added basic packaging structure

LICENSE

@@ -0,0 +1,14 @@
+/*
+* ----------------------------------------------------------------------------
+* "THE BEER-WARE LICENSE" (Revision 42):
+* <frey@imtek.de> 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.

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

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

README.md

@@ -0,0 +1,5 @@
+Mtor Image Analysis
+===================
+
+Image analysis for the mTor project
+

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)

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

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
+

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
+

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,
+)