fix: links + allow markdown as source

Author: mgxd

README.rst

@@ -1,4 +1,4 @@
-heudiconv: A Heuristic-centric DICOM Converter
+.. topic:: `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/
@@ -29,7 +29,7 @@ About
 - 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
+- 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/conf.py

@@ -49,8 +49,8 @@
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ['.rst', '.md']
+# source_suffix = '.rst'
 
 # The master toctree document.
 master_doc = 'index'

docs/index.rst

@@ -9,7 +9,7 @@ Contents
 --------
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    installation
    ../CHANGELOG.md

docs/installation.rst

@@ -7,31 +7,31 @@ Installation
 
 Local
 -----
-Released versions of HeuDiConv are available on `PyPI <https://pypi.org/project/heudiconv/>`
- and `conda <https://github.com/conda-forge/heudiconv-feedstock#installing-heudiconv>`.
+Released versions of HeuDiConv are available on `PyPI <https://pypi.org/project/heudiconv/>`_
+ and `conda <https://github.com/conda-forge/heudiconv-feedstock#installing-heudiconv>`_.
  If installing through ``PyPI``, eg::
 
     pip install heudiconv[all]
 
-Manual installation of `dcm2niix <https://github.com/rordenlab/dcm2niix#install>`
+Manual installation of `dcm2niix <https://github.com/rordenlab/dcm2niix#install>`_
  is required.
 
- On Debian-based systems we recommend using `NeuroDebian <http://neuro.debian.net>`
- which provides the `heudiconv package <http://neuro.debian.net/pkgs/heudiconv.html>`.
+ On Debian-based systems we recommend using `NeuroDebian <http://neuro.debian.net>`_
+ which provides the `heudiconv package <http://neuro.debian.net/pkgs/heudiconv.html>`_.
 
 
 Docker
 ------
-If `Docker <https://docs.docker.com/install/>` is available on your system, you
- can visit `our page on Docker Hub <https://hub.docker.com/r/nipy/heudiconv/tags>`
+If `Docker <https://docs.docker.com/install/>`_ is available on your system, you
+ can visit `our page on Docker Hub <https://hub.docker.com/r/nipy/heudiconv/tags>`_
  to view available releases. To pull the latest release, run::
 
     $ docker pull nipy/heudiconv:0.5.4
 
 
 Singularity
 -----------
-If `Singularity <https://www.sylabs.io/singularity/>` is available on your system,
+If `Singularity <https://www.sylabs.io/singularity/>`_ is available on your system,
  you can use it to pull and convert our Docker images! For example, to pull and
  build the latest release, you can run::
 

docs/tutorials.rst

@@ -1,13 +1,9 @@
 Luckily(?), we live in an era of plentiful information. Below are some links to
- other users' tutorials covering their experience with ``heudiconv``.
+other users' tutorials covering their experience with ``heudiconv``.
 
- - `YouTube tutorial <https://www.youtube.com/watch?v=O1kZAuR7E00>` by
- `James Kent <https://github.com/jdkent>`
- - `Walkthrough <http://reproducibility.stanford.edu/bids-tutorial-series-part-2a/>`
- by the `Standard Center for Reproducible Neuroscience <http://reproducibility.stanford.edu/>`
- - `Sample Conversion: Coastal Coding 2019 <http://www.repronim.org/coco2019-training/presentations/heudiconv/#1>`
- - `U of A Neuroimaging Core <https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/heudiconv.html>`
- by `Dianne Patterson <https://github.com/dkp>`
+ - `YouTube tutorial <https://www.youtube.com/watch?v=O1kZAuR7E00>`_ by `James Kent <https://github.com/jdkent>`_.
+ - `Walkthrough <http://reproducibility.stanford.edu/bids-tutorial-series-part-2a/>`_ by the `Standard Center for Reproducible Neuroscience <http://reproducibility.stanford.edu/>`_.
+ - `Sample Conversion: Coastal Coding 2019 <http://www.repronim.org/coco2019-training/presentations/heudiconv/#1>`_.
+ - `U of A Neuroimaging Core <https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/heudiconv.html>`_ by `Dianne Patterson <https://github.com/dkp>`_.
 
- * Note: some of these tutorials may not be 100% up to date with the latest releases
-  of ``heudiconv``, so refer to this documentation first.
+** Note: some of these tutorials may not be 100% up to date with the latest releases of ``heudiconv``, so refer to this documentation first.