diff --git a/.coveralls.yml b/.coveralls.yml new file mode 100644 index 0000000..0721e5c --- /dev/null +++ b/.coveralls.yml @@ -0,0 +1 @@ +repo_token: 5onYy27mPi7cCRUIQrlPNnnHdAe7jnIGh diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 88ec3ba..9cc5457 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,7 +8,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, windows-latest] + os: [ubuntu-latest, windows-latest, macos-latest] python-ver: [3.6, 3.7] experimental: [false] include: @@ -18,6 +18,9 @@ jobs: - python-ver: 3.8 os: windows-latest experimental: true + - python-ver: 3.8 + os: macos-latest + experimental: true runs-on: ${{ matrix.os }} continue-on-error: ${{ matrix.experimental }} @@ -59,19 +62,19 @@ jobs: export DISPLAY=":1" export LD_LIBRARY_PATH=$pythonLocation"/lib/python3.6/site-packages/PySide2/Qt/plugins/platfoms" coverage erase - coverage run -a --source ./sksurgeryvtk -m pytest + coverage run -a --source ./sksurgeryutils -m pytest coverage report -m - name: Run tests Windows/Mac if: contains(matrix.os, 'o') run: | coverage erase - coverage run -a --source ./sksurgeryvtk -m pytest + coverage run -a --source ./sksurgeryutils -m pytest coverage report -m - name: Linting run: | - pylint --rcfile=tests/pylintrc sksurgeryvtk + pylint --rcfile=tests/pylintrc sksurgeryutils - name: Run coveralls run: | diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml deleted file mode 100644 index 0ec8f55..0000000 --- a/.gitlab-ci.yml +++ /dev/null @@ -1,118 +0,0 @@ -#Tell Gitlab to load these environental vars from the variables list -variables: - PYPI_USER: SECURE - PYPI_PASS: SECURE - -stages: - - build - - installer - - test - - deploy - - -build docs: - stage: build - script: - - tox -e docs - tags: - - shared-linux - artifacts: - paths: - - doc/ - expire_in: 1 week - - -build linux installer: - stage: build - script: - - tox -e installer - tags: - - shared-linux - artifacts: - paths: - - dist/ - expire_in: 1 week - - -build mac installer: - stage: build - script: - - tox -e installer - tags: - - shared-mac - artifacts: - paths: - - dist/ - expire_in: 1 week - - -build windows installer: - stage: build - script: - - tox -e installer - tags: - - shared-win - artifacts: - paths: - - dist/ - expire_in: 1 week - - -test Linux: - stage: test - variables: - LD_LIBRARY_PATH: ${CI_PROJECT_DIR}/.tox/py36/lib/python3.6/site-packages/PySide2/Qt/plugins/platforms - DISPLAY: localhost:1 - script: - - echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" - - echo "DISPLAY=${DISPLAY}" - - tox - tags: - - shared-linux, gui - coverage: '/^TOTAL.*\s+(\d+\%)$/' - - -test macOS: - stage: test - script: - - tox - tags: - - shared-mac, gui - - -test Windows: - stage: test - script: - - tox - tags: - - shared-win, gui - -deploy pip to PyPI: - - stage: deploy - when: manual - only: - - tags - - environment: - name: PyPI - url: https://pypi.python.org/pypi/scikit-surgeryutils - - tags: - - pip-production - - artifacts: - paths: - - dist/ - - script: - # Install packages required to build/publish - # remove any previous distribution files - - pip install wheel twine setuptools - - rm -rf dist - - # bundle installer - - python setup.py bdist_wheel - - # Upload to pypi - - twine upload --repository pypi dist/* --username $PYPI_USER --password $PYPI_PASS diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index 64326a1..bb194e4 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.rst @@ -10,7 +10,7 @@ We welcome contributions to scikit-surgeryutils. Reporting bugs and feature requests ----------------------------------- -Please create a new issue on https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/issues/new +Please create a new issue on https://github.com/UCL/scikit-surgeryutils/issues/new When reporting a bug, please include: * The version of scikit-surgeryutils 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/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/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/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/issues/new +1. Look through the issues on https://github.com/UCL/scikit-surgeryutils/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-surgeryutils/issues/new 2. Read the design considerations below. -3. Fork the repository: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/forks/new +3. Fork the repository: https://github.com/UCL/scikit-surgeryutils/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 #`, 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/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/merge_requests/new +7. Submit a merge request: https://github.com/UCL/scikit-surgeryutils/merge_requests/new Design Considerations --------------------- diff --git a/README.rst b/README.rst index c0c9312..c57a3b8 100644 --- a/README.rst +++ b/README.rst @@ -1,21 +1,22 @@ scikit-surgeryutils =============================== -.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/raw/master/project-icon.png +.. image:: https://github.com/UCL/scikit-surgeryutils /raw/master/project-icon.png :height: 128px :width: 128px - :target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils + :target: https://github.com/UCL/scikit-surgeryutils + :alt: Logo -.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/badges/master/pipeline.svg - :target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/pipelines - :alt: GitLab-CI test status +.. image:: https://github.com/UCL/scikit-surgeryutils/workflows/.github/workflows/ci.yml/badge.svg + :target: https://github.com/UCL/scikit-surgeryutils/actions + :alt: GitHub Actions CI statuss -.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/badges/master/coverage.svg - :target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/commits/master +.. image:: https://coveralls.io/repos/github/UCL/scikit-surgeryutils/badge.svg?branch=master&service=github + :target: https://coveralls.io/github/UCL/scikit-surgeryutils?branch=master :alt: Test coverage -.. image:: https://readthedocs.org/projects/scikit-surgeryutils/badge/?version=latest - :target: http://scikit-surgeryutils.readthedocs.io/en/latest/?badge=latest +.. image:: https://readthedocs.org/projects/scikit-surgeryutils /badge/?version=latest + :target: http://scikit-surgeryutils .readthedocs.io/en/latest/?badge=latest :alt: Documentation Status scikit-surgeryutils is a python project containing small demo apps, @@ -36,7 +37,7 @@ You can pip install directly from the repository as follows: :: - pip install git+https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils + pip install git+https://github.com/UCL/scikit-surgeryutils Developing @@ -49,7 +50,7 @@ You can clone the repository using the following command: :: - git clone https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils + git clone https://github.com/UCL/scikit-surgeryutils Running the tests @@ -93,12 +94,12 @@ 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/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils +.. _`source code repository`: https://github.com/UCL/scikit-surgeryutils .. _`Documentation`: https://scikit-surgeryutils.readthedocs.io .. _`SNAPPY`: https://weisslab.cs.ucl.ac.uk/WEISS/PlatformManagement/SNAPPY/wikis/home .. _`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/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/blob/master/CONTRIBUTING.rst -.. _`license file`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/blob/master/LICENSE +.. _`contributing guidelines`: https://github.com/UCL/scikit-surgeryutils/blob/master/CONTRIBUTING.rst +.. _`license file`: https://github.com/UCL/scikit-surgeryutils/blob/master/LICENSE .. _`common issues`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery/wikis/Common-Issues diff --git a/requirements-dev.txt b/requirements-dev.txt index 7583a58..89ae570 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -15,3 +15,5 @@ pyinstaller pytest pytest-qt tox +coveralls +pyyaml diff --git a/setup.py b/setup.py index 587f2b5..45716cf 100644 --- a/setup.py +++ b/setup.py @@ -17,7 +17,7 @@ description='scikit-surgeryutils - Tests/demos utilities, based around opencv-contrib and PySide2', long_description=long_description, long_description_content_type='text/x-rst', - url='https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils', + url='https://github.com/UCL/scikit-surgeryutils', author='Matt Clarkson', author_email='m.clarkson@ucl.ac.uk', license='BSD-3 license',