Merge pull request #327 from nipy/doc/rtd

DOC: readthedocs

Author: yarikoptic

.gitignore

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

CHANGELOG.md

@@ -16,9 +16,14 @@ TODO Summary
 
 ### Fixed
 
+- TODO: fix: embedding issue (([#306][]))
+- TODO: ([#304][]) from mgxd/fix/queue
+- TODO: ([#301][]) from franklin-feingold/master
+- TODO: fix/queue
+- TODO: ([#293][]) from mgxd/multiecho
 - correctly handle the case when `outtype` of heuristic has "dicom"
   before '.nii.gz'. Previously would have lead to absent additional metadata
-  extraction etc
+  extraction etc ([#310][])
 
 ### Removed
 
@@ -122,28 +127,28 @@ 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
@@ -173,3 +178,8 @@ 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

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

docs/api/dicoms.rst

@@ -0,0 +1,5 @@
+======
+DICOMS
+======
+
+.. automodule:: heudiconv.dicoms

docs/api/parser.rst

@@ -0,0 +1,5 @@
+=======
+Parsing
+=======
+
+.. automodule:: heudiconv.parser

docs/api/queue.rst

@@ -0,0 +1,5 @@
+=============
+Batch Queuing
+=============
+
+.. automodule:: heudiconv.queue