Commit e857b302 authored by Thomas Dowrick's avatar Thomas Dowrick
Browse files

Update files after renaming repo

parent 991f6219
Pipeline #1487 failed with stages
in 3 minutes and 55 seconds
[run]
omit =
./sksurgeryardavinci/_version.py
./sksurgeryardavinci/__init__.py
./sksurgeryardavinci/__main__.py
./sksurgeryardavinci/ui/sksurgeryardavinci_command_line.py
./sksurgerydavinci/_version.py
./sksurgerydavinci/__init__.py
./sksurgerydavinci/__main__.py
./sksurgerydavinci/ui/sksurgerydavinci_command_line.py
sksurgeryardavinci/_version.py export-subst
sksurgerydavinci/_version.py export-subst
......@@ -90,12 +90,12 @@ 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
- rsync -avz -e'ssh -v' --numeric-ids --delete doc/build/html/* staging_docs_rsync:WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci 2>&1
tags:
- docs-staging
environment:
name: staging
url: http://weisslab-lin.cs.ucl.ac.uk/staging/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci
url: http://weisslab-lin.cs.ucl.ac.uk/staging/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci
only:
- master
dependencies:
......@@ -106,7 +106,7 @@ 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
- rsync -avz -e'ssh -v' --numeric-ids --delete doc/build/html/* production_docs_rsync:WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci 2>&1
tags:
- docs-production
environment:
......@@ -125,7 +125,7 @@ deploy pip to PyPI:
environment:
name: PyPI
url: https://pypi.python.org/pypi/scikit-surgeryARDavinci
url: https://pypi.python.org/pypi/scikit-surgery-davinci
tags:
- pip-production
......
.. highlight:: shell
===============================================
Contributing to scikit-surgeryARDavinci
Contributing to scikit-surgery-davinci
===============================================
We welcome contributions to scikit-surgeryARDavinci.
We welcome contributions to scikit-surgery-davinci.
Reporting bugs and feature requests
-----------------------------------
Please create a new issue on https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/issues/new
Please create a new issue on https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/issues/new
When reporting a bug, please include:
* The version of scikit-surgeryARDavinci you are using
* The version of scikit-surgery-davinci you are using
* Your OS version (for example Windows 10 64-bit, macOS High Sierra, Ubuntu 16.04)
* Detailed steps to reproduce the bug.
......@@ -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-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
1. Look through the issues on https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/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-surgery-davinci/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
3. Fork the repository: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/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
7. Submit a merge request: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/merge_requests/new
Design Considerations
---------------------
......
include versioneer.py
include sksurgeryardavinci/_version.py
include sksurgerydavinci/_version.py
scikit-surgeryARDavinci
scikit-surgery-davinci
===============================
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci/raw/master/project-icon.png
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/raw/master/project-icon.png
:height: 128px
:width: 128px
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci
: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
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/badges/master/build.svg
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/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
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/badges/master/coverage.svg
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/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
.. image:: https://readthedocs.org/projects/scikit-surgery-davinci/badge/?version=latest
:target: http://scikit-surgery-davinci.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
Augmented reality for image-guided laproscopic surgery.
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-surgery-davinci is part of the `SNAPPY`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
.. figure:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryardavinci/raw/master/doc/ardavin_demo.gif
Author: Thomas Dowrick
scikit-surgeryARDavinci supports Python 3.6.
scikit-surgery-davinci supports Python 3.6.
Installing
----------
......@@ -37,7 +37,7 @@ You can install using pip:
::
pip install scikit-surgeryARDavinci
pip install scikit-surgery-davinci
Example Usage
--------------
......@@ -45,7 +45,7 @@ Example Usage
Single video feed:
::
python sksurgeryardavinci -v 0 -m MODEL_DIR
python sksurgerydavinci -v 0 -m MODEL_DIR
-m specifies the location of a directory containing vtl/stl/vtp/ply models.
......@@ -53,23 +53,23 @@ Stereo video feed:
::
python sksurgeryardavinci -v 0 1 -m MODEL_DIR
python sksurgerydavinci -v 0 1 -m MODEL_DIR
Mock stereo feed using only one input:
::
python sksurgeryardavinci -v 0 -1 -m MODEL_DIR
python sksurgerydavinci -v 0 -1 -m MODEL_DIR
If 3 or more screens are available, each video feed will run full screen on a separate display.
Video feeds can be assigned to specific displays using the -o arugment:
::
python sksurgeryardavinci -v 0 1 -o 2 3 1
python sksurgerydavinci -v 0 1 -o 2 3 1
More details on command line arguments can be viewed using:
::
python sksurgeryardavinci -h
python sksurgerydavinci -h
Contributing
^^^^^^^^^^^^
......@@ -88,7 +88,7 @@ Licensing and copyright
-----------------------
Copyright 2019 University College London.
scikit-surgeryARDavinci is released under the BSD-3 license. Please see the `license file`_ for details.
scikit-surgery-davinci is released under the BSD-3 license. Please see the `license file`_ for details.
Acknowledgements
......@@ -98,12 +98,12 @@ 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-surgeryARDavinci
.. _`Documentation`: https://scikit-surgeryARDavinci.readthedocs.io
.. _`source code repository`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci
.. _`Documentation`: https://scikit-surgery-davinci.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
.. _`contributing guidelines`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/blob/master/CONTRIBUTING.rst
.. _`license file`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci/blob/master/LICENSE
/sksurgeryardavinci.rst
/sksurgeryardavinci.*.rst
/sksurgerydavinci.rst
/sksurgerydavinci.*.rst
/modules.rst
/versioneer.rst
/build
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# scikit-surgeryARDavinci documentation build configuration file, created by
# scikit-surgery-davinci 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
......@@ -100,13 +100,13 @@ source_suffix = '.rst'
master_doc = 'index'
# This allows modules to be indexed under the submodule name rather than all appearing under sksurgeryardavinci
# This allows modules to be indexed under the submodule name rather than all appearing under sksurgerydavinci
modindex_common_prefix = [
'sksurgeryardavinci.'
'sksurgerydavinci.'
]
# General information about the project.
project = u'scikit-surgeryARDavinci'
project = u'scikit-surgery-davinci'
copyright = u"2019, University College London"
author = u'Thomas Dowrick'
......@@ -120,9 +120,9 @@ version = u''
release = u''
# The short X.Y version.
# version = sksurgeryardavinci.__version__
# version = sksurgerydavinci.__version__
# The full version, including alpha/beta/rc tags.
# release = sksurgeryardavinci.__version__
# release = sksurgerydavinci.__version__
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
......@@ -200,7 +200,7 @@ html_sidebars = {
# -- Options for HTMLHelp output ------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'scikit-surgeryARDavincidoc'
htmlhelp_basename = 'scikit-surgery-davincidoc'
# -- Options for LaTeX output ---------------------------------------------
......@@ -226,8 +226,8 @@ latex_elements = {
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
('index', 'scikit-surgeryARDavinci.tex',
u'scikit-surgeryARDavinci Documentation',
('index', 'scikit-surgery-davinci.tex',
u'scikit-surgery-davinci Documentation',
u'Thomas Dowrick', 'manual'),
]
......@@ -236,8 +236,8 @@ latex_documents = [
# 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',
('index', 'scikit-surgery-davinci',
u'scikit-surgery-davinci Documentation',
[u'Thomas Dowrick'], 1)
]
......@@ -248,10 +248,10 @@ man_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'scikit-surgeryARDavinci',
u'scikit-surgeryARDavinci Documentation',
('index', 'scikit-surgery-davinci',
u'scikit-surgery-davinci Documentation',
u'Thomas Dowrick',
'scikit-surgeryARDavinci',
'scikit-surgery-davinci',
'One line description of project.',
'Miscellaneous'),
]
......@@ -4,5 +4,5 @@ universal=1
[versioneer]
VCS = git
style = pep440
versionfile_source = sksurgeryardavinci/_version.py
versionfile_source = sksurgerydavinci/_version.py
tag_prefix = v
# coding=utf-8
"""
Setup for scikit-surgeryARDavinci
Setup for scikit-surgery-davinci
"""
from setuptools import setup, find_packages
......@@ -11,13 +11,13 @@ with open('README.rst') as f:
long_description = f.read()
setup(
name='scikit-surgeryARDavinci',
name='scikit-surgery-davinci',
version=versioneer.get_version(),
cmdclass=versioneer.get_cmdclass(),
description='Augmented Reality for Davinci Surgical Robot',
long_description=long_description,
long_description_content_type='text/x-rst',
url='https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryARDavinci',
url='https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery-davinci',
author='Thomas Dowrick',
author_email='YOUR-EMAIL@ucl.ac.uk',
license='BSD-3 license',
......@@ -61,7 +61,7 @@ setup(
entry_points={
'console_scripts': [
'sksurgeryardavinci=sksurgeryardavinci.__main__:main',
'sksurgerydavinci=sksurgerydavinci.__main__:main',
],
},
)
......@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
import sys
from sksurgeryardavinci.ui.sksurgeryardavinci_command_line import main
from sksurgerydavinci.ui.sksurgerydavinci_command_line import main
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
# coding=utf-8
"""scikit-surgeryARDavinci"""
"""scikit-surgery-davinci"""
from ._version import get_versions
__version__ = get_versions()['version']
......
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""scikit-surgeryARDavinci"""
"""scikit-surgery-davinci"""
import sys
if __name__ == "__main__" and not __package__:
# To allow the package's main function to be executed without the -m switch,
# i.e. "python sksurgeryardavinci", we have to explicitly set the
# i.e. "python sksurgerydavinci", we have to explicitly set the
# module name and append the parent directory to the sys.path (see PEP 366)
from os import path
__package__ = "sksurgeryardavinci" # pylint: disable=redefined-builtin
__package__ = "sksurgerydavinci" # pylint: disable=redefined-builtin
sys.path.append(path.dirname(path.dirname(path.abspath(__file__))))
sys.path.append(path.dirname(path.dirname(__file__)))
# pylint: disable=wrong-import-position
from sksurgeryardavinci.ui.sksurgeryardavinci_command_line import main
from sksurgerydavinci.ui.sksurgerydavinci_command_line import main
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
# coding=utf-8
"""scikit-surgeryARDavinci"""
"""scikit-surgery-davinci"""
......@@ -4,8 +4,8 @@
import argparse
import logging
from sksurgeryardavinci import __version__
from sksurgeryardavinci.ui.sksurgeryardavinci_demo import run_demo
from sksurgerydavinci import __version__
from sksurgerydavinci.ui.sksurgerydavinci_demo import run_demo
logging.basicConfig(level=logging.INFO)
LOGGER = logging.getLogger(__name__)
......
......@@ -7,7 +7,7 @@ from PySide2.QtWidgets import QApplication
from sksurgeryvtk.models.vtk_surface_model_directory_loader \
import VTKSurfaceModelDirectoryLoader
from sksurgeryardavinci.widgets.Viewers\
from sksurgerydavinci.widgets.Viewers\
import MonoViewer, StereoViewer, MockStereoViewer
......
......@@ -4,7 +4,7 @@ from PySide2 import QtWidgets
from sksurgeryvtk.widgets.vtk_overlay_window import VTKOverlayWindow
from sksurgeryutils.common_overlay_apps import OverlayOnVideoFeed
from sksurgeryutils.utils.screen_utils import ScreenController
from sksurgeryardavinci.ui.gui import UI
from sksurgerydavinci.ui.gui import UI
LOGGER = logging.getLogger(__name__)
......
import os
import sys
import pytest
from sksurgeryardavinci.widgets import Viewers
from sksurgerydavinci.widgets import Viewers
from sksurgeryvtk.models.vtk_surface_model_directory_loader \
import VTKSurfaceModelDirectoryLoader
......
......@@ -2,7 +2,7 @@ import os
import sys
import pytest
import numpy as np
from sksurgeryardavinci.widgets import Viewers
from sksurgerydavinci.widgets import Viewers
from sksurgeryutils.common_overlay_apps import OverlayOnVideoFeed
# pyint:disable=line-too-long
......
......@@ -13,14 +13,14 @@ deps=-rrequirements-dev.txt
whitelist_externals=coverage,pip
# See .coveragerc for list of omitted files
commands = coverage erase
coverage run -a --source ./sksurgeryardavinci -m pytest -v -s ./tests/
coverage run -a --source ./sksurgerydavinci -m pytest -v -s ./tests/
coverage report -m
[testenv:lint]
basepython=python3.6
deps=pylint
{[testenv]deps}
commands=pylint --rcfile=tests/pylintrc sksurgeryardavinci
commands=pylint --rcfile=tests/pylintrc sksurgerydavinci
[testenv:docs]
basepython=python3.6
......@@ -29,18 +29,18 @@ commands = sphinx-build -M html . build
[testenv:installer]
basepython=python3.6
commands=pyinstaller --onefile sksurgeryardavinci.py --noconfirm --windowed
commands=pyinstaller --onefile sksurgerydavinci.py --noconfirm --windowed
[testenv:pip2]
basepython=python2.7
changedir=pip_test
skip_install=True
commands = pip install {posargs}
sksurgeryardavinci --help
sksurgerydavinci --help
[testenv:pip3]
basepython=python3.6
changedir=pip_test
skip_install=True
commands = pip install {posargs}
sksurgeryardavinci --help
sksurgerydavinci --help
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