Commit cf20734e authored by Thomas Dowrick's avatar Thomas Dowrick

Issue N/A: Rename scikit-surgeryvideoutils to scikit-surgeryutils

parent c089755c
Pipeline #1182 passed with stages
in 21 minutes and 58 seconds
[run]
omit =
./sksurgeryvideoutils/_version.py
./sksurgeryvideoutils/__init__.py
./sksurgeryvideoutils/__main__.py
./sksurgeryutils/_version.py
./sksurgeryutils/__init__.py
./sksurgeryutils/__main__.py
sksurgeryvideoutils/_version.py export-subst
sksurgeryutils/_version.py export-subst
......@@ -92,12 +92,12 @@ 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-surgeryvideoutils 2>&1
- rsync -avz -e'ssh -v' --numeric-ids --delete doc/build/html/* staging_docs_rsync:WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils 2>&1
tags:
- docs-staging
environment:
name: staging
url: http://weisslab-lin.cs.ucl.ac.uk/staging/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils
url: http://weisslab-lin.cs.ucl.ac.uk/staging/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils
only:
- master
dependencies:
......@@ -108,7 +108,7 @@ 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-surgeryvideoutils 2>&1
- rsync -avz -e'ssh -v' --numeric-ids --delete doc/build/html/* production_docs_rsync:WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils 2>&1
tags:
- docs-production
environment:
......@@ -127,7 +127,7 @@ deploy pip to PyPI:
environment:
name: PyPI
url: https://pypi.python.org/pypi/scikit-surgeryvideoutils
url: https://pypi.python.org/pypi/scikit-surgeryutils
tags:
- pip-production
......
.. highlight:: shell
===============================================
Contributing to scikit-surgeryvideoutils
Contributing to scikit-surgeryutils
===============================================
We welcome contributions to scikit-surgeryvideoutils.
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-surgeryvideoutils/issues/new
Please create a new issue on https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/issues/new
When reporting a bug, please include:
* The version of scikit-surgeryvideoutils you are using
* The version of scikit-surgeryutils 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-surgeryvideoutils/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-surgeryvideoutils/issues/new
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
2. Read the design considerations below.
3. Fork the repository: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils/forks/new
3. Fork the repository: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/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 #<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-surgeryvideoutils/merge_requests/new
7. Submit a merge request: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/merge_requests/new
Design Considerations
---------------------
......
include versioneer.py
include sksurgeryvideoutils/_version.py
include sksurgeryutils/_version.py
scikit-surgeryvideoutils
scikit-surgeryutils
===============================
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils/raw/master/project-icon.png
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/raw/master/project-icon.png
:height: 128px
:width: 128px
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils/badges/master/build.svg
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils/pipelines
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/badges/master/build.svg
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils/pipelines
:alt: GitLab-CI test status
.. image:: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils/badges/master/coverage.svg
:target: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils/commits/master
.. 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
:alt: Test coverage
.. image:: https://readthedocs.org/projects/scikit-surgeryvideoutils/badge/?version=latest
:target: http://scikit-surgeryvideoutils.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-surgeryvideoutils is a python project containing a few test and demo
scikit-surgeryutils is a python project containing a few test and demo
utilities, based around opencv-contrib-python for video processing and
PySide2 for GUI windows and widgets.
* sksurgeryvideolag.py - shows a millisecond timer and video image to measure lag
* sksurgerycharucotest.py - extracts charuco points and annotates video image with each id detected.
scikit-surgeryvideoutils 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-surgeryutils is part of the `SNAPPY`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
Installing
......@@ -35,7 +35,7 @@ You can pip install directly from the repository as follows:
::
pip install git+https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils
pip install git+https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils
Developing
......@@ -48,7 +48,7 @@ You can clone the repository using the following command:
::
git clone https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils
git clone https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils
Running the tests
......@@ -78,7 +78,7 @@ Licensing and copyright
-----------------------
Copyright 2018 University College London.
scikit-surgeryvideoutils is released under the BSD-3 license. Please see the `license file`_ for details.
scikit-surgeryutils is released under the BSD-3 license. Please see the `license file`_ for details.
Acknowledgements
......@@ -88,12 +88,12 @@ 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-surgeryvideoutils
.. _`Documentation`: https://scikit-surgeryvideoutils.readthedocs.io
.. _`source code repository`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/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-surgeryvideoutils/blob/master/CONTRIBUTING.rst
.. _`license file`: https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryvideoutils/blob/master/LICENSE
.. _`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
/sksurgeryvideoutils.rst
/sksurgeryvideoutils.*.rst
/sksurgeryutils.rst
/sksurgeryutils.*.rst
/sksurgeryvideolag.rst
/sksurgerycharucotest.rst
/modules.rst
......
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# scikit-surgeryvideoutils documentation build configuration file, created by
# scikit-surgeryutils 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 sksurgeryvideoutils
# This allows modules to be indexed under the submodule name rather than all appearing under sksurgeryutils
modindex_common_prefix = [
'sksurgeryvideoutils.'
'sksurgeryutils.'
]
# General information about the project.
project = u'scikit-surgeryvideoutils'
project = u'scikit-surgeryutils'
copyright = u"2018, University College London"
author = u'Matt Clarkson'
......@@ -120,9 +120,9 @@ version = u''
release = u''
# The short X.Y version.
# version = sksurgeryvideoutils.__version__
# version = sksurgeryutils.__version__
# The full version, including alpha/beta/rc tags.
# release = sksurgeryvideoutils.__version__
# release = sksurgeryutils.__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-surgeryvideoutilsdoc'
htmlhelp_basename = 'scikit-surgeryutilsdoc'
# -- 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-surgeryvideoutils.tex',
u'scikit-surgeryvideoutils Documentation',
('index', 'scikit-surgeryutils.tex',
u'scikit-surgeryutils Documentation',
u'Matt Clarkson', '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-surgeryvideoutils',
u'scikit-surgeryvideoutils Documentation',
('index', 'scikit-surgeryutils',
u'scikit-surgeryutils Documentation',
[u'Matt Clarkson'], 1)
]
......@@ -248,10 +248,10 @@ man_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'scikit-surgeryvideoutils',
u'scikit-surgeryvideoutils Documentation',
('index', 'scikit-surgeryutils',
u'scikit-surgeryutils Documentation',
u'Matt Clarkson',
'scikit-surgeryvideoutils',
'scikit-surgeryutils',
'One line description of project.',
'Miscellaneous'),
]
......@@ -4,7 +4,7 @@ Some Hints for Developing with PyCharm
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PyCharm is a popular python editor. This is a quickstart guide setting up
PyCharm for developing sksurgeryvideoutils.
PyCharm for developing sksurgeryutils.
This assumes you have PyCharm installed and configured to support virtual environments.
1. Start PyCharm
......@@ -25,6 +25,6 @@ This assumes you have PyCharm installed and configured to support virtual enviro
16. `tox`
17. Expand the project
18. Right-click on the Tests folder and choose "Run Unittests in tests". This will create a new configuration for running tests
19. Right-click on sksurgeryvideoutils and select Run sksurgeryvideoutils. This will create a new configuration for running the project.
19. Right-click on sksurgeryutils and select Run sksurgeryutils. This will create a new configuration for running the project.
20. Switch between the program and test configurations using the drop-down at the top of the screen, and the green arrow to run or the green bug to debug.
......@@ -3,12 +3,12 @@
.. _requirements:
===============================================
Requirements for scikit-surgeryvideoutils
Requirements for scikit-surgeryutils
===============================================
This is the software requirements file for scikit-surgeryvideoutils, part of the
This is the software requirements file for scikit-surgeryutils, part of the
SNAPPY project. The requirements listed below should define
what scikit-surgeryvideoutils does. Each requirement can be matched to a unit test that
what scikit-surgeryutils does. Each requirement can be matched to a unit test that
checks whether the requirement is met.
Requirements
......
......@@ -4,5 +4,5 @@ universal=1
[versioneer]
VCS = git
style = pep440
versionfile_source = sksurgeryvideoutils/_version.py
versionfile_source = sksurgeryutils/_version.py
tag_prefix = v
# coding=utf-8
"""
Setup for scikit-surgeryvideoutils
Setup for scikit-surgeryutils
"""
from setuptools import setup, find_packages
......@@ -11,13 +11,13 @@ with open('README.rst') as f:
long_description = f.read()
setup(
name='scikit-surgeryvideoutils',
name='scikit-surgeryutils',
version=versioneer.get_version(),
cmdclass=versioneer.get_cmdclass(),
description='scikit-surgeryvideoutils - Tests/demos utilities, based around opencv-contrib and PySide2',
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-surgeryvideoutils',
url='https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgeryutils',
author='Matt Clarkson',
author_email='m.clarkson@ucl.ac.uk',
license='BSD-3 license',
......@@ -60,8 +60,8 @@ setup(
entry_points={
'console_scripts': [
'sksurgeryvideolag=sksurgeryvideoutils.ui.sksurgeryvideolag_command_line:main',
'sksurgerycharucotest=sksurgeryvideoutils.ui.sksurgerycharucotest_command_line:main',
'sksurgeryvideolag=sksurgeryutils.ui.sksurgeryvideolag_command_line:main',
'sksurgerycharucotest=sksurgeryutils.ui.sksurgerycharucotest_command_line:main',
],
},
)
......@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
import sys
from sksurgeryvideoutils.ui.sksurgerycharucotest_command_line import main
from sksurgeryutils.ui.sksurgerycharucotest_command_line import main
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
# coding=utf-8
"""scikit-surgeryvideoutils"""
"""scikit-surgeryutils"""
from ._version import get_versions
__version__ = get_versions()['version']
......
# coding=utf-8
"""scikit-surgeryvideoutils"""
"""scikit-surgeryutils"""
......@@ -3,8 +3,8 @@
""" Command line processing for charucotest app. """
import argparse
from sksurgeryvideoutils import __version__
from sksurgeryvideoutils.ui.sksurgerycharucotest_demo import run_demo
from sksurgeryutils import __version__
from sksurgeryutils.ui.sksurgerycharucotest_demo import run_demo
def main(args=None):
......
......@@ -8,7 +8,7 @@ from cv2 import aruco
from PySide2 import QtCore, QtWidgets
from PySide2.QtCore import Slot
import sksurgeryimage.calibration.aruco as ar
import sksurgeryvideoutils.utils.image_utils as iu
import sksurgeryutils.utils.image_utils as iu
# pylint: disable=too-many-instance-attributes
......
......@@ -3,8 +3,8 @@
""" Command line processing for videolag app. """
import argparse
from sksurgeryvideoutils import __version__
from sksurgeryvideoutils.ui.sksurgeryvideolag_demo import run_demo
from sksurgeryutils import __version__
from sksurgeryutils.ui.sksurgeryvideolag_demo import run_demo
def main(args=None):
......
......@@ -7,7 +7,7 @@ import six
import cv2
from PySide2 import QtCore, QtWidgets, QtGui
from PySide2.QtCore import Slot
import sksurgeryvideoutils.utils.image_utils as iu
import sksurgeryutils.utils.image_utils as iu
# pylint: disable=too-many-instance-attributes
......
......@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
import sys
from sksurgeryvideoutils.ui.sksurgeryvideolag_command_line import main
from sksurgeryutils.ui.sksurgeryvideolag_command_line import main
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
......@@ -2,7 +2,7 @@
"""sksurgeryarucotest tests"""
from sksurgeryvideoutils.ui.sksurgerycharucotest_demo import run_demo
from sksurgeryutils.ui.sksurgerycharucotest_demo import run_demo
def test_sksurgeryarucotest():
......
......@@ -2,7 +2,7 @@
"""sksurgeryvideolag tests"""
from sksurgeryvideoutils.ui.sksurgeryvideolag_demo import run_demo
from sksurgeryutils.ui.sksurgeryvideolag_demo import run_demo
def test_sksurgeryvideolag():
......
......@@ -2,7 +2,7 @@
import pytest
import numpy as np
import sksurgeryvideoutils.utils.image_utils as iu
import sksurgeryutils.utils.image_utils as iu
def test_image_to_pixel_invalid_because_input_is_none():
......
......@@ -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 ./sksurgeryvideoutils -m pytest -v -s
coverage run -a --source ./sksurgeryutils -m pytest -v -s
coverage report -m
[testenv:lint]
basepython=python3.6
deps=pylint
{[testenv]deps}
commands=pylint --rcfile=tests/pylintrc sksurgeryvideoutils
commands=pylint --rcfile=tests/pylintrc sksurgeryutils
[testenv:docs]
basepython=python3.6
......
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