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#### PyBILT is a Python toolkit developed to analyze molecular simulation trajectories of lipid bilayers systems. The toolkit includes a variety of analyses from various lipid bilayer molecular simulation publications.
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# Install
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|**! Warning**|
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| :--- |
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| PyBILT is still under heavy development and may rapidly change. |
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#### PyBILT run dependencies
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PyBILT has the following major dependencies:
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* MDAnalysis - https://www.mdanalysis.org/
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* NumPy - http://www.numpy.org/
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* SciPy - https://www.scipy.org/
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* Matplotlib - https://matplotlib.org/
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* Seaborn - https://seaborn.pydata.org/
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* six - https://pypi.org/project/six/
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* future - http://python-future.org/
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To run the pybilt test suite:
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* pytest - https://docs.pytest.org/en/latest/
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To use the PyBILT Jupyter Notebooks:
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* Jupyter - http://jupyter.org/
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To build the docs locally requires the following additional packages:
The pybilt package has been tested using [Anaconda Python](https://www.anaconda.com/) 2.7, 3.6, and 3.7.
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The pybilt package has been tested using [Anaconda Python](https://www.anaconda.com/) 2.7 and Python 3.6;
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#### Sunsetting of Python 2
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Please be aware that Python 2 is scheduled to be sunset on January 1 2020. You can read about it here: [https://www.python.org/doc/sunset-python-2/](https://www.python.org/doc/sunset-python-2/)
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Parallel to the sunsetting of Python 2 many open source packages are also dropping support for Python 2 ([https://python3statement.org/](https://python3statement.org/)), including some of PyBILT's core dependencies. As such, after January 1, 2020, PyBILT will also likely sunset its support for Python 2.7.
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The following section describes the process for setting up the dependencies and
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installing the 'pybilt' package using a conda environment and the setup.py
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script.
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## Setup and install using Anaconda's conda tool
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### Method 1 (manual package installation)
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First, clone or download the GitHub repo
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```
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git clone https://github.com/blakeaw/PyBILT.git
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### pip install
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You can install the latest version of the `pybilt` package using `pip` sourced from the GitHub repo:
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```
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Then create a new conda environment for pybilt and activate it:
However, this will not automatically install the core dependencies. You will have to do that separately:
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```
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The install the preferred python version:
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* for Python 2.7
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pip install MDAnalysis numpy scipy matplotlib seaborn six future
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```
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conda install python=2.7
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```
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* for Python 3.6
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```
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conda install python=3.6
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```
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Then install all the pybilt run dependencies:
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```
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conda install numpy scipy matplotlib seaborn six future
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conda install -c conda-forge MDAnalysis
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### conda install
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First make sure you have the `conda-forge` channel in your channel list; that is the channel from which MDAnalysis is installed. You can use the following command to add it to the bottom of your channel list:
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```
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Then install pybilt:
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```
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python PyBILT/setup.py install
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conda config --append channels conda-forge
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```
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If you want to run the pybilt tests you can install pytest:
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```
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conda install pytest
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Then you can install the `pybilt` package from the `blakeaw` Anaconda Cloud channel,
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```
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If you want to run the pybilt Jupyter notebooks (PyBILT/jupyter_notebooks), then install Jupyter:
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conda install -c blakeaw pybilt
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```
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conda install jupyter
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```
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Note that the notebooks have not been updated for Python 3 yet.
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The core dependencies will be automatically installed.
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If you want to build local versions of doc pages install the following packages:
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```
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conda install sphinx
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pip install sphinx_rtd_theme
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pip install recommonmark
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```
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### Recommended additional software
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### Method 2 (From environment yaml)
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The following software is not required for the basic operation of **PyBILT**, but provides extra capabilities and features when installed.
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The files environment_py27.yml and environment_py36.yml have been provided to allow for easy setup of a new conda
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environment with all of the most recently tested versions of dependencies.
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Run:
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* For Python 2.7:
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```
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conda env create -f environment_py27.yml
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```
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* For Python 3.6
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```
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conda env create -f environment_py36.yml
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```
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#### pytest
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The pybilt test suite is designed to be run with [pytest](https://docs.pytest.org/en/latest/), so if you want to run the tests then you will need to install pytest.
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which will create a new conda environment named *pybilt* with the appropriate
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dependencies. Then activate the environment
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```
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conda activate pybilt
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```
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Next, run the setup.py script with install,
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```
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python PyBILT/setup.py install
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```
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to install the 'pybilt' package into the *pybilt* environment.
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#### Jupyter
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PyBILT comes with a set of [Jupyter IPython notebooks](./jupyter_notebooks) which supplement the doc pages. If you want to run these notebooks locally then you will need to intall [Jupyter](https://jupyter.org/) (or at least the IPython kernel).
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If you want to run the pybilt Jupyter notebooks (PyBILT/jupyter_notebooks), then install Jupyter:
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```
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conda install jupyter
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```
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Note that the notebooks have not been updated for Python 3 yet.
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#### sphinx, sphinx_rtd_theme, and recommonmark
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If you want to build local versions of doc pages install the following additional packages:
**PyBILT** is composed of 2 primary analysis packages:
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* bilayer_analyzer -- The [bilayer_analyzer](http://pybilt.readthedocs.io/en/latest/pybilt.bilayer_analyzer.html#module-pybilt.bilayer_analyzer.bilayer_analyzer) is an analysis package that
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is designed to analyze (quasi) planar lipid bilayer
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(using matplotlib and seaborn) for some of the properties
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that can be computed from functions in the other modules.
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e.g. mean squared displacement and area per lipid.
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------
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# Documentation
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## Docs
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Visit the PyBILT docs on [Read the Docs](http://pybilt.readthedocs.io/en/latest/index.html).
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Docs can also be viewed offline/locally by opening the [PyBILT/docs/build/html/index.html](docs/build/html/index.html) file from the
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repo in a web browser; however, this build of the docs is not updated often.
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## Jupyter IPython notebooks
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In addition
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to the doc pages, there are currently a few Jupyter IPython
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to the Docs, there are currently a few Jupyter IPython
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[notebooks](jupyter_notebooks) that provide some examples and show some basic
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usage (these have not been updated/tested for/with python 3 yet); updates and more of these are in the pipeline.
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# Contact
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To report problems or bugs please open a
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[GitHub Issue](https://github.com/blakeaw/PyBILT/issues). Additionally, any
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[GitHub Issue](https://github.com/LoLab-VU/PyBILT/issues). Additionally, any
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comments, suggestions, or feature requests for PyBILT can also be submitted as
If you would like to contribute directly to PyBILT's development please
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1. Fork the repo (https://github.com/blakeaw/PyBILT/fork)
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1. Fork the repo (https://github.com/LoLab-VU/PyBILT/fork)
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2. Create a new branch for your feature (git checkout -b feature/foo_bar)
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3. Create test code for your feature
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4. Once your feature passes its own test, run all the tests using [pytest](https://docs.pytest.org/en/latest/) (python -m pytest)
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------
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##License
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# License
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This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
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------
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##Acknowledgments
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# Acknowledgments
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* A special thanks to James Pino (https://github.com/JamesPino) for his inciteful comments and suggestions that have helped improve the quality of this code, and thanks to him for pointing out some very useful coding tools.
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* Thanks to my advisors, Carlos F. Lopez and Arvind Ramanathan, for catalyzing this project and for providing me with the space and means to pursue it.
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------
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## Built With
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*[ANACONDA](https://www.continuum.io/) - ANACONDA Python distribution and CONDA package and environment manager
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*[PyCharm](https://www.jetbrains.com/pycharm/) - Text Editor/IDE
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*[ATOM](https://atom.io/) - Text Editor/IDE
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*[Sublime Text](https://www.sublimetext.com/) - Text Editor used in earlier work
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*[Landscape](https://landscape.io/) - Code quality analysis and tracking
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*[Git](https://git-scm.com/) - Version control
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*[GitHub](https://github.com/) - Development Platform and repository storage
*[recommonmark](https://github.com/rtfd/recommonmark) - A docutils-compatibility bridge to CommonMark
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*[Read the Docs](https://readthedocs.org/) - Documentation hosting
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*[docstring-coverage](https://bitbucket.org/DataGreed/docstring-coverage/wiki/Home) - A simple audit tool for examining python source files for missing docstrings.
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*[Python-Modernize](https://python-modernize.readthedocs.io/en/latest/) - Automatic modernization of Python 2 code for dual Python 2 and 3 support.
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# Citing
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------
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If you use the **PyBILT** software as a part of your research, please cite the GitHub repo.
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Also, please cite the following references as appropriate for scientific/research software used with/via **PyBILT**:
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#### MDAnalysis
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See: https://www.mdanalysis.org/pages/citations/
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#### Packages from the SciPy ecosystem
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These include NumPy, SciPy, and Matplotlib for which references can be obtained from:
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https://www.scipy.org/citing.html
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#### seaborn
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Reference can be exported from the [seaborn Zeondo DOI entry](https://doi.org/10.5281/zenodo.592845)
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