initial commit

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -23,7 +24,6 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -45,7 +45,6 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
-.pytest_cache/
 
 # Translations
 *.mo
@@ -54,7 +53,6 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
 
 # Flask stuff:
 instance/
@@ -81,14 +79,13 @@ celerybeat-schedule
 # SageMath parsed files
 *.sage.py
 
-# Environments
+# dotenv
 .env
+
+# virtualenv
 .venv
-env/
 venv/
 ENV/
-env.bak/
-venv.bak/
 
 # Spyder project settings
 .spyderproject
@@ -101,4 +98,6 @@ venv.bak/
 /site
 
 # mypy
-.mypy_cache/
+_version_save.py
+.pytest_cache
+

.readthedocs.yml

@@ -0,0 +1,7 @@
+formats:
+ - pdf
+requirements_file: docs/requirements.txt
+build:
+    image: latest
+python:
+   version: 3.6

.travis.yml

@@ -0,0 +1,34 @@
+notifications:
+  email: false
+language: python
+python:
+- '3.6'
+env:
+  matrix:
+  - TEST="PYTEST"
+  - TEST="FLAKE8"
+install:
+- travis_retry pip install --no-deps .
+# coverage packages
+- travis_retry pip install flake8
+- travis_retry pip install codecov coverage
+- pip freeze
+script:
+- if [ "${TEST}" == "PYTEST" ]; then
+       coverage run --source=cellsino setup.py test;
+       coverage report -m;
+       codecov;
+  else
+       flake8 drymass;
+       flake8 examples;
+       flake8 tests;
+  fi;
+deploy:
+  provider: pypi
+  user: "ci_qpi"
+  password:
+    secure: "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"
+  on:
+    tags: true
+  distributions: "sdist bdist_wheel"
+  skip_existing: true

CHANGELOG

@@ -0,0 +1,2 @@
+0.0.1
+ - initial release

MANIFEST.in

@@ -0,0 +1,8 @@
+include CHANGELOG
+include LICENSE
+include README.rst
+recursive-include examples *.py *.jpg *.npy *.npz
+recursive-include docs *.py *.md *.txt *.rst *.bib *.gif *.jpg
+recursive-include tests *.py *.md *.zip *.h5
+prune docs/_build
+exclude docs/_version_save.py

README.rst

@@ -0,0 +1,43 @@
+cellsino
+========
+
+|PyPI Version| |Tests Status| |Coverage Status| |Docs Status|
+
+
+**cellsino** is a Python library for generating sinograms (phase and
+fluorescence) of cell phantoms for testing tomographic reconstruction algorithms.
+
+
+Documentation
+-------------
+
+The documentation, including the code reference and examples, is available at
+`cellsino.readthedocs.io <https://cellsino.readthedocs.io/en/stable/>`__.
+
+
+Installation
+------------
+
+::
+
+    pip install cellsino
+
+
+Testing
+-------
+
+::
+
+    pip install -e .
+    python setup.py test
+    
+
+.. |PyPI Version| image:: https://img.shields.io/pypi/v/cellsino.svg
+   :target: https://pypi.python.org/pypi/cellsino
+.. |Tests Status| image:: https://img.shields.io/travis/RI-imaging/cellsino.svg
+   :target: https://travis-ci.org/RI-imaging/cellsino
+.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/RI-imaging/cellsino/master.svg
+   :target: https://codecov.io/gh/RI-imaging/cellsino
+.. |Docs Status| image:: https://readthedocs.org/projects/cellsino/badge/?version=latest
+   :target: https://readthedocs.org/projects/cellsino/builds/
+

setup.cfg

@@ -0,0 +1,6 @@
+[aliases]
+test = pytest
+
+[metadata]
+license_file = LICENSE
+

setup.py

@@ -0,0 +1,45 @@
+from os.path import dirname, realpath, exists
+from setuptools import setup, find_packages
+import sys
+
+
+author = u"Paul Müller"
+authors = [author]
+description = 'in-silico sinograms (phase and fluorescence) of cells'
+name = 'cellsino'
+year = "2019"
+
+sys.path.insert(0, realpath(dirname(__file__))+"/"+name)
+from _version import version
+
+setup(
+    name=name,
+    author=author,
+    author_email='dev@craban.de',
+    url='https://github.com/RI-imaging/cellsino',
+    version=version,
+    packages=find_packages(),
+    package_dir={name: name},
+    include_package_data=True,
+    license="MIT",
+    description=description,
+    long_description=open('README.rst').read() if exists('README.rst') else '',
+    install_requires=["qpimage",
+                      "qpsphere",
+                      "numpy>=1.12.0",
+                      ]
+    setup_requires=['pytest-runner'],
+    tests_require=["pytest"],
+    python_requires='>=3.6, <4',
+    keywords=["phase microscopy",
+              "fluorescence imaging",
+              "optical tomography",
+              "diffraction tomography",
+              ],
+    classifiers= [
+        'Operating System :: OS Independent',
+        'Programming Language :: Python :: 3',
+        'Intended Audience :: Science/Research'
+                 ],
+    platforms=['ALL'],
+    )