diff --git a/.gitmodules b/.gitmodules index 6f548f1..e69de29 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,5 +0,0 @@ -[submodule "tests/data/ds000005-fmriprep"] - path = tests/data/ds000005-fmriprep - url = https://gin.g-node.org/nipreps-data/ds000005-fmriprep - datalad-id = 92e566e4-1c80-434e-a4d7-5bf9fb483d76 - datalad-url = https://gin.g-node.org/nipreps-data/ds000005-fmriprep diff --git a/.zenodo.json b/.zenodo.json index fcc06d6..0bb5985 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -10,7 +10,7 @@ ], "creators": [ { - "affiliation": "Department of Psychology, Florida International University", + "affiliation": "University of Pennsylvania", "name": "Salo, Taylor", "orcid": "0000-0001-9813-3167" }, diff --git a/README.rst b/README.rst index e0313cf..9a9a513 100644 --- a/README.rst +++ b/README.rst @@ -31,6 +31,11 @@ Here are a few of the key features: In this case, the fMRIPost-AROMA workflow will pull a transform from MNI152NLin2009cAsym to MNI152NLin6Asym from TemplateFlow and apply it, along with the boldref-to-MNI152NLin2009cAsym transform, to the boldref-space derivatives. + - fMRIPrep with ``--level full`` and raw BOLD data. + In this case, the fMRIPost workflow will apply minimal preprocessing steps internally + to generate the required derivatives. + This will rarely be used, but may be useful for fMRIPost workflows that require raw data, + like fMRIPost-phase. .. warning:: @@ -40,3 +45,20 @@ Here are a few of the key features: 4. General NiPreps infrastructure for running a BIDS App, such as a config file, a command-line interface, and tools to generate HTML reports. + + +***** +Usage +***** + +If you use this template to create a new fMRIPost workflow, you will need to: + +1. Replace all instances of ``fmripost_template`` with the name of your new workflow. +2. Replace all instances of ``fMRIPost-template`` with the name of your new workflow. +3. Modify the workflows and interfaces to apply your desired processing steps. +4. Update the documentation to reflect the new workflow. + +Please also include something like the following in your boilerplate: + +> Data were postprocessed using *fMRIPost-*, +> which is based on *fMRIPost-template* ([cite fMRIPost-template version and DOI here]). diff --git a/src/fmripost_template/__main__.py b/src/fmripost_template/__main__.py deleted file mode 100644 index 7ed8e41..0000000 --- a/src/fmripost_template/__main__.py +++ /dev/null @@ -1,9 +0,0 @@ -# SPDX-FileCopyrightText: 2023-present Chris Markiewicz -# -# SPDX-License-Identifier: Apache-2.0 -import sys - -if __name__ == '__main__': - from .cli import fmripost_template - - sys.exit(fmripost_template()) diff --git a/src/fmripost_template/_version.pyi b/src/fmripost_template/_version.pyi deleted file mode 100644 index e704d43..0000000 --- a/src/fmripost_template/_version.pyi +++ /dev/null @@ -1,26 +0,0 @@ -# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- -# vi: set ft=python sts=4 ts=4 sw=4 et: -# -# Copyright 2024 The NiPreps Developers -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# -# We support and encourage derived works from this project, please read -# about our expectations at -# -# https://www.nipreps.org/community/licensing/ -# -__version__: str -__version_tuple__: tuple[str, ...] -version: str -version_tuple: tuple[str, ...] diff --git a/src/fmripost_template/cli/__init__.py b/src/fmripost_template/cli/__init__.py index 3138c99..75ad542 100644 --- a/src/fmripost_template/cli/__init__.py +++ b/src/fmripost_template/cli/__init__.py @@ -1,13 +1,36 @@ -# SPDX-FileCopyrightText: 2023-present Chris Markiewicz +# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- +# vi: set ft=python sts=4 ts=4 sw=4 et: # -# SPDX-License-Identifier: Apache-2.0 -import click - -from .. import __version__ - +# Copyright 2024 The NiPreps Developers +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# +# We support and encourage derived works from this project, please read +# about our expectations at +# +# https://www.nipreps.org/community/licensing/ +# +"""Command-line interface modules for fMRIPost-template.""" +from . import ( + parser, + run, + version, + workflow, +) -@click.group(context_settings={'help_option_names': ['-h', '--help']}, invoke_without_command=True) -@click.version_option(version=__version__, prog_name='fmripost-template') -@click.pass_context -def fmripost_template(ctx: click.Context): - click.echo('Hello world!') +__all__ = [ + 'parser', + 'run', + 'version', + 'workflow', +]