+.. image:: https://codecov.io/gh/nipy/heudiconv/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/nipy/heudiconv
+  :alt: CodeCoverage
+
+.. image:: https://readthedocs.org/projects/heudiconv/badge/?version=latest
+  :target: http://heudiconv.readthedocs.io/en/latest/?badge=latest
+  :alt: Readthedocs
+
+About
+-----
+
+``heudiconv`` is a flexible DICOM converter for organizing brain imaging data
+into structured directory layouts.
+
+- it allows flexible directory layouts and naming schemes through customizable heuristics implementations
+- it only converts the necessary DICOMs, not everything in a directory
+- you can keep links to DICOM files in the participant layout
+- using dcm2niix under the hood, it's fast
+- it can track the provenance of the conversion from DICOM to NIfTI in W3C PROV format
+- it provides assistance in converting to `BIDS <http://bids.neuroimaging.io/>`_.
+- it integrates with `DataLad <https://www.datalad.org/>`_ to place converted and original data under git/git-annex version control, while automatically annotating files with sensitive information (e.g., non-defaced anatomicals, etc)

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api.rst

@@ -0,0 +1,13 @@
+=============
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 1
+
+   api/bids
+   api/convert
+   api/dicoms
+   api/parser
+   api/queue
+   api/utils

docs/api/bids.rst

@@ -0,0 +1,5 @@
+====
+BIDS
+====
+
+.. automodule:: heudiconv.bids

docs/api/convert.rst

@@ -0,0 +1,5 @@
+==========
+Conversion
+==========
+
+.. automodule:: heudiconv.convert