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Cleaned up README.rst
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tclose authored Aug 16, 2023
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Expand Up @@ -14,20 +14,7 @@ Pydra task package for fastsurfer
:alt: Latest Version


This package contains a collection of Pydra task interfaces for the fastsurfer toolkit.
The basis of this collection has been formed by the semi-automatic conversion of
existing `Nipype <https://github.com/nipy/nipype>`__ interfaces to Pydra using the
`Nipype2Pydra <https://github.com/nipype/nipype2pydra>`__ tool


Automatically-generated vs manually-curated tasks
-------------------------------------------------

Automatically generated tasks can be found in the `pydra.tasks.fastsurfer.auto` package.
These packages should be treated with extreme caution as they likely do not pass testing.
Generated tasks that have been edited and pass testing are imported into one or more of the
`pydra.tasks.fastsurfer.v*` packages, corresponding to the version of the fastsurfer toolkit
they are designed for.
This package contains a Pydra interface for the fastsurfer toolkit.

Tests
-----
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$ pytest --doctest-modules --timeout-pass 0 pydra/tasks/*
Continuous integration
----------------------

This template uses `GitHub Actions <https://docs.github.com/en/actions/>`__` to run tests and
deploy packages to PYPI. New packages are built and uploaded when releases are created on
GitHub, or new releases of Nipype or the Nipype2Pydra conversion tool are released.
Releases triggered by updates to Nipype or Nipype2Pydra are signified by the `postN`
suffix where `N = <nipype-version><nipype2pydra-version>` with the '.'s stripped, e.g.
`v0.2.3post185010` corresponds to the v0.2.3 tag of this repository with auto-generated
packages from Nipype 1.8.5 using Nipype2Pydra 0.1.0.


Contributing to this package
----------------------------

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$ pip install -e .[test,dev]
$ pre-commit install
Next install the requirements for running the auto-conversion script and generate the
Pydra task interfaces from their Nipype counterparts

.. code-block::
$ pip install -r nipype-auto-conv/requirements.txt
The run the conversion script to convert Nipype interfaces to Pydra

.. code-block::
$ nipype-auto-conv/generate
## Methodology

The development of this package is expected to have two phases

1. Where the corresponding Nipype interfaces are considered to be the ground truth, and
the Pydra tasks are generated from them
2. When the Pydra tasks are considered be mature and they are edited by hand

Different tasks will probably mature at different times so there will probably be an
intermediate phase between 1 and 2.

Auto-conversion phase
~~~~~~~~~~~~~~~~~~~~~

The auto-converted Pydra tasks are generated from their corresponding Nipype interface
in combination with "conversion hints" contained in YAML specs
located in `nipype-auto-conv/specs/`. The self-documented conversion specs are
to be edited by hand in order to assist the auto-converter produce valid pydra tasks.
After editing one or more conversion specs the `pydra.tasks.fastsurfer.auto` package should
be regenerated by running

.. code-block::
$ nipype-auto-conv/generate
The tests should be run on the auto-generated tasks to see if they are valid

.. code-block::
$ pytest --doctest-modules pydra/tasks/fastsurfer/auto/tests/test_<the-name-of-the-task-you-edited>.py
If the test passes you should then edit the `pydra/tasks/fastsurfer/v<tool-version>/__init__.py` file
to import the now valid task interface to signify that it has been validated and is ready
for use, e.g.

.. code-block::python
from pydra.tasks.fastsurfer.auto import <the-task-you-have-validated>
Typing and sample test data
~~~~~~~~~~~~~~~~~~~~~~~~~~~

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