| Name | pydra-freesurfer JSON |
| Version |
0.1.1
JSON |
| download |
| home_page | None |
| Summary | Pydra tasks package for freesurfer |
| upload_time | 2024-05-18 10:26:21 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. "Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. "Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. "Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. "Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." "Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright [yyyy] [name of copyright owner] 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. |
| keywords |
pydra
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# pydra-freesurfer
[![PyPI - Version][pypi-version]][pypi-project]
[![PyPI - Python Version][pypi-pyversions]][pypi-project]
[![PyPI - Downloads][pypi-downloads]][pypi-project]
[![Status-docs][status-docs-badge]][status-docs-link]
[![Status-CICD][status-cicd-badge]][status-cicd-link]
----
Pydra tasks for FreeSurfer.
[Pydra][pydra] is a dataflow engine
which provides a set of lightweight abstractions
for DAG construction, manipulation, and distributed execution.
[FreeSurfer][freesurfer] is a neuroimaging toolkit
for processing, analyzing, and visualizing human brain MR images.
This project exposes some of FreeSurfer's utilities as Pydra tasks
to facilitate their integration into more advanced processing workflows.
**Table of contents**
- [Tested interfaces](#available-interfaces)
- [Installation](#installation)
- [Automatic Conversion](#nipype-auto-conv)
- [Development](#development)
- [Licensing](#licensing)
## Tested interfaces
| Module | Interfaces |
|-----------|-----------------------------------------------------------------------------------------------------|
| gtmseg | GTMSeg |
| mri | Aparc2Aseg, Binarize, Convert, Coreg, Label2Vol, RobustRegister, RobustTemplate, Surf2Surf, Vol2Vol |
| mris | AnatomicalStats, CALabel, CATrain, Expand, Preproc |
| recon_all | ReconAll, BaseReconAll, LongReconAll |
## Installation
```console
pip install pydra-freesurfer
```
A separate installation of FreeSurfer is required to use this package.
Please review the following [instructions][freesurfer-install]
and [licensing details][freesurfer-license].
## Automatic Conversion
Automatically generated tasks can be found in the `pydra.tasks.freesurfer.auto` sub-package.
These interfaces should be treated with caution as they likely do not pass testing.
Generated tasks that have been edited and pass testing will be imported into one or more of the
`pydra.tasks.freesurfer.v*` sub-packages (e.g. `pydra.tasks.freesurfer.v7_4`) corresponding
to the version of the freesurfer toolkit they are designed for.
### 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.
## Development
### 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.
### Developer installation
Before the pydra task interfaces can be generated and installed, the file-format classes
[fileformats](https://arcanaframework.github.io/fileformats/) packages
corresponding to Freesurfer specific file formats will need to be installed
```console
pip install -e ./related-packages/fileformats[dev]
pip install -e ./related-packages/fileformats-extras[dev]
```
Next install the requirements for running the auto-conversion script and generate the
Pydra task interfaces from their Nipype counterparts
```console
pip install -r nipype-auto-conv/requirements.txt
```
The run the conversion script to convert Nipype interfaces to Pydra
```console
nipype-auto-conv/generate
```
Install repo in developer mode from the source directory and install pre-commit to
ensure consistent code-style and quality.
```console
pip install -e .[test,dev]
pre-commit install
```
### 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.freesurfer.auto` package should
be regenerated by running
```console
nipype-auto-conv/generate
```
The tests should be run on the auto-generated tasks to see if they are valid
```console
pytest pydra/tasks/freesurfer/auto/tests/test_<the-name-of-the-task-you-edited>.py
```
If the test passes you should then edit the `pydra/tasks/freesurfer/v*/__init__.py` file
to import the auto-generated task interface to signify that it has been validated and is
ready for use, where v* corresponds to the version of Freesurfer that you have tested
it against e.g.
```console
from pydra.tasks.freesurfer.auto import <the-task-you-have-validated>
```
and copy the test file `pydra/tasks/freesurfer/auto/tests/test_<validated-task>.py`
into `pydra/tasks/freesurfer/v*/tests`.
### File-formats and sample test data
The automatically generated tests will attempt to provided the task instance to be tested
with sensible default values based on the type of the field and any constraints it has
on it. However, these will often need to be manually overridden after consulting the
underlying tool's documentation.
For file-based data, automatically generated file-system objects will be created for
selected format types, e.g. Nifti, Dicom. Therefore, it is important to specify the
format of the file using the "mime-like" string corresponding to a
[fileformats](https://github.com/ArcanaFramework/fileformats) class
in the `inputs > types` and `outputs > types` dicts of the YAML spec.
If the required file-type is not found implemented within fileformats, please see the `fileformats`
docs [https://arcanaframework.github.io/fileformats/developer.html] for instructions on how to define
new fileformat types, and see
[fileformats-medimage-extras](https://github.com/ArcanaFramework/fileformats-medimage-extras/blob/6c2dabe91e95687eebc2639bb6f034cf9595ecfc/fileformats/extras/medimage/nifti.py#L30-L48)
for an example on how to implement methods to generate sample data for them. Implementations of
new fileformats that are specific to Freesurfer, and functions to
generate sample data for them, should be defined in `related-packages/fileformats`
and `related-packages/fileformats-extras`, respectively.
## Licensing
This project is distributed under the terms of the [Apache License, Version 2.0][license].
[freesurfer]: https://surfer.nmr.mgh.harvard.edu
[freesurfer-install]: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
[freesurfer-license]: https://surfer.nmr.mgh.harvard.edu/registration.html
[license]: https://opensource.org/licenses/Apache-2.0
[pydra]: https://nipype.github.io/pydra
[pypi-downloads]: https://static.pepy.tech/badge/pydra-freesurfer
[pypi-project]: https://pypi.org/project/pydra-freesurfer
[pypi-pyversions]: https://img.shields.io/pypi/pyversions/pydra-freesurfer.svg
[pypi-version]: https://img.shields.io/pypi/v/pydra-freesurfer.svg
[status-docs-badge]: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
[status-cicd-badge]: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg
[status-docs-link]: https://nipype.github.io/pydra-freesurfer/
[status-cicd-link]: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml
Raw data
{
"_id": null,
"home_page": null,
"name": "pydra-freesurfer",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": "Nipype developers <neuroimaging@python.org>",
"keywords": "pydra",
"author": null,
"author_email": "Nipype developers <neuroimaging@python.org>",
"download_url": "https://files.pythonhosted.org/packages/80/77/3dfe3b1b805a47d812533b698e9c06b3f696687e667c82499bcadecd0acc/pydra_freesurfer-0.1.1.tar.gz",
"platform": null,
"description": "# pydra-freesurfer\n\n[![PyPI - Version][pypi-version]][pypi-project]\n[![PyPI - Python Version][pypi-pyversions]][pypi-project]\n[![PyPI - Downloads][pypi-downloads]][pypi-project]\n[![Status-docs][status-docs-badge]][status-docs-link]\n[![Status-CICD][status-cicd-badge]][status-cicd-link]\n\n----\n\nPydra tasks for FreeSurfer.\n\n[Pydra][pydra] is a dataflow engine\nwhich provides a set of lightweight abstractions\nfor DAG construction, manipulation, and distributed execution.\n\n[FreeSurfer][freesurfer] is a neuroimaging toolkit\nfor processing, analyzing, and visualizing human brain MR images.\n\nThis project exposes some of FreeSurfer's utilities as Pydra tasks\nto facilitate their integration into more advanced processing workflows.\n\n**Table of contents**\n\n- [Tested interfaces](#available-interfaces)\n- [Installation](#installation)\n- [Automatic Conversion](#nipype-auto-conv)\n- [Development](#development)\n- [Licensing](#licensing)\n\n## Tested interfaces\n\n| Module | Interfaces |\n|-----------|-----------------------------------------------------------------------------------------------------|\n| gtmseg | GTMSeg |\n| mri | Aparc2Aseg, Binarize, Convert, Coreg, Label2Vol, RobustRegister, RobustTemplate, Surf2Surf, Vol2Vol |\n| mris | AnatomicalStats, CALabel, CATrain, Expand, Preproc |\n| recon_all | ReconAll, BaseReconAll, LongReconAll |\n\n## Installation\n\n```console\npip install pydra-freesurfer\n```\n\nA separate installation of FreeSurfer is required to use this package.\nPlease review the following [instructions][freesurfer-install]\nand [licensing details][freesurfer-license].\n\n## Automatic Conversion\n\nAutomatically generated tasks can be found in the `pydra.tasks.freesurfer.auto` sub-package.\nThese interfaces should be treated with caution as they likely do not pass testing.\nGenerated tasks that have been edited and pass testing will be imported into one or more of the\n`pydra.tasks.freesurfer.v*` sub-packages (e.g. `pydra.tasks.freesurfer.v7_4`) corresponding\nto the version of the freesurfer toolkit they are designed for. \n\n\n### Continuous integration\n\nThis template uses [GitHub Actions](https://docs.github.com/en/actions/) to run tests and\ndeploy packages to PYPI. New packages are built and uploaded when releases are created on\nGitHub, or new releases of Nipype or the Nipype2Pydra conversion tool are released.\nReleases triggered by updates to Nipype or Nipype2Pydra are signified by the `postN`\nsuffix where `N = <nipype-version><nipype2pydra-version>` with the '.'s stripped, e.g.\n`v0.2.3post185010` corresponds to the v0.2.3 tag of this repository with auto-generated\npackages from Nipype 1.8.5 using Nipype2Pydra 0.1.0.\n\n## Development\n\n### Methodology\n\nThe development of this package is expected to have two phases\n\n1. Where the corresponding Nipype interfaces are considered to be the ground truth, and\n the Pydra tasks are generated from them\n2. When the Pydra tasks are considered be mature and they are edited by hand\n\nDifferent tasks will probably mature at different times so there will probably be an\nintermediate phase between 1 and 2.\n\n### Developer installation\n\nBefore the pydra task interfaces can be generated and installed, the file-format classes\n[fileformats](https://arcanaframework.github.io/fileformats/) packages\ncorresponding to Freesurfer specific file formats will need to be installed\n\n```console\npip install -e ./related-packages/fileformats[dev]\npip install -e ./related-packages/fileformats-extras[dev]\n```\n\nNext install the requirements for running the auto-conversion script and generate the\nPydra task interfaces from their Nipype counterparts\n\n```console\npip install -r nipype-auto-conv/requirements.txt\n```\n\nThe run the conversion script to convert Nipype interfaces to Pydra\n\n```console\nnipype-auto-conv/generate\n```\n\nInstall repo in developer mode from the source directory and install pre-commit to\nensure consistent code-style and quality.\n\n```console\npip install -e .[test,dev]\npre-commit install\n```\n\n### Auto-conversion phase\n\nThe auto-converted Pydra tasks are generated from their corresponding Nipype interface\nin combination with \"conversion hints\" contained in YAML specs\nlocated in `nipype-auto-conv/specs/`. The self-documented conversion specs are\nto be edited by hand in order to assist the auto-converter produce valid pydra tasks.\nAfter editing one or more conversion specs the `pydra.tasks.freesurfer.auto` package should\nbe regenerated by running\n\n```console\nnipype-auto-conv/generate\n```\n\nThe tests should be run on the auto-generated tasks to see if they are valid\n\n```console\npytest pydra/tasks/freesurfer/auto/tests/test_<the-name-of-the-task-you-edited>.py\n```\n\nIf the test passes you should then edit the `pydra/tasks/freesurfer/v*/__init__.py` file\nto import the auto-generated task interface to signify that it has been validated and is\nready for use, where v* corresponds to the version of Freesurfer that you have tested\nit against e.g.\n\n```console\nfrom pydra.tasks.freesurfer.auto import <the-task-you-have-validated>\n```\n\nand copy the test file `pydra/tasks/freesurfer/auto/tests/test_<validated-task>.py`\ninto `pydra/tasks/freesurfer/v*/tests`.\n\n\n### File-formats and sample test data\n\nThe automatically generated tests will attempt to provided the task instance to be tested\nwith sensible default values based on the type of the field and any constraints it has\non it. However, these will often need to be manually overridden after consulting the\nunderlying tool's documentation.\n\nFor file-based data, automatically generated file-system objects will be created for\nselected format types, e.g. Nifti, Dicom. Therefore, it is important to specify the\nformat of the file using the \"mime-like\" string corresponding to a\n[fileformats](https://github.com/ArcanaFramework/fileformats) class\nin the `inputs > types` and `outputs > types` dicts of the YAML spec.\n\nIf the required file-type is not found implemented within fileformats, please see the `fileformats`\ndocs [https://arcanaframework.github.io/fileformats/developer.html] for instructions on how to define\nnew fileformat types, and see \n[fileformats-medimage-extras](https://github.com/ArcanaFramework/fileformats-medimage-extras/blob/6c2dabe91e95687eebc2639bb6f034cf9595ecfc/fileformats/extras/medimage/nifti.py#L30-L48)\nfor an example on how to implement methods to generate sample data for them. Implementations of\nnew fileformats that are specific to Freesurfer, and functions to\ngenerate sample data for them, should be defined in `related-packages/fileformats`\nand `related-packages/fileformats-extras`, respectively.\n\n\n\n## Licensing\n\nThis project is distributed under the terms of the [Apache License, Version 2.0][license].\n\n[freesurfer]: https://surfer.nmr.mgh.harvard.edu\n\n[freesurfer-install]: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall\n\n[freesurfer-license]: https://surfer.nmr.mgh.harvard.edu/registration.html\n\n[license]: https://opensource.org/licenses/Apache-2.0\n\n[pydra]: https://nipype.github.io/pydra\n\n[pypi-downloads]: https://static.pepy.tech/badge/pydra-freesurfer\n\n[pypi-project]: https://pypi.org/project/pydra-freesurfer\n\n[pypi-pyversions]: https://img.shields.io/pypi/pyversions/pydra-freesurfer.svg\n\n[pypi-version]: https://img.shields.io/pypi/v/pydra-freesurfer.svg\n\n[status-docs-badge]: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat\n\n[status-cicd-badge]: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg\n\n[status-docs-link]: https://nipype.github.io/pydra-freesurfer/\n\n[status-cicd-link]: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml",
"bugtrack_url": null,
"license": "Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. \"License\" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. \"Licensor\" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. \"Legal Entity\" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, \"control\" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. \"You\" (or \"Your\") shall mean an individual or Legal Entity exercising permissions granted by this License. \"Source\" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. \"Object\" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. \"Work\" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). \"Derivative Works\" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. \"Contribution\" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, \"submitted\" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as \"Not a Contribution.\" \"Contributor\" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a \"NOTICE\" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets \"[]\" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same \"printed page\" as the copyright notice for easier identification within third-party archives. Copyright [yyyy] [name of copyright owner] 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.",
"summary": "Pydra tasks package for freesurfer",
"version": "0.1.1",
"project_urls": {
"Documentation": "https://aramis-lab.github.io/pydra-freesurfer",
"Issues": "https://github.com/aramis-lab/pydra-freesurfer/issues",
"Repository": "https://github.com/aramis-lab/pydra-freesurfer"
},
"split_keywords": [
"pydra"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "266ea792f95d472c5edaf2e5ba53532953dc92457df55e618e0d90a3482766e6",
"md5": "0503879bc90c9cceb199b15fdf3eeaee",
"sha256": "ff6be042db93f789c6f32b3c34a5f06ef0c6ffa1f3a45e645a54a3d486a7f0ef"
},
"downloads": -1,
"filename": "pydra_freesurfer-0.1.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "0503879bc90c9cceb199b15fdf3eeaee",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 233303,
"upload_time": "2024-05-18T10:26:19",
"upload_time_iso_8601": "2024-05-18T10:26:19.898158Z",
"url": "https://files.pythonhosted.org/packages/26/6e/a792f95d472c5edaf2e5ba53532953dc92457df55e618e0d90a3482766e6/pydra_freesurfer-0.1.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "80773dfe3b1b805a47d812533b698e9c06b3f696687e667c82499bcadecd0acc",
"md5": "decff7498a6bf9fffa4c51288d00db8a",
"sha256": "a656fd1ec7066cf4bd777687640293b6dada1ba67f86e51410469fd3eb8a621e"
},
"downloads": -1,
"filename": "pydra_freesurfer-0.1.1.tar.gz",
"has_sig": false,
"md5_digest": "decff7498a6bf9fffa4c51288d00db8a",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 216244,
"upload_time": "2024-05-18T10:26:21",
"upload_time_iso_8601": "2024-05-18T10:26:21.331790Z",
"url": "https://files.pythonhosted.org/packages/80/77/3dfe3b1b805a47d812533b698e9c06b3f696687e667c82499bcadecd0acc/pydra_freesurfer-0.1.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-05-18 10:26:21",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "aramis-lab",
"github_project": "pydra-freesurfer",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "pydra-freesurfer"
}
