Merge pull request #19 from SciKit-Surgery/18-move-tosks

18 move tosks

.coveralls.yml

@@ -1,2 +1 @@
-service_name: travis-ci
-repo_token: BY7CsmZLxsoGVRr5MUfIHBKf80Jp4CDYp
+repo_token: IttknVKD3g94z7XGhphBKd6XUgp3LorGf

.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
 
@@ -53,7 +53,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install pip-tools
-          pip-compile requirements.txt
           pip install -r requirements-dev.txt
 
       - name: Run tests using xvfb (Ubuntu)

CITATION.cff

@@ -0,0 +1,47 @@
+cff-version: 1.2.0
+message: "If you use SnappySonic, 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: "SnappySonic"
+doi: 10.5281/zenodo.3491054
+url: "https://github.com/SciKit-Surgery/snappysonic"
+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: "Xiao"
+    given-names: "Guofang"
+  - family-names: "Ramalhinho"
+    given-names: "Jo{\~a}o"
+  - family-names: "Robu"
+    given-names: "Maria"
+  - family-names: "Ahmad"
+    given-names: "Mian"
+    orcid: "https://orcid.org/0000-0002-4706-4146"
+  - family-names: "Taylor"
+    given-names: "Dan"
+  - family-names: "Clarkson"
+    given-names: "Matthew"
+    orcid: "https://orcid.org/0000-0002-5565-1252"
+  doi: 10.5334/jors.289
+  journal: "Journal of Open Research Software"
+  title: "SnappySonic: An Ultrasound Acquisition Replay Simulator"
+  volume: 8
+  issue: 1
+  year: 2020

README.rst

@@ -1,18 +1,19 @@
 SnappySonic
 ===============================
 
-.. image:: https://github.com/UCL/snappysonic/raw/master/project-icon.png
-   :height: 128px
-   :width: 128px
-   :target: https://github.com/UCL/snappysonic
+.. image:: https://github.com/SciKit-Surgery/snappysonic/raw/master/snappysonic.gif
+   :height: 134px
+   :target: https://github.com/SciKit-Surgery/snappysonic
    :alt: Logo
 
-.. image:: https://github.com/UCL/snappysonic/workflows/.github/workflows/ci.yml/badge.svg
-   :target: https://github.com/UCL/snappysonic/actions
+|
+
+.. image:: https://github.com/SciKit-Surgery/snappysonic/workflows/.github/workflows/ci.yml/badge.svg
+   :target: https://github.com/SciKit-Surgery/snappysonic/actions
    :alt: GitHub Actions CI status
 
-.. image:: https://coveralls.io/repos/github/UCL/snappysonic/badge.svg?branch=master&service=github
-    :target: https://coveralls.io/github/UCL/snappysonic?branch=master 
+.. image:: https://coveralls.io/repos/github/SciKit-Surgery/snappysonic/badge.svg?branch=master&service=github
+    :target: https://coveralls.io/github/SciKit-Surgery/snappysonic?branch=master 
     :alt: Test coverage
 
 .. image:: https://readthedocs.org/projects/snappysonic/badge/?version=latest
@@ -23,18 +24,17 @@ SnappySonic
     :target: http://doi.org/10.5334/jors.289
     :alt: The SnappySonic Paper
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3491054.svg
-   :target: https://doi.org/10.5281/zenodo.3491054
-   :alt: Software DOI
-
-.. image:: https://api.codeclimate.com/v1/badges/326c1b87863bd61bbe83/maintainability
-   :target: https://codeclimate.com/github/UCL/snappysonic/maintainability
+.. image:: https://api.codeclimate.com/v1/badges/78440062319f61c55177/maintainability
+   :target: https://codeclimate.com/github/SciKit-Surgery/snappysonic/maintainability
    :alt: Maintainability
 
 .. image:: https://img.shields.io/badge/-Video%20Tutorial-blueviolet?style=flat&logo=youtube
    :target: https://www.youtube.com/watch?v=BI4qyg9NEOk
    :alt: Tutorial on YouTube
 
+.. 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
@@ -90,7 +90,7 @@ You can clone the repository using the following command:
 
 ::
 
-    git clone https://github.com/UCL/snappysonic
+    git clone https://github.com/SciKit-Surgery/snappysonic
 
 
 Running tests
@@ -112,7 +112,7 @@ You can pip install from pypi with
 or You can pip install directly from the repository as follows:
 ::
 
-    pip install git+https://github.com/UCL/snappysonic
+    pip install git+https://github.com/SciKit-Surgery/snappysonic
 
 How to Cite
 -----------
@@ -147,14 +147,14 @@ 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/snappysonic
-.. _`here`: https://github.com/UCL/snappysonic/config.json
-.. _`source code repository data directory`: https://github.com/UCL/snappysonic/data
+.. _`source code repository`: https://github.com/SciKit-Surgery/snappysonic
+.. _`here`: https://github.com/SciKit-Surgery/snappysonic/config.json
+.. _`source code repository data directory`: https://github.com/SciKit-Surgery/snappysonic/data
 .. _`Documentation`: https://snappysonic.readthedocs.io
-.. _`SciKit-Surgery`: https://github.com/UCL/scikit-surgery/wikis/home
+.. _`SciKit-Surgery`: https://github.com/SciKit-Surgery/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/UCL/snappysonic/blob/master/CONTRIBUTING.rst
-.. _`license file`: https://github.com/UCL/snappysonic/blob/master/LICENSE
+.. _`contributing guidelines`: https://github.com/SciKit-Surgery/snappysonic/blob/master/CONTRIBUTING.rst
+.. _`license file`: https://github.com/SciKit-Surgery/snappysonic/blob/master/LICENSE
 .. _`SnappySonic paper`: http://doi.org/10.5334/jors.289

setup.py

@@ -17,7 +17,7 @@
     description='snappysonic provides an application to simulate an ultrasound probe moving over a body torso, it is intended for public engagement events"',
     long_description=long_description,
     long_description_content_type='text/x-rst',
-    url='https://github.com/UCL/snappysonic',
+    url='https://github.com/SciKit-Surgery/snappysonic',
     author='Stephen Thompson',
     author_email='s.thompson@ucl.ac.uk',
     license='BSD-3 license',

tests/test_requirements.py

@@ -0,0 +1,51 @@
+# coding=utf-8
+
+"""scikit-surgerynditracker tests"""
+
+# Pytest style
+
+def test_requirements_vs_setup():
+    """
+    Test that the requirements.txt matches setup.py
+    """
+
+   # setup=open("setup.py","r")
+   # setuptxt = setup.read()
+   # setup.close()
+
+    with open("setup.py", "r", encoding='us-ascii') as file_to_read:
+        searchlines = file_to_read.readlines()
+
+    install_line = -1
+    for i, line in enumerate(searchlines):
+        if "install_requires" in line:
+            install_line = i
+            break
+
+    end_line = -1
+    for i, line in enumerate(searchlines[install_line:]):
+        if "]" in line:
+            end_line = install_line + i
+            break
+
+    setup_reqs = []
+
+    for line in searchlines[install_line + 1: end_line]:
+        req = line.replace(',', '').replace("'", "")
+        req = req.replace(' ', '').replace('\n', '')
+        setup_reqs.append(req)
+
+
+    with open("requirements.txt", "r", encoding='us-ascii') as file_to_read:
+        searchlines = file_to_read.readlines()
+
+    reqs = []
+    for line in searchlines:
+        if "#" not in line:
+            reqs.append(line.replace('\n', ''))
+
+    for setup_req in setup_reqs:
+        assert setup_req in reqs
+
+    for req in reqs:
+        assert req in setup_reqs