Merge pull request #105 from SciKit-Surgery/103-scikitorg

103 scikitorg

.coveralls.yml

@@ -1 +1 @@
-repo_token: i623ytjvC6uwYrSJOaHBNLb1UV5YVqZU8
+repo_token: rbBr2oClC1vCHYpXLqbBzr60ZvkEfUpyh

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

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 #<issue number>`, 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
 
 
 

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

docs/index.rst

@@ -5,7 +5,7 @@ scikit-surgeryimage documentation
    :start-after: .. features-start
    :end-before: .. features-end
 
-`Source code <https://github.com/UCL/scikit-surgeryimage/>`_ is avaialble on GitHub.
+`Source code <https://github.com/SciKit-Surgery/scikit-surgeryimage/>`_ is avaialble on GitHub.
 
 .. toctree::
    :maxdepth: 2

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',

tox.ini

@@ -1,34 +1,36 @@
 # 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 = *
 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}