| Name | fairly JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | None |
| Summary | A package to create, publish, and download research datasets |
| upload_time | 2024-04-29 15:54:02 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT License Copyright (c) 2022 JupyterFAIR Team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
data management
fairly
open science
research data
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
.. list-table::
:widths: 25 25
:header-rows: 1
* - `fair-software.nl <https://fair-software.nl>`_ recommendations
- Badges
* - \1. Code repository
- |GitHub Badge|
* - \2. License
- |License Badge|
* - \3. Community Registry
- |PyPI Badge|
* - \4. Enable Citation
- |Zenodo Badge|
* - **Other best practices**
-
* - Continuous integration
- |Python Build| |Python Publish|
* - Documentation
- |Documentation Status|
.. |GitHub Badge| image:: https://img.shields.io/github/v/release/ITC-CRIB/fairly
:target: https://github.com/ITC-CRIB/fairly
:alt: GitHub Badge
.. |License Badge| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
:alt: License Badge
.. |PyPI Badge| image:: https://img.shields.io/pypi/v/fairly?colorB=blue
:target: https://pypi.org/project/fairly/
:alt: PyPI Badge
.. |Zenodo Badge| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7759648.svg
:target: https://doi.org/10.5281/zenodo.7759648
:alt: Zenodo Badge
.. |Python Build| image:: https://img.shields.io/github/actions/workflow/status/ITC-CRIB/fairly/test_workflow.yaml
:target: https://github.com/ITC-CRIB/fairly/actions/workflows/test_workflow.yaml
:alt: Python Build
.. |Python Publish| image:: https://img.shields.io/github/actions/workflow/status/ITC-CRIB/fairly/publish.yaml
:target: https://github.com/ITC-CRIB/fairly/actions/workflows/publish.yaml
:alt: Python Publish
.. |Documentation Status| image:: https://readthedocs.org/projects/fairly/badge/?version=latest
:target: https://fairly.readthedocs.io/en/latest/
:alt: Documentation Status
fairly
======
A package to create, publish and clone research datasets.
|License: MIT|
Installation
------------
*fairly* requires Python 3.8 or later, and `ruamel.yaml` version *0.17.26* or later. It can be installed directly
using pip.
.. code:: shell
pip install fairly
Installing from source
~~~~~~~~~~~~~~~~~~~~~~
1. Clone or download the `source
code <https://github.com/ITC-CRIB/fairly>`__:
.. code:: shell
git clone https://github.com/ITC-CRIB/fairly.git
2. Go to the root directory:
.. code:: shell
cd fairly/
3. Compile and install using pip:
.. code:: shell
pip install .
Usage
-----
Basic example to create a local research dataset and deposit it to a
repository:
.. code:: python
import fairly
# Initialize a local dataset
dataset = fairly.init_dataset('/path/dataset')
# Set metadata
dataset.metadata['license'] = 'MIT'
dataset.set_metadata(
title='My dataset',
keywords=['FAIR', 'research', 'data'],
authors=[
'0000-0002-0156-185X',
{'name': 'John', 'surname': 'Doe'}
]
)
# Add data files
dataset.includes.extend([
'README.txt',
'*.csv',
'train/*.jpg'
])
# Save dataset
dataset.save()
# Upload to a data repository
remote_dataset = dataset.upload('zenodo')
Basic example to access a remote dataset and store it locally:
.. code:: python
import fairly
# Open a remote dataset
dataset = fairly.dataset('doi:10.4121/21588096.v1')
# Get dataset information
dataset.id
>>> {'id': '21588096', 'version': '1'}
dataset.url
>>> 'https://data.4tu.nl/articles/dataset/.../21588096/1'
dataset.size
>>> 33339
len(dataset.files)
>>> 6
dataset.metadata
>>> Metadata({'keywords': ['Earthquakes', 'precursor', ...], ...})
# Update metadata
dataset.metadata['keywords'] = ['Landslides', 'precursor']
dataset.save_metadata()
# Store dataset to a local directory (i.e. clone dataset)
local_dataset = dataset.store('/path/dataset')
Currently, the package supports the following research data management
platforms:
- `Invenio <https://inveniosoftware.org/>`__
- `Figshare <https://figshare.com/>`__
- `Djehuty <https://github.com/4TUResearchData/djehuty/>`__
(experimental)
All research data repositories based on the listed platforms are
supported.
For more details and examples, consult the `package
documentation <https://fairly.readthedocs.io/en/latest/>`__.
Testing
-------
Unit tests can be run by using ``pytest`` command in the root directory.
Contributions
-------------
Read the `guidelines <CONTRIBUTING.md>`__ to know how you can be part of
this open source project.
JupyterLab Extension
--------------------
An extension for JupyerLab is being developed in a `different
repository. <https://github.com/ITC-CRIB/jupyter-fairly>`__
Citation
--------
Please cite this software using as follows:
*Girgin, S., Garcia Alvarez, M., & Urra Llanusa, J., fairly: a package
to create, publish and clone research datasets [Computer software]*
Acknowledgements
----------------
This research is funded by the `Dutch Research Council (NWO) Open
Science
Fund <https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/>`__,
File No. 203.001.114.
Project members:
- `Center of Expertise in Big Geodata Science, University of Twente,
Faculty ITC <https://itc.nl/big-geodata/>`__
- `Digital Competence Centre, TU Delft <https://dcc.tudelft.nl/>`__
- `4TU.ResearchData <https://data.4tu.nl/>`__
.. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
Raw data
{
"_id": null,
"home_page": null,
"name": "fairly",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "data management, fairly, open science, research data",
"author": null,
"author_email": "Serkan Girgin <s.girgin@utwente.nl>, Manuel Garcia Alvarez <m.g.garciaalvarez@tudelft.nl>, Jose Urra Llanusa <j.c.urrallanusa@tudelft.nl>",
"download_url": "https://files.pythonhosted.org/packages/88/ff/80fd1046a8ed3fd2cdfdee42ea427e29cdc8ed5fb361b37c59f486824b53/fairly-1.0.1.tar.gz",
"platform": null,
"description": ".. list-table::\n :widths: 25 25\n :header-rows: 1\n\n * - `fair-software.nl <https://fair-software.nl>`_ recommendations\n - Badges\n * - \\1. Code repository\n - |GitHub Badge|\n * - \\2. License\n - |License Badge|\n * - \\3. Community Registry\n - |PyPI Badge|\n * - \\4. Enable Citation\n - |Zenodo Badge|\n * - **Other best practices**\n -\n * - Continuous integration\n - |Python Build| |Python Publish|\n * - Documentation\n - |Documentation Status|\n\n.. |GitHub Badge| image:: https://img.shields.io/github/v/release/ITC-CRIB/fairly\n :target: https://github.com/ITC-CRIB/fairly\n :alt: GitHub Badge\n\n.. |License Badge| image:: https://img.shields.io/badge/License-MIT-yellow.svg\n :target: https://opensource.org/licenses/MIT\n :alt: License Badge\n\n.. |PyPI Badge| image:: https://img.shields.io/pypi/v/fairly?colorB=blue\n :target: https://pypi.org/project/fairly/\n :alt: PyPI Badge\n\n.. |Zenodo Badge| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7759648.svg\n :target: https://doi.org/10.5281/zenodo.7759648\n :alt: Zenodo Badge\n\n.. |Python Build| image:: https://img.shields.io/github/actions/workflow/status/ITC-CRIB/fairly/test_workflow.yaml\n :target: https://github.com/ITC-CRIB/fairly/actions/workflows/test_workflow.yaml\n :alt: Python Build\n\n.. |Python Publish| image:: https://img.shields.io/github/actions/workflow/status/ITC-CRIB/fairly/publish.yaml\n :target: https://github.com/ITC-CRIB/fairly/actions/workflows/publish.yaml\n :alt: Python Publish\n\n.. |Documentation Status| image:: https://readthedocs.org/projects/fairly/badge/?version=latest\n :target: https://fairly.readthedocs.io/en/latest/\n :alt: Documentation Status\n\n\nfairly\n======\n\nA package to create, publish and clone research datasets.\n\n|License: MIT|\n\nInstallation\n------------\n\n*fairly* requires Python 3.8 or later, and `ruamel.yaml` version *0.17.26* or later. It can be installed directly\nusing pip.\n\n.. code:: shell\n\n pip install fairly\n\nInstalling from source\n~~~~~~~~~~~~~~~~~~~~~~\n\n1. Clone or download the `source\n code <https://github.com/ITC-CRIB/fairly>`__:\n\n .. code:: shell\n\n git clone https://github.com/ITC-CRIB/fairly.git\n\n2. Go to the root directory:\n\n .. code:: shell\n\n cd fairly/\n\n3. Compile and install using pip:\n\n .. code:: shell\n\n pip install .\n\nUsage\n-----\n\nBasic example to create a local research dataset and deposit it to a\nrepository:\n\n.. code:: python\n\n import fairly\n\n # Initialize a local dataset\n dataset = fairly.init_dataset('/path/dataset')\n\n # Set metadata\n dataset.metadata['license'] = 'MIT'\n dataset.set_metadata(\n title='My dataset',\n keywords=['FAIR', 'research', 'data'],\n authors=[\n '0000-0002-0156-185X',\n {'name': 'John', 'surname': 'Doe'}\n ]\n )\n\n # Add data files\n dataset.includes.extend([\n 'README.txt',\n '*.csv',\n 'train/*.jpg'\n ])\n\n # Save dataset\n dataset.save()\n\n # Upload to a data repository\n remote_dataset = dataset.upload('zenodo')\n\nBasic example to access a remote dataset and store it locally:\n\n.. code:: python\n\n import fairly\n\n # Open a remote dataset\n dataset = fairly.dataset('doi:10.4121/21588096.v1')\n\n # Get dataset information\n dataset.id\n >>> {'id': '21588096', 'version': '1'}\n\n dataset.url\n >>> 'https://data.4tu.nl/articles/dataset/.../21588096/1'\n\n dataset.size\n >>> 33339\n\n len(dataset.files)\n >>> 6\n\n dataset.metadata\n >>> Metadata({'keywords': ['Earthquakes', 'precursor', ...], ...})\n\n # Update metadata\n dataset.metadata['keywords'] = ['Landslides', 'precursor']\n dataset.save_metadata()\n\n # Store dataset to a local directory (i.e. clone dataset)\n local_dataset = dataset.store('/path/dataset')\n\nCurrently, the package supports the following research data management\nplatforms:\n\n- `Invenio <https://inveniosoftware.org/>`__\n- `Figshare <https://figshare.com/>`__\n- `Djehuty <https://github.com/4TUResearchData/djehuty/>`__\n (experimental)\n\nAll research data repositories based on the listed platforms are\nsupported.\n\nFor more details and examples, consult the `package\ndocumentation <https://fairly.readthedocs.io/en/latest/>`__.\n\nTesting\n-------\n\nUnit tests can be run by using ``pytest`` command in the root directory.\n\nContributions\n-------------\n\nRead the `guidelines <CONTRIBUTING.md>`__ to know how you can be part of\nthis open source project.\n\nJupyterLab Extension\n--------------------\n\nAn extension for JupyerLab is being developed in a `different\nrepository. <https://github.com/ITC-CRIB/jupyter-fairly>`__\n\nCitation\n--------\n\nPlease cite this software using as follows:\n\n*Girgin, S., Garcia Alvarez, M., & Urra Llanusa, J., fairly: a package\nto create, publish and clone research datasets [Computer software]*\n\nAcknowledgements\n----------------\n\nThis research is funded by the `Dutch Research Council (NWO) Open\nScience\nFund <https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/>`__,\nFile No.\u00a0203.001.114.\n\nProject members:\n\n- `Center of Expertise in Big Geodata Science, University of Twente,\n Faculty ITC <https://itc.nl/big-geodata/>`__\n- `Digital Competence Centre, TU Delft <https://dcc.tudelft.nl/>`__\n- `4TU.ResearchData <https://data.4tu.nl/>`__\n\n.. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg\n :target: https://opensource.org/licenses/MIT\n",
"bugtrack_url": null,
"license": "MIT License Copyright (c) 2022 JupyterFAIR Team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.",
"summary": "A package to create, publish, and download research datasets",
"version": "1.0.1",
"project_urls": {
"Bug Tracker": "https://github.com/ITC-CRIB/fairly/issues",
"Documentation": "https://fairly.readthedocs.io",
"Funding": "https://nwo.nl/en/researchprogrammes/open-science/open-science-fund",
"Homepage": "https://github.com/ITC-CRIB/fairly"
},
"split_keywords": [
"data management",
" fairly",
" open science",
" research data"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "a31bbaf1aacd625ee121594879cdc995fcc9c090b4b79e5ae247746bd9695798",
"md5": "c2a53acd14dd940cc8df62f2ed3bf42a",
"sha256": "242787daaa5c95842823dfdbdf2243ef1e86a15eec343b89e5e36d8a0f220de6"
},
"downloads": -1,
"filename": "fairly-1.0.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "c2a53acd14dd940cc8df62f2ed3bf42a",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 246344,
"upload_time": "2024-04-29T15:54:00",
"upload_time_iso_8601": "2024-04-29T15:54:00.503706Z",
"url": "https://files.pythonhosted.org/packages/a3/1b/baf1aacd625ee121594879cdc995fcc9c090b4b79e5ae247746bd9695798/fairly-1.0.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "88ff80fd1046a8ed3fd2cdfdee42ea427e29cdc8ed5fb361b37c59f486824b53",
"md5": "0e623c8eedef091650cca865aaa2ac4e",
"sha256": "d93b187f72215a059774134fcf862d51f9f5da687e8f058d208c1d87aa330e05"
},
"downloads": -1,
"filename": "fairly-1.0.1.tar.gz",
"has_sig": false,
"md5_digest": "0e623c8eedef091650cca865aaa2ac4e",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 1512443,
"upload_time": "2024-04-29T15:54:02",
"upload_time_iso_8601": "2024-04-29T15:54:02.623480Z",
"url": "https://files.pythonhosted.org/packages/88/ff/80fd1046a8ed3fd2cdfdee42ea427e29cdc8ed5fb361b37c59f486824b53/fairly-1.0.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-04-29 15:54:02",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "ITC-CRIB",
"github_project": "fairly",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "fairly"
}
