Merge branch 'doc/rtd' into rel-v0.5.4

yarikoptic · yarikoptic · commit 73650444a5ce · 2019-04-01T11:29:23.000-04:00
* doc/rtd:
  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
  doc: styling, heuristics
  fix: links + allow markdown as source
  doc+wip: re-implementation of rtd
  DOC: issue template clarity

 Conflicts:
	CHANGELOG.md - took the verbose version and adjusted for having blank []
                   in references where conflicted and not.
diff --git a/.github/ISSUE_TEMPLATE.md b/.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 -->
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,4 @@
 *.egg-info/
 .idea/
 venvs/
+_build/
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,25 +15,25 @@ This release includes fixes to BIDS multi-echo conversions, the
  tag has been renamed to `unstable`.
 
 ### Added
-- Additional Stanford tutorial added to README ([#301])
+- Additional Stanford tutorial added to README ([#301][])
 
 ### Changed
-- `--sbargs` argument was renamed to `--queue-args` ([#304])
+- `--sbargs` argument was renamed to `--queue-args` ([#304][])
 - Allow usage of `--files` with basic heuristics. This requires
-  use of `--subject` flag, and is limited to one subject. ([#293])
+  use of `--subject` flag, and is limited to one subject. ([#293][])
 
 ### Deprecated
 
 ### Fixed
 
 - 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])
+  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])
+  extraction etc ([#310][])
 
 ### Removed
 
@@ -137,28 +137,28 @@ 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
diff --git a/README.rst b/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)
diff --git a/docs/Makefile b/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)
diff --git a/docs/api.rst b/docs/api.rst
@@ -0,0 +1,13 @@
+=============
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 1
+
+   api/bids
+   api/convert
+   api/dicoms
+   api/parser
+   api/queue
+   api/utils
diff --git a/docs/api/bids.rst b/docs/api/bids.rst
@@ -0,0 +1,5 @@
+====
+BIDS
+====
+
+.. automodule:: heudiconv.bids
diff --git a/docs/api/convert.rst b/docs/api/convert.rst
@@ -0,0 +1,5 @@
+==========
+Conversion
+==========
+
+.. automodule:: heudiconv.convert
diff --git a/docs/api/dicoms.rst b/docs/api/dicoms.rst
@@ -0,0 +1,5 @@
+======
+DICOMS
+======
+
+.. automodule:: heudiconv.dicoms
diff --git a/docs/api/parser.rst b/docs/api/parser.rst
@@ -0,0 +1,5 @@
+=======
+Parsing
+=======
+
+.. automodule:: heudiconv.parser
diff --git a/docs/api/queue.rst b/docs/api/queue.rst
@@ -0,0 +1,5 @@
+=============
+Batch Queuing
+=============
+
+.. automodule:: heudiconv.queue
diff --git a/docs/api/utils.rst b/docs/api/utils.rst
@@ -0,0 +1,5 @@
+=======
+Utility
+=======
+
+.. automodule:: heudiconv.utils
diff --git a/docs/changes.rst b/docs/changes.rst
@@ -0,0 +1,5 @@
+=======
+Changes
+=======
+
+.. mdinclude:: ../CHANGELOG.md
diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,181 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'heudiconv'
+copyright = '2019, Heudiconv team'
+author = 'Heudiconv team'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '0.5.4'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinxarg.ext',
+    'm2r',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
+# source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'heudiconvdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'heudiconv.tex', 'heudiconv Documentation',
+     'Heudiconv team', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'heudiconv', 'heudiconv Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'heudiconv', 'heudiconv Documentation',
+     author, 'heudiconv', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+autodoc_default_options={
+          'members': None}
diff --git a/docs/heuristics.rst b/docs/heuristics.rst
diff --git a/docs/index.rst b/docs/index.rst
diff --git a/docs/installation.rst b/docs/installation.rst
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/tutorials.rst b/docs/tutorials.rst
diff --git a/docs/usage.rst b/docs/usage.rst
diff --git a/utils/link_issues_CHANGELOG b/utils/link_issues_CHANGELOG

-Original file line number
+Diff line change
 *.egg-info/
 .idea/
 venvs/
 +_build/