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@@ -15,6 +15,7 @@ EMMA (Emma's Markov Model Algorithms) | |
.. image:: https://coveralls.io/repos/markovmodel/PyEMMA/badge.svg?branch=devel | ||
:target: https://coveralls.io/r/markovmodel/PyEMMA?branch=devel | ||
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What is it? | ||
----------- | ||
PyEMMA (EMMA = Emma's Markov Model Algorithms) is an open source | ||
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@@ -25,14 +26,15 @@ of: | |
* Clustering and Featurization | ||
* Markov state models (MSMs) | ||
* Hidden Markov models (HMMs) | ||
* multi-ensemble Markov models (MEMMs) | ||
* Multi-ensemble Markov models (MEMMs) | ||
* Time-lagged independent component analysis (TICA) | ||
* Transition Path Theory (TPT) | ||
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PyEMMA can be used from Jupyther (former IPython, recommended), or by | ||
PyEMMA can be used from Jupyter (former IPython, recommended), or by | ||
writing Python scripts. The docs, can be found at | ||
`http://pyemma.org <http://www.pyemma.org/>`__. | ||
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Citation | ||
-------- | ||
If you use PyEMMA in scientific work, please cite: | ||
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@@ -46,17 +48,16 @@ If you use PyEMMA in scientific work, please cite: | |
Installation | ||
------------ | ||
With pip:: | ||
pip install pyemma | ||
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with conda:: | ||
pip install pyemma | ||
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conda install -c omnia pyemma | ||
with conda:: | ||
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conda install -c omnia pyemma | ||
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or install latest devel branch with pip:: | ||
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pip install git+https://github.com/markovmodel/PyEMMA.git@devel | ||
pip install git+https://github.com/markovmodel/PyEMMA.git@devel | ||
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For a complete guide to installation, please have a look at the version | ||
`online <http://www.emma-project.org/latest/INSTALL.html>`__ or offline in file | ||
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@@ -70,9 +71,10 @@ Then build with make:: | |
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cd doc; make html | ||
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Support and development | ||
----------------------- | ||
For bug reports/sugguestions/complains please file an issue on | ||
For bug reports/suggestions/complaints please file an issue on | ||
`GitHub <http://github.com/markovmodel/PyEMMA>`__. | ||
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Or start a discussion on our mailing list: [email protected] | ||
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@@ -83,4 +85,4 @@ External Libraries | |
* mdtraj (LGPLv3): https://mdtraj.org | ||
* bhmm (LGPLv3): http://github.com/bhmm/bhmm | ||
* msmtools (LGLPv3): http://github.com/markovmodel/msmtools | ||
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* thermotools (LGLPv3): http://github.com/markovmodel/thermotools |