Drop Docker wrapper (#52)

* Drop the Docker and Singularity wrappers.

* Keep dropping wrappers.

docs/contributors.rst

@@ -0,0 +1,128 @@
+.. include:: links.rst
+
+------------------------
+Contributing to qsirecon
+------------------------
+
+This document explains how to prepare a new development environment and
+update an existing environment, as necessary.
+
+Development in Docker is encouraged, for the sake of consistency and
+portability.
+By default, work should be built off of `pennlinc/qsirecon:latest
+<https://hub.docker.com/r/pennlinc/qsirecon/>`_ (see the
+installation_ guide for the basic procedure for running).
+
+
+Patching working repositories
+=============================
+In order to test new code without rebuilding the Docker image, it is
+possible to mount working repositories as source directories within the
+container.
+
+When invoking ``docker`` directly, the mount options must be specified
+with the ``-v`` flag::
+
+    -v $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon:ro
+    -v $HOME/projects/nipype/nipype:/usr/local/miniconda/lib/python3.10/site-packages/nipype:ro
+
+For example, ::
+
+    $ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
+        -v $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon:ro \
+        pennlinc/qsirecon:latest /data /out/out participant \
+        -w /out/work/
+
+In order to work directly in the container, use ``--entrypoint=bash`` and omit the qsirecon
+arguments in a ``docker`` command::
+
+    $ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
+        -v $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon:ro --entrypoint=bash \
+        pennlinc/qsirecon:latest
+
+Patching containers can be achieved in Singularity analogous to ``docker``
+using the ``--bind`` (``-B``) option: ::
+
+    $ singularity run \
+        -B $HOME/projects/qsirecon/qsirecon:/usr/local/miniconda/lib/python3.10/site-packages/qsirecon \
+        qsirecon.img \
+        /scratch/dataset /scratch/out participant -w /out/work/
+
+Or you can patch Singularity containers using the PYTHONPATH variable: ::
+
+   $ PYTHONPATH="$HOME/projects/qsirecon" singularity run qsirecon.img \
+        /scratch/dataset /scratch/out participant -w /out/work/
+
+
+Adding dependencies
+===================
+New dependencies to be inserted into the Docker image will either be
+Python or non-Python dependencies.
+Python dependencies may be added in three places, depending on whether
+the package is large or non-release versions are required.
+The image `must be rebuilt <#rebuilding-docker-image>`_ after any
+dependency changes.
+
+Python dependencies should generally be included in the ``REQUIRES``
+list in `qsirecon/info.py
+<https://github.com/pennlinc/qsirecon/blob/29133e5e9f92aae4b23dd897f9733885a60be311/qsirecon/info.py#L46-L61>`_.
+If the latest version in `PyPI <https://pypi.org/>`_ is sufficient,
+then no further action is required.
+
+For large Python dependencies where there will be a benefit to
+pre-compiled binaries, `conda <https://github.com/conda/conda>`_ packages
+may also be added to the ``conda install`` line in the `Dockerfile
+<https://github.com/pennlinc/qsirecon/blob/29133e5e9f92aae4b23dd897f9733885a60be311/Dockerfile#L46>`_.
+
+Non-Python dependencies must also be installed in the Dockerfile, via a
+``RUN`` command.
+For example, installing an ``apt`` package may be done as follows: ::
+
+    RUN apt-get update && \
+        apt-get install -y <PACKAGE>
+
+Rebuilding Docker image
+=======================
+If it is necessary to rebuild the Docker image, a local image named
+``qsirecon`` may be built from within the working qsirecon
+repository, located in ``~/projects/qsirecon``: ::
+
+    ~/projects/qsirecon$ docker build -t qsirecon .
+
+To work in this image, replace ``pennlinc/qsirecon:latest`` with
+``qsirecon`` in any of the above commands.
+
+
+Adding new features to the citation boilerplate
+===============================================
+
+The citation boilerplate is built by adding two dunder attributes
+of workflow objects: ``__desc__`` and ``__postdesc__``.
+Once the full *qsirecon* workflow is built, starting from the
+outer workflow and visiting all sub-workflows in topological
+order, all defined ``__desc__`` are appended to the citation
+boilerplate before descending into sub-workflows.
+Once all the sub-workflows of a given workflow have
+been visited, then the ``__postdesc__`` attribute is appended
+and the execution pops out to higher level workflows.
+The dunder attributes are written in Markdown language, and may contain
+references.
+To add a reference, just add a new Bibtex entry to the references
+database (``/qsirecon/data/boilerplate.bib``).
+You can then use the Bibtex handle within the Markdown text.
+For example, if the Bibtex handle is ``myreference``, a citation
+will be generated in Markdown language with ``@myreference``.
+To generate citations with parenthesis and/or additional content,
+brackets should be used: e.g. ``[see @myreference]`` will produce
+a citation like *(see Doe J. et al 2018)*.
+
+
+An example of how this works is shown here::
+
+    workflow = Workflow(name=name)
+    workflow.__desc__ = """\
+    Head-motion parameters with respect to the DWI reference
+    (transformation matrices, and six corresponding rotation and translation
+    parameters) are estimated before any spatiotemporal filtering using
+    `mcflirt` [FSL {fsl_ver}, @mcflirt].
+    """.format(fsl_ver=fsl.Info().version() or '<ver>')