.. image:: https://img.shields.io/pypi/v/scipion-pyworkflow.svg
:target: https://pypi.python.org/pypi/scipion-pyworkflow
:alt: PyPI release
.. image:: https://sonarcloud.io/api/project_badges/measure?project=scipion-em_scipion-pyworkflow&metric=alert_status
:alt: Quality Gate Status
:target: https://sonarcloud.io/summary/new_code?id=scipion-em_scipion-pyworkflow
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-pyworkflow?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-pyworkflow
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/l/scipion-pyworkflow.svg
:target: https://pypi.python.org/pypi/scipion-pyworkflow
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-pyworkflow.svg
:target: https://pypi.python.org/pypi/scipion-pyworkflow
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/dm/scipion-pyworkflow
:target: https://pypi.python.org/pypi/scipion-pyworkflow
:alt: Downloads
.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
:alt: Contributor Covenant
:target: https://www.contributor-covenant.org/version/2/0/code_of_conduct/
pyworkflow
==========
**pyworkflow** is a simple workflow platform used in scientific applications. It has been initially developed
within the Scipion framework for image processing in Electron Microscopy.
**pyworkflow** allows you to define a working *Domain* by defining the following group of classes:
* Objects: input/outputs that will be generated by different programs
* Protocols: special type of Objects that have defined input parameters and will produce some output
* Viewers: Entities that provide graphical analysis of results.
* Wizards: Small GUIs that can be develop to help users to select given parameter values.
Development
-----------
To install **pyworkflow** for development purposes, one can do:
.. code-block:: bash
# Create a clean virtual environment
conda create -n scipion python=3.8
conda activate
git clone https://github.com/scipion-em/scipion-pyworkflow.git
cd scipion-pyworkflow
pip install -e .
Running tests
-------------
.. code-block:: bash
conda activate scipion
cd scipion-pyworkflow
export SCIPION_DOMAIN="pyworkflowtests/tests/mock_domain"
python -m unittest discover
# Simple project GUI can be shown after running tests:
python pyworkflow/apps/pw_project.py TestProtocolOutputs
All test projects are located in ~/ScipionUserData/Tests/
API documentation
-----------------
https://scipion-em.github.io/docs/release-3.0.0/api/pyworkflow/pyworkflow.html
Raw data
{
"_id": null,
"home_page": "https://github.com/scipion-em/scipion-pyworkflow",
"name": "scipion-pyworkflow",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": "workflows science electron-microscopy cryo-em structural-biology image-processing scipion",
"author": "J.M. De la Rosa Trevin, Roberto Marabini, Grigory Sharov, Josue Gomez Blanco, Pablo Conesa, Yunior Fonseca Reyna",
"author_email": "delarosatrevin@scilifelab.se, roberto@cnb.csic.es, gsharov@mrc-lmb.cam.ac.uk, josue.gomez-blanco@mcgill.ca, pconesa@cnb.csic.es, fonsecareyna@cnb.csic.es",
"download_url": "https://files.pythonhosted.org/packages/0d/d3/a0aa50aa16ee771eda5b2c8faf5ecec40ba692b83f5cc6d8f30920055ea8/scipion_pyworkflow-3.10.5.tar.gz",
"platform": null,
"description": ".. image:: https://img.shields.io/pypi/v/scipion-pyworkflow.svg\n :target: https://pypi.python.org/pypi/scipion-pyworkflow\n :alt: PyPI release\n\n.. image:: https://sonarcloud.io/api/project_badges/measure?project=scipion-em_scipion-pyworkflow&metric=alert_status\n :alt: Quality Gate Status\n :target: https://sonarcloud.io/summary/new_code?id=scipion-em_scipion-pyworkflow\n\n.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-pyworkflow?server=https%3A%2F%2Fsonarcloud.io\n :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-pyworkflow\n :alt: SonarCloud quality gate\n\n.. image:: https://img.shields.io/pypi/l/scipion-pyworkflow.svg\n :target: https://pypi.python.org/pypi/scipion-pyworkflow\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-pyworkflow.svg\n :target: https://pypi.python.org/pypi/scipion-pyworkflow\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/pypi/dm/scipion-pyworkflow\n :target: https://pypi.python.org/pypi/scipion-pyworkflow\n :alt: Downloads\n\n.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg\n :alt: Contributor Covenant\n :target: https://www.contributor-covenant.org/version/2/0/code_of_conduct/\n\npyworkflow\n==========\n\n**pyworkflow** is a simple workflow platform used in scientific applications. It has been initially developed\nwithin the Scipion framework for image processing in Electron Microscopy.\n \n**pyworkflow** allows you to define a working *Domain* by defining the following group of classes:\n\n * Objects: input/outputs that will be generated by different programs\n * Protocols: special type of Objects that have defined input parameters and will produce some output\n * Viewers: Entities that provide graphical analysis of results.\n * Wizards: Small GUIs that can be develop to help users to select given parameter values.\n\nDevelopment\n-----------\n\nTo install **pyworkflow** for development purposes, one can do:\n\n.. code-block:: bash\n\n # Create a clean virtual environment\n conda create -n scipion python=3.8\n conda activate\n git clone https://github.com/scipion-em/scipion-pyworkflow.git\n cd scipion-pyworkflow\n pip install -e .\n\nRunning tests\n-------------\n\n.. code-block:: bash\n\n conda activate scipion\n cd scipion-pyworkflow\n export SCIPION_DOMAIN=\"pyworkflowtests/tests/mock_domain\"\n python -m unittest discover\n\n # Simple project GUI can be shown after running tests:\n python pyworkflow/apps/pw_project.py TestProtocolOutputs\n\nAll test projects are located in ~/ScipionUserData/Tests/\n\nAPI documentation\n-----------------\n\nhttps://scipion-em.github.io/docs/release-3.0.0/api/pyworkflow/pyworkflow.html\n",
"bugtrack_url": null,
"license": null,
"summary": "Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.",
"version": "3.10.5",
"project_urls": {
"Bug Reports": "https://github.com/scipion-em/scipion-pyworkflow/issues",
"Homepage": "https://github.com/scipion-em/scipion-pyworkflow",
"Source": "https://github.com/scipion-em/scipion-pyworkflow/"
},
"split_keywords": [
"workflows",
"science",
"electron-microscopy",
"cryo-em",
"structural-biology",
"image-processing",
"scipion"
],
"urls": [
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "b29971416a813a41e26c2663a80dabec2c70063e64d2fcbdda7389eb32c2f27a",
"md5": "c47811b1c9e0e70eef9a829abb1cc8a4",
"sha256": "f64a5294905a5d3e8a70bf13e5d0bf178908fd8414c1b3accd139cedf451e2ee"
},
"downloads": -1,
"filename": "scipion_pyworkflow-3.10.5-py3-none-any.whl",
"has_sig": false,
"md5_digest": "c47811b1c9e0e70eef9a829abb1cc8a4",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 835706,
"upload_time": "2024-11-13T10:37:33",
"upload_time_iso_8601": "2024-11-13T10:37:33.836113Z",
"url": "https://files.pythonhosted.org/packages/b2/99/71416a813a41e26c2663a80dabec2c70063e64d2fcbdda7389eb32c2f27a/scipion_pyworkflow-3.10.5-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "0dd3a0aa50aa16ee771eda5b2c8faf5ecec40ba692b83f5cc6d8f30920055ea8",
"md5": "f723ba42d8fec6fee1045db5a8875dac",
"sha256": "2628fc3bcab78c973b0917ead6f99dbc8f22acd8ea5c5181c372deaa80dd7359"
},
"downloads": -1,
"filename": "scipion_pyworkflow-3.10.5.tar.gz",
"has_sig": false,
"md5_digest": "f723ba42d8fec6fee1045db5a8875dac",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 1055573,
"upload_time": "2024-11-13T10:37:35",
"upload_time_iso_8601": "2024-11-13T10:37:35.343807Z",
"url": "https://files.pythonhosted.org/packages/0d/d3/a0aa50aa16ee771eda5b2c8faf5ecec40ba692b83f5cc6d8f30920055ea8/scipion_pyworkflow-3.10.5.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-11-13 10:37:35",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "scipion-em",
"github_project": "scipion-pyworkflow",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "scipion-pyworkflow"
}
JSON
