Initial commit

.gitignore

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+.idea/
+__pycache__/
+*.pyc
+*.iml
+*.html
+.coverage
+~*
+*~
+htmlcov/
+*.json
+*.css
+*.png
+*.js
+.*
+!/.gitignore
+!/docs/build/html

LICENSE.md

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+Copyright 2019 Austrian Centre of Industrial Biotechnology, Vienna
+
+Copyright 2020 University of Natural Resources and Life Sciences, Vienna
+
+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:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+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.

Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = docs/source
+BUILDDIR      = docs/build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

README.md

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+# bio_rtd library
+bio_rtd library is a python library for modeling
+residence time distributions (RTD)
+of integrated continuous biomanufacturing processes.
+
+## Version
+Current version: 0.7
+
+## Requirements
+
+Python 3.7.+
+
+Core dependencies:
+
+- numpy
+- scipy
+
+Packages for visual representation in examples:
+
+- bokeh
+- xlrd
+
+Packages for importing data from Excel in examples:
+
+* pandas
+
+## Installation
+
+Download or clone the github repo:
+
+    git clone https://github.com/open-biotech/bio-rtd.git
+
+Set local destination (`/path_to/bio-rtd`) as working directory
+or add it to the python path.
+
+
+## Getting started
+
+Examples can be run as scripts:
+
+    python examples/unit_operations/pcc.py
+
+Model examples ending with `_gui.py`
+can be run via `bokeh serve` command:
+
+    bokeh serve examples/models/mab_a/mab_a_gui.py
+
+or
+
+    python bokeh serve examples/models/mab_a/mab_a_gui.py
+
+For more information see the documentation.
+
+## Documentation
+
+Documentation can be accessed at ... or by building a local copy.
+
+To build a local version of documentation install the following packages:
+
+    pip install sphinx sphinx_autodoc_typehints sphinx_rtd_theme
+
+run command:
+
+    make html
+
+and open `docs/build/html/index.html` with a web browser.
+
+## Contributing
+
+1. Create your feature branch (`git checkout -b feature/myFeature`)
+2. Update the code, documentation and tests
+   * Maintain 100 % code coverage in `bio_rtd`
+3. Commit your changes (`git commit -am 'Describe the changes'`)
+4. Push to the branch (`git push origin feature/myFeature`)
+5. Create a new Pull Request
+
+For additional information, see the
+[Documentation - Development]() (link needs update)
+section.
+
+
+## Meta information
+
+Distributed under the MIT license. See ``LICENSE`` for more information.
+
+For technical issues, bug reports and feature request use
+[issue tracker](https://github.com/open-biotech/bio-rtd/issues).
+
+If you are using the library in your projects please let 
+[us know](mailto:jure.sencar@boku.ac.at).
+This way we know how much interest there is, what is the scope of usage,
+the needs, etc. This information influences the future development of the project.
+
+
+E-mail: [jure.sencar@boku.ac.at](mailto:jure.sencar@boku.ac.at)
+
+University of Natural Resources and Life Sciences (BOKU), Vienna
+
+## Referencing the library
+
+ If you are using this package for a scientific publication,
+ please add the following reference:
+
+* Senčar, J., (2020) GitHub Repository,
+   https://github.com/open-biotech/bio-rtd.
+
+## Acknowledgements
+This work was supported by:
+
+- The Federal Ministry for Digital and
+  Economic Affairs (bmwd), the Federal Ministry for Transport,
+  Innovation and Technology (bmvit),
+  the Styrian Business Promotion Agency SFG,
+  the Standortagentur Tirol,
+  Government of Lower Austria,
+  and ZIT - Technology Agency of the City of Vienna
+  through the COMET-Funding Program managed
+  by the Austrian Research Promotion Agency FFG
+- Baxalta Innovations GmbH (now part of Takeda)
+- Bilfinger Industrietechnik Salzburg GmbH

ToDo.md

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+# ToDo
+
+List of things to do.
+
+## Maintenance
+
+#### Sample Cases
+* Process optimization example.
+
+#### Documentation
+* Update docstrings.
+* Update Examples in Documentation.
+
+#### Testing
+Unit tests:
+* Add tests for data stored in data log.
+
+Integrated tests:
+* Define testing strategy and implement tests.
+
+## New Features
+
+#### Unit Operations
+* PCC with irregular cycles (cycle switch based on bt criteria) and
+  surge tanks that supports such process.
+* `pdf` and `breakthrough_profiles` that support different
+  binding properties for different species.
+
+
+Implementation of new features should not result in expansion
+of **Maintenance** section.