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medvae

https://github.com/nmontanabrown/medvae

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.0%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: NMontanaBrown
  • License: other
  • Language: Python
  • Default Branch: main
  • Size: 77.1 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 3
  • Releases: 0
Created almost 4 years ago · Last pushed almost 4 years ago
Metadata Files
Readme Contributing License Citation

README.rst 

medVAE
===============================

.. image:: https://github.com/NMontanaBrown/medVAE/raw/master/project-icon.png
   :height: 128px
   :width: 128px
   :target: https://github.com/NMontanaBrown/medVAE
   :alt: Logo

.. image:: https://github.com/NMontanaBrown/medVAE/badges/master/build.svg
   :target: https://github.com/NMontanaBrown/medVAE/pipelines
   :alt: GitLab-CI test status

.. image:: https://github.com/NMontanaBrown/medVAE/badges/master/coverage.svg
    :target: https://github.com/NMontanaBrown/medVAE/commits/master
    :alt: Test coverage

.. image:: https://readthedocs.org/projects/medVAE/badge/?version=latest
    :target: http://medVAE.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status



Author: Nina Montana Brown

medVAE is part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.

medVAE is tested on Python 3.7 but should support other modern Python versions.

medVAE is currently a demo project, which will add/multiply two numbers. Example usage:

::

    python medvae.py 5 8
    python medvae.py 3 6 --multiply

Please explore the project structure, and implement your own functionality.

Developing
----------

Cloning
^^^^^^^

You can clone the repository using the following command:

::

    git clone https://github.com/NMontanaBrown/medVAE


Running tests
^^^^^^^^^^^^^
Pytest is used for running unit tests:
::

    pip install pytest
    python -m pytest


Linting
^^^^^^^

This code conforms to the PEP8 standard. Pylint can be used to analyse the code:

::

    pip install pylint
    pylint --rcfile=tests/pylintrc medvae


Installing
----------

You can pip install directly from the repository as follows:

::

    pip install git+https://github.com/NMontanaBrown/medVAE



Contributing
^^^^^^^^^^^^

Please see the `contributing guidelines`_.


Useful links
^^^^^^^^^^^^

* `Source code repository`_
* `Documentation`_


Licensing and copyright
-----------------------

Copyright 2022 University College London.
medVAE is released under the BSD-3 license. Please see the `license file`_ for details.


Acknowledgements
----------------

Supported by `Wellcome`_ and `EPSRC`_.


.. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss
.. _`source code repository`: https://github.com/NMontanaBrown/medVAE
.. _`Documentation`: https://medVAE.readthedocs.io
.. _`SciKit-Surgery`: https://github.com/SciKit-Surgery
.. _`University College London (UCL)`: http://www.ucl.ac.uk/
.. _`Wellcome`: https://wellcome.ac.uk/
.. _`EPSRC`: https://www.epsrc.ac.uk/
.. _`contributing guidelines`: https://github.com/NMontanaBrown/medVAE/blob/master/CONTRIBUTING.rst
.. _`license file`: https://github.com/NMontanaBrown/medVAE/blob/master/LICENSE

Owner

  • Name: Nina Montana-Brown
  • Login: NMontanaBrown
  • Kind: user
  • Location: London

PhD Student Medical Imaging @ UCL WEISS + CMIC || ML Engineer @ Verdure Imaging Inc. || she/they ||

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use any SciKit-Surgery packages in your research, please cite it as below."
authors:
- family-names: "Thompson"
  given-names: "Stephen"
  orcid: "https://orcid.org/0000-0001-7286-1326"
- family-names: "Dowrick"
  given-names: "Thomas"
  orcid: "https://orcid.org/0000-0002-2712-4447"
- family-names: "Ahmad"
  given-names: "Mian"
  orcid: "https://orcid.org/0000-0002-4706-4146"
- family-names: "Clarkson"
  given-names: "Matthew"
  orcid: "https://orcid.org/0000-0002-5565-1252"
title: "SciKit-Surgery"
url: "https://github.com/SciKit-Surgery/scikit-surgery"
preferred-citation:
  type: article
  authors:
  - family-names: "Thompson"
    given-names: "Stephen"
    orcid: "https://orcid.org/0000-0001-7286-1326"
  - family-names: "Dowrick"
    given-names: "Thomas"
    orcid: "https://orcid.org/0000-0002-2712-4447"
  - family-names: "Ahmad"
    given-names: "Mian"
    orcid: "https://orcid.org/0000-0002-4706-4146"
  - family-names: "Xiao"
    given-names: "Guofang"
  - family-names: "Koo"
    given-names: "Bongjin"
    orcid: "https://orcid.org/0000-0002-3611-4988"
  - family-names: "Bonmati"
    given-names: "Ester"
    orcid: "https://orcid.org/0000-0001-9217-5438"
  - family-names: "Kahl"
    given-names: "Kim"
  - family-names: "Clarkson"
    given-names: "Matthew"
    orcid: "https://orcid.org/0000-0002-5565-1252"
  doi: 10.1007/s11548-020-02180-5
  journal: "International journal of computer assisted radiology and surgery"
  start: 1075
  end: 1084
  title: "SciKit-Surgery: Compact Libraries for Surgical Navigation"
  volume: 15
  issue: 7
  year: 2020

GitHub Events

Total
Last Year

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 1
  • Total Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nina Montana-Brown n****5@u****k 1
Committer Domains (Top 20 + Academic)
ucl.ac.uk: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • NMontanaBrown (3)
Pull Request Authors
Top Labels
Issue Labels
enhancement (1) question (1)
Pull Request Labels

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/checkout master composite
  • actions/setup-python v1 composite
  • pypa/gh-action-pypi-publish master composite
requirements-dev.txt pypi
  • coverage * development
  • ipykernel * development
  • mock * development
  • nbsphinx * development
  • parameterized * development
  • pyfakefs * development
  • pyinstaller * development
  • pylint * development
  • pytest * development
  • sphinx * development
  • sphinx_rtd_theme * development
  • tox * development
requirements.txt pypi
  • numpy *
setup.py pypi
  • numpy *