From 4fb83afb9fccc6e827e036f2b64884c096153898 Mon Sep 17 00:00:00 2001 From: Patrick Cleeve Date: Mon, 3 Oct 2022 17:13:32 +1100 Subject: [PATCH] update package / install info --- .coveragerc | 13 ---------- .flake8 | 10 -------- LICENSE | 42 +++++++++++++------------------ requirements.txt | 11 -------- setup.cfg | 31 +++++++++++++++-------- setup.py | 65 ++---------------------------------------------- 6 files changed, 40 insertions(+), 132 deletions(-) delete mode 100644 .coveragerc delete mode 100644 .flake8 delete mode 100644 requirements.txt diff --git a/.coveragerc b/.coveragerc deleted file mode 100644 index e15786c2..00000000 --- a/.coveragerc +++ /dev/null @@ -1,13 +0,0 @@ -[run] -source = - liftout -[report] -omit = - */python?.?/* - */site-packages/nose/* - # ignore _version.py and versioneer.py - .*version.* - *_version.py - -exclude_lines = - if __name__ == '__main__': diff --git a/.flake8 b/.flake8 deleted file mode 100644 index 53cbfaa2..00000000 --- a/.flake8 +++ /dev/null @@ -1,10 +0,0 @@ -[flake8] -exclude = - .git, - __pycache__, - build, - dist, - versioneer.py, - liftout/_version.py, - docs/source/conf.py -max-line-length = 115 diff --git a/LICENSE b/LICENSE index 8cab152f..6629fb24 100644 --- a/LICENSE +++ b/LICENSE @@ -1,29 +1,21 @@ -BSD 3-Clause License +MIT License -Copyright (c) 2020, Genevieve Buckley -All rights reserved. +Copyright (c) 2022 DeMarcoLab -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: -1. Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. -2. 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. - -3. 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. +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index efed0f80..00000000 --- a/requirements.txt +++ /dev/null @@ -1,11 +0,0 @@ -click -ipython -matplotlib -numpy -opencv-python -pillow -pyyaml -scipy -scikit-image -petname -pandas diff --git a/setup.cfg b/setup.cfg index 0ec6c0a5..292957cc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,12 +1,23 @@ -[versioneer] -VCS = git -style = pep440-post -versionfile_source = liftout/_version.py -versionfile_build = liftout/_version.py -tag_prefix = v +[metadata] +name = autoliftout +version = 0.0.1 +author = Patrick Cleeve +author_email = Patrick.Cleeve@monash.edu +description = automated cryo-liftout +long_description = file: README.md +long_description_content_type = text/markdown +url = https://github.com/DeMarcoLab/autoliftout +project_urls = + Bug Tracker = https://github.com/DeMarcoLab/autoliftout/issues +classifiers = + Programming Language :: Python :: 3 + License :: OSI Approved :: MIT License + Operating System :: OS Independent -[bdist_wheel] -universal = 1 +[options] +packages = find: +python_requires = >=3.9 -[flake8] -exclude = docs / conf.py +[options.entry_points] +console_scripts = + autoliftout_ui = autoliftout.gui.main:main \ No newline at end of file diff --git a/setup.py b/setup.py index a70a71c7..864b617c 100644 --- a/setup.py +++ b/setup.py @@ -1,63 +1,2 @@ -from os import path -from setuptools import setup, find_packages -import sys -import versioneer - - -# NOTE: This file must remain Python 2 compatible for the foreseeable future, -# to ensure that we error out properly for people with outdated setuptools -# and/or pip. -min_version = (3, 6) -if sys.version_info < min_version: - error = """ -liftout does not support Python {0}.{1}. -Python {2}.{3} and above is required. Check your Python version like so: - -python3 --version - -This may be due to an out-of-date pip. Make sure you have pip >= 9.0.1. -Upgrade pip like so: - -pip install --upgrade pip -""".format(*(sys.version_info[:2] + min_version)) - sys.exit(error) - -here = path.abspath(path.dirname(__file__)) - -with open(path.join(here, 'README.md'), encoding='utf-8') as readme_file: - readme = readme_file.read() - -with open(path.join(here, 'requirements.txt')) as requirements_file: - # Parse requirements.txt, ignoring any commented-out lines. - requirements = [line for line in requirements_file.read().splitlines() - if not line.startswith('#')] - - -setup( - name='liftout', - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - description="Automated cryo-liftout for electron microscopy.", - long_description=readme, - author="Genevieve Buckley", - author_email='', - url='https://github.com/GenevieveBuckley/liftout', - python_requires='>={}'.format('.'.join(str(n) for n in min_version)), - packages=find_packages(exclude=['docs', 'tests']), - entry_points={"console_scripts": ["liftout = liftout.main:main_cli"]}, - include_package_data=True, - package_data={ - 'liftout': [ - # When adding files here, remember to update MANIFEST.in as well, - # or else they will not be included in the distribution on PyPI! - # 'path/to/data_file', - ] - }, - install_requires=requirements, - license="BSD (3-clause)", - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'Natural Language :: English', - 'Programming Language :: Python :: 3', - ], -) +import setuptools +setuptools.setup() \ No newline at end of file