Merge pull request #29 from SciKit-Surgery/28-movetosks

28 movetosks

.github/workflows/ci.yml

@@ -9,22 +9,19 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-ver: [3.6, 3.7]
+        python-ver: [3.7, 3.8]
         experimental: [false]
         exclude:
           - os: macos-latest
             python-ver: 3.6
         include:
-          - os: macos-latest
-            python-ver: 3.6
-            experimental: true
-          - python-ver: 3.8
+          - python-ver: 3.9
             os: ubuntu-latest
             experimental: true
-          - python-ver: 3.8
+          - python-ver: 3.9
             os: windows-latest
             experimental: true
-          - python-ver: 3.8
+          - python-ver: 3.9
             os: macos-latest
             experimental: true
 

CITATION.cff

@@ -0,0 +1,41 @@
+cff-version: 1.2.0
+message: "If you use SciKit-Surgery Tutorial01 in your research, please cite it as below."
+authors:
+- family-names: "Thompson"
+  given-names: "Stephen"
+  orcid: "https://orcid.org/0000-0001-7286-1326"
+title: "SciKit-SurgeryTutorial01"
+url: "https://github.com/SciKit-Surgery/scikit-surgerytutorial01"
+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

CODE_OF_CONDUCT.md

@@ -0,0 +1,134 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
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+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+<s.thompson@ucl.ac.uk>.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

CONTRIBUTING.rst

@@ -10,7 +10,7 @@ We welcome contributions to SciKit-SurgeryTutorial01.
 Reporting bugs and feature requests
 -----------------------------------
 
-Please create a new issue on https://github.com/UCL/SciKit-SurgeryTutorial01/issues/new
+Please create a new issue on https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/issues/new
 
 When reporting a bug, please include:
 * The version of SciKit-SurgeryTutorial01 you are using
@@ -23,13 +23,13 @@ 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-SurgeryTutorial01/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-SurgeryTutorial01/issues/new
+1. Look through the issues on https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/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-SurgeryTutorial01/issues/
 2. Read the design considerations below.
-3. Fork the repository: https://github.com/UCL/SciKit-SurgeryTutorial01/forks/new
+3. Fork the repository: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/forks/
 4. 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
 5. Make your changes following the coding guidelines below.
 6. 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.
-7. Submit a merge request: https://github.com/UCL/SciKit-SurgeryTutorial01/merge_requests/new
+7. Submit a pull request: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/pulls
 
 Design Considerations
 ---------------------

README.rst

@@ -1,10 +1,10 @@
 SciKit-Surgery Augmented Reality Tutorial
 =========================================
 
-.. image:: https://github.com/UCL/scikit-surgerytutorial01/raw/master/project-icon.gif
+.. image:: https://github.com/SciKit-Surgery/scikit-surgerytutorial01/raw/master/project-icon.gif
    :height: 128px
    :width: 128px
-   :target: https://github.com/UCL/scikit-surgeryturorial01
+   :target: https://github.com/SciKit-Surgery/scikit-surgeryturorial01
    :alt: Logo
 
 |
@@ -17,10 +17,17 @@ SciKit-Surgery Augmented Reality Tutorial
    :target: https://doi.org/10.1007/s11548-020-02180-5
    :alt: The SciKit-Surgery paper
 
+.. image:: https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg
+   :target: CODE_OF_CONDUCT.md
+
 .. image:: https://img.shields.io/badge/MICCAI%20Educational%20Challenge-Finalist-yellow
    :target: https://miccai-sb.github.io/materials.html#mec2019
    :alt: Finalist in 2019 MICCAI Educational Challenge
 
+.. 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
+
 Author: Stephen Thompson
 
 This is the SciKit-Surgery Augmented Reality Tutorial. It will teach you how to write an augmented reality application, showing a rendered model on top of a live video feed.
@@ -50,7 +57,7 @@ You can clone the repository using the following command:
 
 ::
 
-    git clone https://github.com/UCL/SciKit-SurgeryTutorial01
+    git clone https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01
 
 
 Contributing
@@ -80,12 +87,12 @@ 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-SurgeryTutorial01
+.. _`source code repository`: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01
 .. _`Documentation`: https://SciKit-SurgeryTutorial01.readthedocs.io
-.. _`SciKit-Surgery`: https://github.com/UCL/scikit-surgery/wiki
+.. _`SciKit-Surgery`: https://github.com/SciKit-Surgery/scikit-surgery/wiki
 .. _`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-SurgeryTutorial01/blob/master/CONTRIBUTING.rst
-.. _`license file`: https://github.com/UCL/SciKit-SurgeryTutorial01/blob/master/LICENSE
+.. _`contributing guidelines`: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/blob/master/CONTRIBUTING.rst
+.. _`license file`: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/blob/master/LICENSE
 

doc/00_Introduction.rst

@@ -30,7 +30,7 @@ unseen anatomy can be overlaid on the surgical scene, to help the surgeon
 find anatomy of interest. The example below is from the `SmartLiver`_ system, 
 developed using the `NifTK`_ platform.
 
-.. figure:: https://github.com/UCL/SciKit-SurgeryTutorial01/raw/master/doc/croppedOverlayVideo.gif
+.. figure:: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/raw/master/doc/croppedOverlayVideo.gif
 
 Making an augmented reality application from scratch can be quite complicated.
 The developer will require an

doc/01_VTK_Overlay_App.rst

@@ -9,7 +9,7 @@ Making a simple model overlay application
 In the first instance, let's just get a 3D rendering
 of a model, overlaid on live video from your webcam, something like this ...
 
-.. figure:: https://github.com/UCL/SciKit-SurgeryTutorial01/raw/master/doc/vtk_overlay_example.gif
+.. figure:: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/raw/master/doc/vtk_overlay_example.gif
 
 00 - Simple overlay application
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -99,5 +99,5 @@ for each frame update.
 .. _`OpenCV` : https://pypi.org/project/opencv-contrib-python
 .. _`VTK` : https://pypi.org/project/vtk
 .. _`OverlayBaseApp` : https://scikit-surgeryutils.readthedocs.io/en/latest/sksurgeryutils.common_overlay_apps.html#module-sksurgeryutils.common_overlay_apps.OverlayBaseApp
-.. _`finished example` : https://github.com/UCL/SciKit-SurgeryTutorial01/blob/master/sksurgerytutorial01/vtkoverlay_app.py
-.. _`project repository` : https://github.com/UCL/SciKit-SurgeryTutorial01/blob/master/models
+.. _`finished example` : https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/blob/master/sksurgerytutorial01/vtkoverlay_app.py
+.. _`project repository` : https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/blob/master/models

doc/02_VTK_Overlay_With_Movement.rst

@@ -11,7 +11,7 @@ the position of model elements. Here we add a few lines of code to
 our update function to make the overlaid model move. You should end up 
 with something like this ...
 
-.. figure:: https://github.com/UCL/SciKit-SurgeryTutorial01/raw/master/doc/vtk_overlay_with_movement_example.gif
+.. figure:: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/raw/master/doc/vtk_overlay_with_movement_example.gif
 
 
 01 - Add some movement to the models
@@ -74,4 +74,4 @@ Next we will add some code to detect an ArUco marker and "pin" the model to it
 .. _`OpenCV` : https://pypi.org/project/opencv-contrib-python
 .. _`VTK` : https://pypi.org/project/vtk
 .. _`OverlayBaseApp` : https://scikit-surgeryutils.readthedocs.io/en/latest/sksurgeryutils.common_overlay_apps.html#module-sksurgeryutils.common_overlay_apps.OverlayBaseApp
-.. _`finished example` : https://github.com/UCL/SciKit-SurgeryTutorial01/blob/master/sksurgerytutorial01/vtkoverlay_with_movement_app.py
+.. _`finished example` : https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/blob/master/sksurgerytutorial01/vtkoverlay_with_movement_app.py

doc/03_VTK_Overlay_With_Aruco_Tag.rst

@@ -16,7 +16,7 @@ uses computer vision to track a tag.
 We should end up with a 3D rendering that follows a tag as you move
 it in front of the camera. Something like ...
 
-.. figure:: https://github.com/UCL/SciKit-SurgeryTutorial01/raw/master/doc/vtk_overlay_aruco_example.gif
+.. figure:: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/raw/master/doc/vtk_overlay_aruco_example.gif
 
 02 - Add a feature detector and follower
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -175,11 +175,11 @@ You can download a
 You can also download the completed tutorial, either using git;
 ::
 
-  git clone https://github.com/UCL/SciKit-SurgeryTutorial01
+  git clone https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01
 
 or by downloading the files directly from
 
-https://github.com/UCL/SciKit-SurgeryTutorial01
+https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01
 
 That completes this tutorial. Please get in touch with any feedback or issues. You can
 use the issue tracker at the `Project homepage`_.
@@ -191,7 +191,7 @@ use the issue tracker at the `Project homepage`_.
 .. _`OpenCV` : https://pypi.org/project/opencv-contrib-python
 .. _`VTK` : https://pypi.org/project/vtk
 .. _`OverlayBaseApp` : https://scikit-surgeryutils.readthedocs.io/en/latest/sksurgeryutils.common_overlay_apps.html#module-sksurgeryutils.common_overlay_apps.OverlayBaseApp
-.. _`finished example` : https://github.com/UCL/SciKit-SurgeryTutorial01/blob/master/sksurgerytutorial01/vtk_aruco_app.py
+.. _`finished example` : https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/blob/master/sksurgerytutorial01/vtk_aruco_app.py
 .. _`OpenCV ArUco tutorial` : https://docs.opencv.org/3.4/d5/dae/tutorial_aruco_detection.html
-.. _`Project homepage` : https://github.com/UCL/SciKit-SurgeryTutorial01
-.. _`this one`: https://github.com/UCL/SciKit-SurgeryTutorial01/blob/master/tags/tag_sheet_sksurgery01.pdf
+.. _`Project homepage` : https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01
+.. _`this one`: https://github.com/SciKit-Surgery/SciKit-SurgeryTutorial01/blob/master/tags/tag_sheet_sksurgery01.pdf