1- ===============================
1+ ===========================
22Pydra task package for afni
3- ===============================
3+ ===========================
44
55.. image :: https://github.com/nipype/pydra-afni/actions/workflows/pythonpackage.yaml/badge.svg
66 :target: https://github.com/nipype/pydra-afni/actions/workflows/pythonpackage.yaml
7- .. .. image:: https://codecov.io/gh/nipype/pydra-afni/branch/main/graph/badge.svg?token=UIS0OGPST7
8- .. :target: https://codecov.io/gh/nipype/pydra-afni
7+ .. image :: https://codecov.io/gh/nipype/pydra-afni/branch/main/graph/badge.svg?token=UIS0OGPST7
8+ :target: https://codecov.io/gh/nipype/pydra-afni
99.. image :: https://img.shields.io/pypi/pyversions/pydra-afni.svg
1010 :target: https://pypi.python.org/pypi/pydra-afni/
1111 :alt: Supported Python versions
@@ -14,10 +14,10 @@ Pydra task package for afni
1414 :alt: Latest Version
1515
1616
17- This package contains a collection of Pydra task interfaces for the afni toolkit.
18- The basis of this collection has been formed by the semi-automatic conversion of
19- existing `Nipype <https://github.com/nipy/nipype >`__ interfaces to Pydra using the
20- `Nipype2Pydra <https://github.com/nipype/nipype2pydra >`__ tool
17+ This package contains a collection of Pydra task interfaces for the ` AFNI < https://afni.nimh.nih.gov/ >`__
18+ software toolkit. The basis of this collection has been formed by the semi-automatic
19+ conversion of existing `Nipype <https://github.com/nipy/nipype >`__ interfaces to Pydra
20+ using the `Nipype2Pydra <https://github.com/nipype/nipype2pydra >`__ tool
2121
2222
2323Automatically-generated vs manually-curated tasks
@@ -26,8 +26,7 @@ Automatically-generated vs manually-curated tasks
2626Automatically generated tasks can be found in the `pydra.tasks.afni.auto ` package.
2727These packages should be treated with extreme caution as they likely do not pass testing.
2828Generated tasks that have been edited and pass testing are imported into one or more of the
29- `pydra.tasks.afni.v* ` packages, corresponding to the version of the afni toolkit
30- they are designed for.
29+ `pydra.tasks.afni.v* ` packages, corresponding to the version of AFNI they are designed for.
3130
3231Tests
3332-----
@@ -39,7 +38,8 @@ the necessary dependencies to run the tests
3938
4039 $ pip install -e .[test]
4140
42- Then the tests, including `doctests ` <https://docs.python.org/3/library/doctest.html>`__, can be launched using
41+ Then the tests, including `doctests ` <https://docs.python.org/3/library/doctest.html>`__,
42+ can be launched using
4343
4444.. code-block ::
4545
@@ -71,14 +71,22 @@ Contributing to this package
7171Developer installation
7272~~~~~~~~~~~~~~~~~~~~~~
7373
74+ Install the `fileformats <https://arcanaframework.github.io/fileformats/ >`__ packages
75+ corresponding to AFNI specific file formats
76+
77+
78+ .. code-block ::
79+
80+ $ pip install -e ./related-packages/fileformats[dev]
81+ $ pip install -e ./related-packages/fileformats-extras[dev]
7482
7583 Install repo in developer mode from the source directory and install pre-commit to
7684ensure consistent code-style and quality.
7785
7886.. code-block ::
7987
8088 $ pip install -e .[test,dev]
81- $ pre-commit install
89+ $ pre-commit install
8290
8391 Next install the requirements for running the auto-conversion script and generate the
8492Pydra task interfaces from their Nipype counterparts
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