diff --git a/.coveralls.yml b/.coveralls.yml index 481104f..b64db3a 100644 --- a/.coveralls.yml +++ b/.coveralls.yml @@ -1 +1 @@ -repo_token: i623ytjvC6uwYrSJOaHBNLb1UV5YVqZU8 +repo_token: rbBr2oClC1vCHYpXLqbBzr60ZvkEfUpyh diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..13cab5f --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,50 @@ +cff-version: 1.2.0 +message: "If you use this in software 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-SurgeryImage" +url: "https://github.com/SciKit-Surgery/scikit-surgeryimage" +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 diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index aa4ef30..02675b5 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.rst @@ -10,7 +10,7 @@ We welcome contributions to scikit-surgeryimage. Reporting bugs and feature requests ----------------------------------- -Please create a new issue on https://github.com/UCL/scikit-surgeryimage/issues +Please create a new issue on https://github.com/SciKit-Surgery/scikit-surgeryimage/issues When reporting a bug, please include: * The version of scikit-surgeryimage you are using @@ -25,12 +25,12 @@ Fixing bugs or implement features The easiest way to contribute is to follow these guidelines: -1. Look through the issues on https://github.com/UCL/scikit-surgeryimage/issues and assign the relevant issue to yourself. If there is not an existing issue that covers your work, please create one: https://github.com/UCL/scikit-surgeryimage/issues -2. Fork the repository: https://github.com/UCL/scikit-surgeryimage/fork +1. Look through the issues on https://github.com/SciKit-Surgery/scikit-surgeryimage/issues and assign the relevant issue to yourself. If there is not an existing issue that covers your work, please create one: https://github.com/SciKit-Surgery/scikit-surgeryimage/issues +2. Fork the repository: https://github.com/SciKit-Surgery/scikit-surgeryimage/fork 3. Create a branch for your changes. The branch name should start with the issue number, followed by hyphen separated words describing the issue. For example: 1-update-contribution-guidelines 4. Make your changes following the coding guidelines below. 5. Commit and push your changes to your fork. The commit message should start with `Issue #`, for example: "Issue #1: Fixed typo". Commit in small, related chunks. Review each commit and explain its purpose in the commit message. -6. Submit a merge request: https://github.com/UCL/scikit-surgeryimage/pulls +6. Submit a merge request: https://github.com/SciKit-Surgery/scikit-surgeryimage/pulls diff --git a/README.rst b/README.rst index 9d622b7..3b4344a 100644 --- a/README.rst +++ b/README.rst @@ -1,26 +1,39 @@ scikit-surgeryimage ==================== -.. image:: https://github.com/UCL/scikit-surgeryimage/raw/master/weiss_logo.png +.. image:: https://github.com/SciKit-Surgery/scikit-surgeryimage/raw/master/weiss_logo.png :height: 128px :width: 128px - :target: https://github.com/UCL/scikit-surgeryimage + :target: https://github.com/SciKit-Surgery/scikit-surgeryimage :alt: Logo | -.. image:: https://github.com/UCL/scikit-surgeryimage/workflows/.github/workflows/ci.yml/badge.svg - :target: https://github.com/UCL/scikit-surgeryimage/actions +.. image:: https://github.com/SciKit-Surgery/scikit-surgeryimage/workflows/.github/workflows/ci.yml/badge.svg + :target: https://github.com/SciKit-Surgery/scikit-surgeryimage/actions :alt: GitHub Actions CI status -.. image:: https://coveralls.io/repos/github/UCL/scikit-surgeryimage/badge.svg?branch=master&service=github - :target: https://coveralls.io/github/UCL/scikit-surgeryimage?branch=master +.. image:: https://coveralls.io/repos/github/SciKit-Surgery/scikit-surgeryimage/badge.svg?branch=master&service=github + :target: https://coveralls.io/github/SciKit-Surgery/scikit-surgeryimage?branch=master :alt: Test coverage .. image:: https://readthedocs.org/projects/scikit-surgeryimage/badge/?version=latest :target: http://scikit-surgeryimage.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status +.. image:: https://img.shields.io/badge/Cite-SciKit--Surgery-informational + :target: https://doi.org/10.1007/s11548-020-02180-5 + :alt: The SciKit-Surgery paper + +.. image:: https://img.shields.io/twitter/url?style=social&url=http%3A%2F%2Fscikit-surgery.org + :target: https://twitter.com/intent/tweet?screen_name=scikit_surgery&ref_src=twsrc%5Etfw + :alt: Get in touch via twitter + +.. image:: https://img.shields.io/twitter/follow/scikit_surgery?style=social + :target: https://twitter.com/scikit_surgery?ref_src=twsrc%5Etfw + :alt: Follow scikit_surgery on twitter + + scikit-surgeryimage is a python only project to implement image processing algorithms @@ -61,7 +74,7 @@ You can clone the repository using the following command: :: - git clone https://github.com/UCL/scikit-surgeryimage + git clone https://github.com/SciKit-Surgery/scikit-surgeryimage Running the tests @@ -105,11 +118,11 @@ 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/UCL/scikit-surgeryimage +.. _`source code repository`: https://github.com/SciKit-Surgery/scikit-surgeryimage .. _`Documentation`: https://scikit-surgeryimage.readthedocs.io .. _`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/UCL/scikit-surgeryimage/blob/master/CONTRIBUTING.rst -.. _`license file`: https://github.com/UCL/scikit-surgeryimage/blob/master/LICENSE -.. _`common issues`: https://github.com/UCL/scikit-surgery/wikis/Common-Issues +.. _`contributing guidelines`: https://github.com/SciKit-Surgery/scikit-surgeryimage/blob/master/CONTRIBUTING.rst +.. _`license file`: https://github.com/SciKit-Surgery/scikit-surgeryimage/blob/master/LICENSE +.. _`common issues`: https://github.com/SciKit-Surgery/scikit-surgery/wikis/Common-Issues diff --git a/docs/index.rst b/docs/index.rst index 633b871..b1d11aa 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -5,7 +5,7 @@ scikit-surgeryimage documentation :start-after: .. features-start :end-before: .. features-end -`Source code `_ is avaialble on GitHub. +`Source code `_ is avaialble on GitHub. .. toctree:: :maxdepth: 2 diff --git a/setup.py b/setup.py index 1f93530..5e2c6b7 100644 --- a/setup.py +++ b/setup.py @@ -17,7 +17,7 @@ description='scikit-surgeryimage implements image processing tools and alogrithms for Image Guided Surgery.', long_description=long_description, long_description_content_type='text/x-rst', - url='https://github.com/UCL/scikit-surgeryimage', + url='https://github.com/SciKit-Surgery/scikit-surgeryimage', author='Stephen Thompson', author_email='s.thompson@ucl.ac.uk', license='BSD-3 license', diff --git a/tox.ini b/tox.ini index 41a94c2..ee8ebfe 100644 --- a/tox.ini +++ b/tox.ini @@ -1,11 +1,13 @@ # content of: tox.ini , put in same dir as setup.py [tox] -envlist = py36,lint +envlist = py37,lint skipsdist = True +requires = setuptools >= 47.1 + [travis] python = - 3.6: py36, docs, lint + 3.7: py37, docs, lint [testenv] passenv = * @@ -13,22 +15,22 @@ deps=-rrequirements-dev.txt whitelist_externals=coverage,pip # See .coveragerc for list of omitted files commands = coverage erase - coverage run -a --source ./sksurgeryimage -m pytest + coverage run -a --source ./sksurgeryimage -m pytest -s coverage report -m [testenv:lint] -basepython=python3.6 +basepython=python3.7 deps=pylint {[testenv]deps} commands=pylint --rcfile=tests/pylintrc --extension-pkg-whitelist=cv2 sksurgeryimage [testenv:docs] -basepython=python3.6 -changedir = doc +basepython=python3.7 +changedir = docs commands = sphinx-build -M html . build [testenv:installer] -basepython=python3.6 +basepython=python3.7 commands=pyinstaller --onefile sksurgeryimage.py --noconfirm --windowed [testenv:pip2] @@ -39,7 +41,7 @@ commands = pip install {posargs} sksurgeryimage --help [testenv:pip3] -basepython=python3.6 +basepython=python3.7 changedir=pip_test skip_install=True commands = pip install {posargs}