Merge pull request #5 from thompson318/4-update-and-release

4 update and release

.coveralls.yml

@@ -0,0 +1,2 @@
+repo_token: pimxLpnWK3uJUfmMCBoLfww8iHhEIaoXs
+

.github/workflows/ci.yml

@@ -0,0 +1,61 @@
+on: push
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Run tox on ubuntu
+        if: startsWith(matrix.os, 'ubuntu')
+        run: |
+          tox
+
+      - name: Run tox on windows/mac
+        # Matches the 'o' in 'windows' or 'macos'
+        if: contains(matrix.os, 'o')
+        run: |
+          tox
+
+      - name: Run coveralls
+        run: |
+          pip install coveralls pyyaml
+          coveralls
+
+  deploy:
+    runs-on: ubuntu-18.04
+    needs: test
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/checkout@master
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+
+      - name: Install dependencies
+        run: python -m pip install wheel twine setuptools
+
+      - name: Build wheel
+        run: |
+          python setup.py sdist
+
+      - name: Publish package if tagged release
+        if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

CONTRIBUTING.rst

@@ -10,7 +10,7 @@ We welcome contributions to scikit-surgery-sphere-fitting.
 Reporting bugs and feature requests
 -----------------------------------
 
-Please create a new issue on https://weisslab.cs.ucl.ac.uk/StephenThompson/sksurgeryspherefitting/issues/new
+Please create a new issue on https://github.com/thompson318/sksurgeryspherefitting/issues/new
 
 When reporting a bug, please include:
 * The version of scikit-surgery-sphere-fitting 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://weisslab.cs.ucl.ac.uk/StephenThompson/sksurgeryspherefitting/issues and assign the relevant issue to yourself. If there is not an existing issue that covers your work, please create one: https://weisslab.cs.ucl.ac.uk/StephenThompson/sksurgeryspherefitting/issues/new
+1. Look through the issues on https://github.com/thompson318/sksurgeryspherefitting/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/thompson318/sksurgeryspherefitting/issues/new
 2. Read the design considerations below.
-3. Fork the repository: https://weisslab.cs.ucl.ac.uk/StephenThompson/sksurgeryspherefitting/forks/new
+3. Fork the repository: https://github.com/thompson318/sksurgeryspherefitting/forks/new
 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://weisslab.cs.ucl.ac.uk/StephenThompson/sksurgeryspherefitting/merge_requests/new
+7. Submit a merge request: https://github.com/thompson318/sksurgeryspherefitting/merge_requests/new
 
 Design Considerations
 ---------------------

README.rst

@@ -1,29 +1,28 @@
 scikit-surgery-sphere-fitting
-===============================
+=============================
 
-.. image:: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting/raw/master/project-icon.png
+.. image:: https://github.com/thompson318/scikit-surgery-sphere-fitting/raw/master/project-icon.png
    :height: 128px
    :width: 128px
-   :target: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting
+   :target: https://github.com/thompson318/scikit-surgery-sphere-fitting
    :alt: Logo
 
-.. image:: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting/badges/master/build.svg
-   :target: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting/pipelines
-   :alt: GitLab-CI test status
+.. image:: https://github.com/thompson318/scikit-surgery-sphere-fitting/workflows/.github/workflows/ci.yml/badge.svg
+   :target: https://github.com/thompson318/scikit-surgery-sphere-fitting/actions
+   :alt: GitHub Actions CI status
 
-.. image:: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting/badges/master/coverage.svg
-    :target: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting/commits/master
+.. image:: https://coveralls.io/repos/github/thompson318/scikit-surgery-sphere-fitting/badge.svg?branch=master&service=github
+    :target: https://coveralls.io/github/thompson318/scikit-surgery-sphere-fitting?branch=master
     :alt: Test coverage
 
 .. image:: https://readthedocs.org/projects/scikit-surgery-sphere-fitting/badge/?version=latest
     :target: http://scikit-surgery-sphere-fitting.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
 
-
 Author: Stephen Thompson
 
-scikit-surgery-sphere-fitting is part of the `SNAPPY`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
+scikit-surgery-sphere-fitting is part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
 
 scikit-surgery-sphere-fitting supports Python 3.6.
 
@@ -39,6 +38,13 @@ It was created in part to provide a simple demonstration of algorithm developmen
 program of SNAPPY Tutorials, but also provides a useful service should you want to fit a sphere
 to some data.
 
+Citing
+------
+If you use SciKit-Surgery-Sphere-Fitting in your research or teaching please cite it. Individual releases can be cited via the Zenodo tag above. SciKit-Surgery should be cited as:
+
+Thompson S, Dowrick T, Ahmad M, et al. "SciKit-Surgery: compact libraries for surgical navigation." International Journal of Computer Assisted Radiology and Surgery. 2020 May. DOI: `10.1007/s11548-020-02180-5`_.
+
+
 Developing
 ----------
 
@@ -49,7 +55,7 @@ You can clone the repository using the following command:
 
 ::
 
-    git clone https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting
+    git clone https://github.com/thompson318/scikit-surgery-sphere-fitting
 
 
 Running tests
@@ -79,7 +85,7 @@ You can pip install directly from the repository as follows:
 
 ::
 
-    pip install git+https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting
+    pip install git+https://github.com/thompson318/scikit-surgery-sphere-fitting
 
 or directly from pypi
 
@@ -115,12 +121,12 @@ Supported by `Wellcome`_ and `EPSRC`_.
 
 
 .. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss
-.. _`source code repository`: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting
+.. _`source code repository`: https://github.com/thompson318/scikit-surgery-sphere-fitting
 .. _`Documentation`: https://scikit-surgery-sphere-fitting.readthedocs.io
-.. _`SNAPPY`: https://weisslab.cs.ucl.ac.uk/WEISS/PlatformManagement/SNAPPY/wikis/home
+.. _`SciKit-Surgery`: https://github.com/UCL/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://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting/blob/master/CONTRIBUTING.rst
-.. _`license file`: https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting/blob/master/LICENSE
-
+.. _`contributing guidelines`: https://github.com/thompson318/scikit-surgery-sphere-fitting/blob/master/CONTRIBUTING.rst
+.. _`license file`: https://github.com/thompson318/scikit-surgery-sphere-fitting/blob/master/LICENSE
+.. _`10.1007/s11548-020-02180-5`: https://doi.org/10.1007/s11548-020-02180-5

requirements.txt

@@ -4,5 +4,5 @@
 # doc/requirements.rst
 numpy>=1.11
 scipy
-vtk
+vtk<9.0
 scikit-surgeryvtk

setup.py

@@ -53,7 +53,7 @@
     install_requires=[
         'numpy>=1.11',
         'scipy',
-        'vtk',
+        'vtk<9.0',
         'scikit-surgeryvtk'
     ],
 

tox.ini

@@ -1,11 +1,11 @@
 # content of: tox.ini , put in same dir as setup.py
 [tox]
-envlist = py36,lint
+envlist = py37,lint
 skipsdist = True
 
 [travis]
 python =
-  3.6: py36, docs, lint
+  3.7: py37, docs, lint
 
 [testenv]
 deps=-rrequirements-dev.txt
@@ -16,22 +16,22 @@ commands = coverage erase
            coverage report -m
 
 [testenv:lint]
-basepython=python3.6
+basepython=python3.7
 deps=pylint
      {[testenv]deps}
 commands=pylint --rcfile=tests/pylintrc sksurgeryspherefitting tests
 
 [testenv:docs]
-basepython=python3.6
+basepython=python3.7
 changedir = doc
 commands = sphinx-build -M html . build
 
 [testenv:installer]
-basepython=python3.6
+basepython=python3.7
 commands=pyinstaller --onefile sksurgeryspherefitting.py --noconfirm --windowed
 
 [testenv:pip3]
-basepython=python3.6
+basepython=python3.7
 changedir=pip_test
 skip_install=True
 commands = pip install {posargs}