Initial commit

.coveragerc

+[run]
+omit = 
+        ./sksurgeryardavinci/_version.py
+        ./sksurgeryardavinci/__init__.py
+        ./sksurgeryardavinci/__main__.py
+        ./sksurgeryardavinci/ui/sksurgeryardavinci_command_line.py

.gitattributes

+sksurgeryardavinci/_version.py export-subst

.gitignore

+# Pycharm
+/.idea
+
+# Generated files
+.tox
+.coverage
+*.pyc
+.pytest_cache/
+
+# PyInstaller
+build/
+dist/

.gitlab-ci.yml

+#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
+  script:
+      - tox
+  tags:
+    - shared-linux
+  coverage: '/^TOTAL.*\s+(\d+\%)$/'
+
+
+test macOS:
+  stage: test
+  script:
+      - tox
+  tags:
+    - shared-mac
+
+
+test Windows:
+  stage: test
+  script:
+      - tox
+  tags:
+    - shared-win
+
+
+deploy docs to staging:
+  stage: deploy
+  script:
+    # Note: the group/username directory must already exist on the server before calling this command
+    - rsync -avz -e'ssh -v' --numeric-ids --delete doc/build/html/* staging_docs_rsync:WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci 2>&1
+  tags:
+    - docs-staging
+  environment:
+    name: staging
+    url: http://weisslab-lin.cs.ucl.ac.uk/staging/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci
+  only:
+    - master
+  dependencies:
+    - build docs
+
+
+deploy docs to production:
+  stage: deploy
+  script:
+    # Note: the group/username directory must already exist on the server before calling this command
+    - rsync -avz -e'ssh -v' --numeric-ids --delete doc/build/html/* production_docs_rsync:WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci 2>&1
+  tags:
+    - docs-production
+  environment:
+    name: production
+  only:
+    - public
+  dependencies:
+    - build docs
+
+deploy pip to PyPI:
+
+  stage: deploy
+  when: manual
+  only:
+    - tags
+    
+  environment:
+    name: PyPI
+    url: https://pypi.python.org/pypi/scikit-surgeryARDavinci
+    
+  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

CONTRIBUTING.rst

+.. highlight:: shell
+
+===============================================
+Contributing to scikit-surgeryARDavinci
+===============================================
+
+We welcome contributions to scikit-surgeryARDavinci.
+
+
+Reporting bugs and feature requests
+-----------------------------------
+
+Please create a new issue on https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/issues/new
+
+When reporting a bug, please include:
+* The version of scikit-surgeryARDavinci you are using
+* Your OS version (for example Windows 10 64-bit, macOS High Sierra, Ubuntu 16.04)
+* Detailed steps to reproduce the bug.
+
+
+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-surgeryARDavinci/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-surgeryARDavinci/issues/new
+2. Read the design considerations below.
+3. Fork the repository: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/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/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/merge_requests/new
+
+Design Considerations
+---------------------
+
+1. As few dependencies as possible. Try to stick to standard scipy packages like numpy and pandas.
+2. Discuss extra dependencies with the team and maybe the outcome will be to create a new separate package, where you can be more specific and more modular.
+3. Unit test well, using pytest, with good coverage.
+4. All errors as exceptions rather than return codes.
+
+
+Coding guidelines
+-----------------
+
+1. Please follow PEP8 guidelines https://www.python.org/dev/peps/pep-0008/
+2. Create a python virtual environment (virtualenv) for development
+3. Make sure that pylint passes. You may disable specific warnings within the code where it is reasonable to do so
+4. Add unit tests for new and modified code
+5. Make sure all existing and new tests pass
+6. Make sure all docstrings have been added
+7. Make sure all dependencies have been added to requirements
+8. Make sure your code works for all required versions of Python
+9. Make sure your code works for all required operating systems
+

LICENSE

+
+BSD License
+
+Copyright (c) 2019, University College London
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+OF THE POSSIBILITY OF SUCH DAMAGE.
+
+

MANIFEST.in

+include versioneer.py
+include sksurgeryardavinci/_version.py

README.rst

+scikit-surgeryARDavinci
+===============================
+
+.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/raw/master/project-icon.png
+   :height: 128px
+   :width: 128px
+   :target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci
+   :alt: Logo
+
+.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/badges/master/build.svg
+   :target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/pipelines
+   :alt: GitLab-CI test status
+
+.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/badges/master/coverage.svg
+    :target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/commits/master
+    :alt: Test coverage
+
+.. image:: https://readthedocs.org/projects/scikit-surgeryARDavinci/badge/?version=latest
+    :target: http://scikit-surgeryARDavinci.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+
+
+Author: Thomas Dowrick
+
+scikit-surgeryARDavinci 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-surgeryARDavinci supports Python 2.7 and Python 3.6.
+
+Installing
+----------
+
+You can pip install directly from the repository as follows:
+
+::
+
+    pip install git+https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci
+
+
+Developing
+----------
+
+Cloning
+^^^^^^^
+
+You can clone the repository using the following command:
+
+::
+
+    git clone https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci
+
+
+Running the tests
+^^^^^^^^^^^^^^^^^
+
+You can run the unit tests by installing and running tox:
+
+::
+
+    pip install tox
+    tox
+
+Contributing
+^^^^^^^^^^^^
+
+Please see the `contributing guidelines`_.
+
+
+Useful links
+^^^^^^^^^^^^
+
+* `Source code repository`_
+* `Documentation`_
+
+
+Licensing and copyright
+-----------------------
+
+Copyright 2019 University College London.
+scikit-surgeryARDavinci is released under the BSD-3 license. Please see the `license file`_ for details.
+
+
+Acknowledgements
+----------------
+
+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-surgeryARDavinci
+.. _`Documentation`: https://scikit-surgeryARDavinci.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-surgeryARDavinci/blob/master/CONTRIBUTING.rst
+.. _`license file`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/blob/master/LICENSE
+

doc/.gitignore

+/sksurgeryardavinci.rst
+/sksurgeryardavinci.*.rst
+/modules.rst
+/versioneer.rst
+/build

doc/conf.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# scikit-surgeryARDavinci documentation build configuration file, created by
+# sphinx-quickstart on Tue Dec 19 17:02:44 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import subprocess
+import os
+import sys
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+working_dir = os.path.abspath(os.path.dirname(__file__))
+root_dir_rel = os.path.join('..')
+root_dir_abs = os.path.abspath(root_dir_rel)
+module_path = root_dir_abs
+sys.path.insert(0, module_path)
+logo_file = 'project-icon.png'
+logo_path = os.path.join('..', logo_file)
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = [
+    'tests',
+    'run_*',
+    'setup.py',
+    '_build',
+    'Thumbs.db',
+    '.DS_Store',
+    '_verion.py',
+    'versioneer.py'
+
+]
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+static_folder = 'static'
+html_static_path = [static_folder]
+
+
+def generate_apidocs(*args):
+    """Generate API docs automatically by trawling the available modules"""
+
+    global working_dir, module_path
+    output_path = working_dir
+    apidoc_command_path = 'sphinx-apidoc'
+    if hasattr(sys, 'real_prefix'):  # called from a virtualenv
+        apidoc_command_path = os.path.join(sys.prefix, 'bin', 'sphinx-apidoc')
+        apidoc_command_path = os.path.abspath(apidoc_command_path)
+    subprocess.check_call(
+        [apidoc_command_path, '--force', '--separate'] +
+        ['-o', output_path, module_path] +
+        [os.path.join(root_dir_abs, pattern) for pattern in exclude_patterns])
+
+
+def setup(app):
+    # Hook to allow for automatic generation of API docs
+    # before doc deployment begins.
+    app.connect('builder-inited', generate_apidocs)
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinx.ext.imgmath']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+
+# This allows modules to be indexed under the submodule name rather than all appearing under sksurgeryardavinci
+modindex_common_prefix = [
+    'sksurgeryardavinci.'
+]
+
+# General information about the project.
+project = u'scikit-surgeryARDavinci'
+copyright = u"2019, University College London"
+author = u'Thomas Dowrick'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u''
+# The full version, including alpha/beta/rc tags.
+release = u''
+
+# The short X.Y version.
+# version = sksurgeryardavinci.__version__
+# The full version, including alpha/beta/rc tags.
+# release = sksurgeryardavinci.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+doc_black = '#0A0A0A'
+doc_red = '#E03C31'
+doc_gray = '#979999'
+doc_blue = '#00627D'
+doc_dark_red = '#C53B2C'
+doc_white = '#FEFEFE'
+html_theme_options = {
+    'footerbgcolor': doc_gray,
+    'footertextcolor': doc_black,
+    'sidebarbgcolor': doc_white,
+    'sidebartextcolor': doc_black,
+    'sidebarlinkcolor': doc_red,
+    'relbarbgcolor': doc_white,
+    'relbartextcolor': doc_black,
+    'relbarlinkcolor': doc_red,
+    'bgcolor': doc_white,
+    'textcolor': doc_black,
+    'linkcolor': doc_red,
+    'visitedlinkcolor': doc_dark_red,
+    'headbgcolor': doc_white,
+    'headtextcolor': doc_black,
+    'headlinkcolor': doc_red,
+    'codebgcolor': doc_blue,
+    'codetextcolor': doc_black,
+    'stickysidebar': 'true',
+}
+
+html_logo = logo_path
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'scikit-surgeryARDavincidoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    ('index', 'scikit-surgeryARDavinci.tex',
+     u'scikit-surgeryARDavinci Documentation',
+     u'Thomas Dowrick', 'manual'),
+]
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'scikit-surgeryARDavinci',
+     u'scikit-surgeryARDavinci Documentation',
+     [u'Thomas Dowrick'], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    ('index', 'scikit-surgeryARDavinci',
+     u'scikit-surgeryARDavinci Documentation',
+     u'Thomas Dowrick',
+     'scikit-surgeryARDavinci',
+     'One line description of project.',
+     'Miscellaneous'),
+]

doc/index.rst

+.. include:: ../README.rst
+
+Contents
+~~~~~~~~
+.. toctree::
+  :maxdepth: 1
+
+  requirements
+  pycharm
+  Module Contents <modules>
+
+* :ref:`modindex`
+* :ref:`genindex`