| Name | nipype2pydra JSON |
| Version |
0.3.3
JSON |
| download |
| home_page | |
| Summary | Tool for converting Nipype tasks and workflows into Pydra syntax |
| upload_time | 2024-03-17 23:36:16 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.7 |
| license | Creative Commons Attribution 4.0 International Public License By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions. Section 1 – Definitions. Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. 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| keywords |
converters
data
nipype
pydra
workflows
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
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Nipype2Pydra
============
.. image:: https://github.com/nipype/nipype2pydra/actions/workflows/ci-cd.yml/badge.svg
:target: https://github.com/nipype/nipype2pydra/actions/workflows/ci-cd.yml
.. image:: https://codecov.io/gh/nipype/nipype2pydra/branch/main/graph/badge.svg?token=UIS0OGPST7
:target: https://codecov.io/gh/nipype/nipype2pydra
.. image:: https://img.shields.io/pypi/pyversions/nipype2pydra.svg
:target: https://pypi.python.org/pypi/nipype2pydra/
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/v/nipype2pydra.svg
:target: https://pypi.python.org/pypi/nipype2pydra/
:alt: Latest Version
Nipype2Pydra is a command-line tool for semi-automatically porting command interfaces
and workflows written from the Nipype_ workflow engine to its successor Pydra_. It has
been designed so that any required manual-specifications are stored in separate YAML
specification files, which is read ahead of the conversion, so once designed the
conversion can be re-run to pick up changes in newer versions of the Nipype_ code without
having to redo the manual steps.
Basic Usage
-----------
To convert a Nipype_ interface to a Pydra_ task run the `nipype2pydra task` command and
pass it the conversion specification YAML file and the root of the package to save the
generated module, e.g.::
$ nipype2pydra task ants_registration_registration.yaml /path/to/package/root
This will create a module file under the package root directory based on the `output_module`
field in the specification, e.g::
/path/to/package/root/output/module/path
If that is missing and the nipype interface is in the standard `nipype.interfaces`
package, then it will be stored at `pydra.tasks.` with the same path end.
Conversion Specifications
-------------------------
While the conversions aim to as automatic as possible, there are structural
differences between Nipype_ and Pydra_ that require manual specification, and it might
be desirable to rename some of the inputs/outputs to more intuitive names. Such
specifications are stored in YAML_ format, such as the ANTs registration conversion
specification,
.. code-block:: yaml
task_name: n4_bias_field_correction
nipype_name: N4BiasFieldCorrection
nipype_module: nipype.interfaces.ants.segmentation
inputs:
omit:
# list[str] - fields to omit from the Pydra interface
rename:
# dict[str, str] - fields to rename in the Pydra interface
types:
# dict[str, type] - override inferred types (use "mime-like" string for file-format types,
# e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
# from the nipype interface, but you may want to be more specific, particularly
# for file types, where specifying the format also specifies the file that will be
# passed to the field in the automatically generated unittests.
input_image: medimage/nifti1
mask_image: medimage/nifti1
weight_image: medimage/nifti1
bias_image: medimage/nifti1
metadata:
# dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)
outputs:
omit:
# list[str] - fields to omit from the Pydra interface
rename:
# dict[str, str] - fields to rename in the Pydra interface
types:
# dict[str, type] - override inferred types (use "mime-like" string for file-format types,
# e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
# from the nipype interface, but you may want to be more specific, particularly
# for file types, where specifying the format also specifies the file that will be
# passed to the field in the automatically generated unittests.
output_image: medimage/nifti1
bias_image: medimage/nifti1
callables:
# dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
# to set to the `callable` attribute of output fields
templates:
# dict[str, str] - `output_file_template` values to be provided to output fields
requirements:
# dict[str, list[str]] - input fields that are required to be provided for the output field to be present
*Detailed description of the different options to go here*
Installation
------------
*Nipype2Pydra* can be installed for Python >= 3.7 from PyPI with
.. code-block:: bash
$ python3 -m pip install nipype2pydra
License
-------
This work is licensed under a
`Creative Commons Attribution 4.0 International License <http://creativecommons.org/licenses/by/4.0/>`_
.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png
:target: http://creativecommons.org/licenses/by/4.0/
:alt: Creative Commons Attribution 4.0 International License
.. _Pydra: https://pydra.readthedocs.io
.. _Nipype: https://nipype.readthedocs.io/en/latest/
.. _YAML: https://yaml.org
Raw data
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"requires_python": ">=3.7",
"maintainer_email": "\"Thomas G. Close\" <tom.g.close@gmail.com>",
"keywords": "converters,data,nipype,pydra,workflows",
"author": "",
"author_email": "\"Thomas G. Close\" <tom.g.close@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/8a/fb/9c6f02cb6a2bcee33c6cef6b0ae3c160b9ef488cef90fda4242534f35f21/nipype2pydra-0.3.3.tar.gz",
"platform": null,
"description": "Nipype2Pydra\n============\n.. image:: https://github.com/nipype/nipype2pydra/actions/workflows/ci-cd.yml/badge.svg\n :target: https://github.com/nipype/nipype2pydra/actions/workflows/ci-cd.yml\n.. image:: https://codecov.io/gh/nipype/nipype2pydra/branch/main/graph/badge.svg?token=UIS0OGPST7\n :target: https://codecov.io/gh/nipype/nipype2pydra\n.. image:: https://img.shields.io/pypi/pyversions/nipype2pydra.svg\n :target: https://pypi.python.org/pypi/nipype2pydra/\n :alt: Supported Python versions\n.. image:: https://img.shields.io/pypi/v/nipype2pydra.svg\n :target: https://pypi.python.org/pypi/nipype2pydra/\n :alt: Latest Version\n\nNipype2Pydra is a command-line tool for semi-automatically porting command interfaces\nand workflows written from the Nipype_ workflow engine to its successor Pydra_. It has\nbeen designed so that any required manual-specifications are stored in separate YAML\nspecification files, which is read ahead of the conversion, so once designed the\nconversion can be re-run to pick up changes in newer versions of the Nipype_ code without\nhaving to redo the manual steps.\n\n\nBasic Usage\n-----------\n\nTo convert a Nipype_ interface to a Pydra_ task run the `nipype2pydra task` command and\npass it the conversion specification YAML file and the root of the package to save the\ngenerated module, e.g.::\n\n $ nipype2pydra task ants_registration_registration.yaml /path/to/package/root\n\nThis will create a module file under the package root directory based on the `output_module`\nfield in the specification, e.g::\n \n /path/to/package/root/output/module/path\n\nIf that is missing and the nipype interface is in the standard `nipype.interfaces`\npackage, then it will be stored at `pydra.tasks.` with the same path end.\n\nConversion Specifications\n-------------------------\n\nWhile the conversions aim to as automatic as possible, there are structural\ndifferences between Nipype_ and Pydra_ that require manual specification, and it might\nbe desirable to rename some of the inputs/outputs to more intuitive names. Such\nspecifications are stored in YAML_ format, such as the ANTs registration conversion\nspecification,\n\n.. code-block:: yaml\n\n task_name: n4_bias_field_correction\n nipype_name: N4BiasFieldCorrection\n nipype_module: nipype.interfaces.ants.segmentation\n inputs:\n omit:\n # list[str] - fields to omit from the Pydra interface\n rename:\n # dict[str, str] - fields to rename in the Pydra interface\n types:\n # dict[str, type] - override inferred types (use \"mime-like\" string for file-format types,\n # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred\n # from the nipype interface, but you may want to be more specific, particularly\n # for file types, where specifying the format also specifies the file that will be\n # passed to the field in the automatically generated unittests.\n input_image: medimage/nifti1\n mask_image: medimage/nifti1\n weight_image: medimage/nifti1\n bias_image: medimage/nifti1\n metadata:\n # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)\n outputs:\n omit:\n # list[str] - fields to omit from the Pydra interface\n rename:\n # dict[str, str] - fields to rename in the Pydra interface\n types:\n # dict[str, type] - override inferred types (use \"mime-like\" string for file-format types,\n # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred\n # from the nipype interface, but you may want to be more specific, particularly\n # for file types, where specifying the format also specifies the file that will be\n # passed to the field in the automatically generated unittests.\n output_image: medimage/nifti1\n bias_image: medimage/nifti1\n callables:\n # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`\n # to set to the `callable` attribute of output fields\n templates:\n # dict[str, str] - `output_file_template` values to be provided to output fields\n requirements:\n # dict[str, list[str]] - input fields that are required to be provided for the output field to be present\n\n*Detailed description of the different options to go here*\n\nInstallation\n------------\n\n*Nipype2Pydra* can be installed for Python >= 3.7 from PyPI with\n\n.. code-block:: bash\n\n $ python3 -m pip install nipype2pydra\n\n\nLicense\n-------\n\nThis work is licensed under a\n`Creative Commons Attribution 4.0 International License <http://creativecommons.org/licenses/by/4.0/>`_\n\n.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png\n :target: http://creativecommons.org/licenses/by/4.0/\n :alt: Creative Commons Attribution 4.0 International License\n\n.. _Pydra: https://pydra.readthedocs.io\n.. _Nipype: https://nipype.readthedocs.io/en/latest/\n.. _YAML: https://yaml.org\n",
"bugtrack_url": null,
"license": "Creative Commons Attribution 4.0 International Public License By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License (\"Public License\"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions. Section 1 \u2013 Definitions. Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image. Adapter's License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License. Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights. Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements. Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material. Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License. Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license. Licensor means the individual(s) or entity(ies) granting rights under this Public License. Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them. Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world. You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning. Section 2 \u2013 Scope. License grant. Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to: reproduce and Share the Licensed Material, in whole or in part; and produce, reproduce, and Share Adapted Material. Exceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions. Term. The term of this Public License is specified in Section 6(a). Media and formats; technical modifications allowed. The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material. Downstream recipients. Offer from the Licensor \u2013 Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License. No downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material. No endorsement. Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i). Other rights. Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise. Patent and trademark rights are not licensed under this Public License. To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties. Section 3 \u2013 License Conditions. Your exercise of the Licensed Rights is expressly made subject to the following conditions. Attribution. If You Share the Licensed Material (including in modified form), You must: retain the following if it is supplied by the Licensor with the Licensed Material: identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated); a copyright notice; a notice that refers to this Public License; a notice that refers to the disclaimer of warranties; a URI or hyperlink to the Licensed Material to the extent reasonably practicable; indicate if You modified the Licensed Material and retain an indication of any previous modifications; and indicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License. You may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information. If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable. If You Share Adapted Material You produce, the Adapter's License You apply must not prevent recipients of the Adapted Material from complying with this Public License. Section 4 \u2013 Sui Generis Database Rights. 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