diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..99bf746 --- /dev/null +++ b/LICENSE @@ -0,0 +1,14 @@ +/* +* ---------------------------------------------------------------------------- +* "THE BEER-WARE LICENSE" (Revision 42): +* wrote this file. As long as you retain this notice you +* can do whatever you want with this stuff. If we meet some day, and you think +* this stuff is worth it, you can buy me a beer in return. Holger Frey +* ---------------------------------------------------------------------------- +*/ + + +The example content for the test cases involving database connections was +assembled from https://en.wikipedia.org/wiki/List_of_cheeses and other pages in +the domain of en.wikipedia.org. This content was provided by the Wikimedia +Foundation under the Creative Commons Attribution-ShareAlike License. \ No newline at end of file diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..fa01dd8 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,8 @@ +include LICENSE +include README.md + +recursive-include tests * +recursive-exclude * __pycache__ +recursive-exclude * *.py[co] + +recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif diff --git a/Makefile b/Makefile index 7ac6b1a..39c8f8d 100644 --- a/Makefile +++ b/Makefile @@ -61,3 +61,11 @@ coverage: ## check code coverage with the default Python coverage report -m coverage html $(BROWSER) htmlcov/index.html + +dist: clean ## builds source and wheel package + python setup.py sdist + python setup.py bdist_wheel + ls -l dist + +install: clean ## install the package to the active Python's site-packages + python setup.py install diff --git a/README.md b/README.md new file mode 100644 index 0000000..3bf91b5 --- /dev/null +++ b/README.md @@ -0,0 +1,5 @@ +Mtor Image Analysis +=================== + +Image analysis for the mTor project + diff --git a/mtor/__init__.py b/mtor/__init__.py index b56c1c6..5c53421 100644 --- a/mtor/__init__.py +++ b/mtor/__init__.py @@ -11,6 +11,8 @@ from .workflows import ( warnings.filterwarnings("ignore") +__version__ = "0.1.0" + def run(): # pw = prescan_workflow("mtor-bilder", 50, 910, 300, 660) pw = prescan_workflow("mtor-bilder", 50, 725 + 150, 300, 725) diff --git a/mtor/cli.py b/mtor/cli.py new file mode 100644 index 0000000..72535c3 --- /dev/null +++ b/mtor/cli.py @@ -0,0 +1,18 @@ +# -*- coding: utf-8 -*- + +"""Console script for mtor.""" +import sys +import click + + +@click.command() +def main(args=None): + """Console script for mtor.""" + click.echo("Replace this message by putting your code into " + "mtor.cli.main") + click.echo("See click documentation at http://click.pocoo.org/") + return 0 + + +if __name__ == "__main__": + sys.exit(main()) # pragma: no cover diff --git a/requirements_dev.txt b/requirements_dev.txt new file mode 100644 index 0000000..2c0229b --- /dev/null +++ b/requirements_dev.txt @@ -0,0 +1,11 @@ +pip==18.1 +bumpversion==0.5.3 +wheel==0.32.1 +watchdog==0.9.0 +flake8==3.5.0 +tox==3.5.2 +coverage==4.5.1 +Sphinx==1.8.1 +twine==1.12.1 +black==18.9b0 + diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..908937a --- /dev/null +++ b/setup.cfg @@ -0,0 +1,19 @@ +[bumpversion] +current_version = 0.1.0 +commit = True +tag = True + +[bumpversion:file:setup.py] +search = version='{current_version}' +replace = version='{new_version}' + +[bumpversion:file:mtor/__init__.py] +search = __version__ = '{current_version}' +replace = __version__ = '{new_version}' + +[bdist_wheel] +universal = 1 + +[aliases] +# Define setup.py command aliases here + diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..2a196e5 --- /dev/null +++ b/setup.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +"""The setup script.""" + +from setuptools import setup, find_packages + +with open("README.md") as readme_file: + readme = readme_file.read() + +with open("HISTORY.rst") as history_file: + history = history_file.read() + +requirements = [ + "Click>=6.0", + "pandas>=0.24", + "seaborn>=0.9", + "xlrd>=1.2", + "scikit-image>=0.15", + "scikit-learn>=0.20", + "peakutils>=1.3", + "tqdm>=4.31", + "openpyxl>=2.6", + "scipy>=1.2", + "xlwt>=1.3", + "xlsxwriter>=1.1", + "reportlab>=3.5", +] + +setup_requirements = [ ] + +test_requirements = [ ] + +setup( + author="Holger Frey", + author_email="mail@holgerfrey.de", + classifiers=[ + "Development Status :: 2 - Pre-Alpha", + "Intended Audience :: Developers", + "License :: Other", + "Natural Language :: English", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + ], + description="Image analysis for the mTor project", + entry_points={ + "console_scripts": [ + "mtor=mtor.cli:main", + ], + }, + install_requires=requirements, + license="Beerware license", + long_description=readme, + include_package_data=True, + keywords="mtor", + name="mtor", + packages=find_packages(include=["mtor"]), + setup_requires=setup_requirements, + url="ttps://git.cpi.imtek.uni-freiburg.de/holgi/mtor", + version="0.1.0", + zip_safe=False, +)