From 428e46969ba50ee749e5b7f9e2f9c0ab31141e44 Mon Sep 17 00:00:00 2001 From: Stephen Thompson Date: Wed, 23 Feb 2022 17:22:59 +0000 Subject: [PATCH 1/3] Issue #28 updated links --- CODE_OF_CONDUCT.md | 134 +++++++++++++++++++++++++++++++++++++++++++++ CONTRIBUTING.rst | 8 +-- README.rst | 21 ++++--- 3 files changed, 152 insertions(+), 11 deletions(-) create mode 100644 CODE_OF_CONDUCT.md diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..d947787 --- /dev/null +++ b/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 +* Publishing others' private information, such as a physical or email address, + 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 +. +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 + diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index 5026d9b..e745644 100644 --- a/CONTRIBUTING.rst +++ b/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 #`, 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 --------------------- diff --git a/README.rst b/README.rst index 025e2ab..f249a86 100644 --- a/README.rst +++ b/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 From 42fded2bde6f0cd26ae869407b76dac90234f2e6 Mon Sep 17 00:00:00 2001 From: Stephen Thompson Date: Wed, 23 Feb 2022 17:29:12 +0000 Subject: [PATCH 2/3] Issue #28 updated more links, added citation file --- CITATION.cff | 41 +++++++++++++++++++++++++++ doc/00_Introduction.rst | 2 +- doc/01_VTK_Overlay_App.rst | 6 ++-- doc/02_VTK_Overlay_With_Movement.rst | 4 +-- doc/03_VTK_Overlay_With_Aruco_Tag.rst | 12 ++++---- 5 files changed, 53 insertions(+), 12 deletions(-) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..23281ba --- /dev/null +++ b/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 diff --git a/doc/00_Introduction.rst b/doc/00_Introduction.rst index fbf3534..5ca034a 100644 --- a/doc/00_Introduction.rst +++ b/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 diff --git a/doc/01_VTK_Overlay_App.rst b/doc/01_VTK_Overlay_App.rst index fe3d319..664b264 100644 --- a/doc/01_VTK_Overlay_App.rst +++ b/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 diff --git a/doc/02_VTK_Overlay_With_Movement.rst b/doc/02_VTK_Overlay_With_Movement.rst index 81ccdbf..00c1aed 100644 --- a/doc/02_VTK_Overlay_With_Movement.rst +++ b/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 diff --git a/doc/03_VTK_Overlay_With_Aruco_Tag.rst b/doc/03_VTK_Overlay_With_Aruco_Tag.rst index 6b27889..febfc7c 100644 --- a/doc/03_VTK_Overlay_With_Aruco_Tag.rst +++ b/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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -173,11 +173,11 @@ 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`_. @@ -189,7 +189,7 @@ 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 From 8d2aeef27a1d0e1d4cfbc5e20589b2df54fd7e60 Mon Sep 17 00:00:00 2001 From: Stephen Thompson Date: Wed, 23 Feb 2022 17:34:53 +0000 Subject: [PATCH 3/3] Issue #28 removed py36 from ci.yml --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e1b7884..6fcf51e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,16 +9,16 @@ 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] include: - - 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