Copy from msmbuilder-3.8.0

MANIFEST.in

@@ -0,0 +1,4 @@
+graft examples
+graft msmbuilder
+include basesetup.py
+include LICENSE

README.md

@@ -0,0 +1,62 @@
+MSMBuilder
+==========
+
+[![Build Status](https://travis-ci.org/msmbuilder/msmbuilder.svg?branch=master)](https://travis-ci.org/msmbuilder/msmbuilder)
+[![PyPi version](https://badge.fury.io/py/msmbuilder.svg)](https://pypi.python.org/pypi/msmbuilder/)
+[![License](https://img.shields.io/badge/license-LGPLv2.1+-red.svg?style=flat)](https://pypi.python.org/pypi/msmbuilder/)
+[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg?style=flat)](http://msmbuilder.org)
+
+MSMBuilder is a python package which implements a series of statistical
+models for high-dimensional time-series. It is particularly focused on the
+analysis of atomistic simulations of biomolecular dynamics. For example,
+MSMBuilder has been used to model protein folding and conformational change
+from molecular dynamics (MD) simulations. MSMBuilder is available under the
+LGPL (v2.1 or later).
+
+Capabilities include:
+
+- Feature extraction into dihedrals, contact maps, and more
+- Geometric clustering with a variety of algorithms.
+- Dimensionality reduction using time-structure independent component
+  analysis (tICA) and principal component analysis (PCA).
+- Markov state model (MSM) construction
+- Rate-matrix MSM construction
+- Hidden markov model (HMM) construction
+- Timescale and transition path analysis.
+
+Check out the documentation at [msmbuilder.org](http://msmbuilder.org) and
+join the [mailing list](https://mailman.stanford.edu/mailman/listinfo/msmbuilder-user).
+For a broader overview of MSMBuilder, take a look at our [slide deck](http://rawgit.com/msmbuilder/talk/master/index.html).
+
+Installation
+------------
+
+The preferred installation mechanism for `msmbuilder` is with `conda`:
+
+```bash
+$ conda install -c omnia msmbuilder
+```
+
+If you don't have conda, or are new to scientific python, we recommend that
+you download the [Anaconda scientific python distribution](https://store.continuum.io/cshop/anaconda/).
+
+
+Workflow
+--------
+
+An example workflow might be as follows:
+
+1. Set up a system for molecular dynamics, and run one or more simulations
+   for as long as you can on as many CPUs or GPUs as you have access to.
+   There are a lot of great software packages for running MD, e.g [OpenMM]
+   (https://simtk.org/home/openmm), [Gromacs](http://www.gromacs.org/),
+   [Amber](http://ambermd.org/), [CHARMM](http://www.charmm.org/), and
+   many others. MSMBuilder is not one of them.
+
+2. Transform your MD coordinates into an appropriate set of features.
+
+3. Perform some sort of dimensionality reduction with tICA or PCA.
+   Reduce your data into discrete states by using clustering.
+
+4. Fit an MSM, rate matrix MSM, or HMM. Perform model selection using
+   cross-validation with the [generalized matrix Rayleigh quotient](http://arxiv.org/abs/1407.8083)

appveyor.yml

@@ -0,0 +1,24 @@
+environment:
+
+  global:
+    PYTHONUNBUFFERED: on
+
+  matrix:
+    - PYDIR: "C:\\Miniconda35"
+      CONDA_PY: "35"
+      CONDA_NPY: "1.10"
+
+    - PYDIR: "C:\\Miniconda35-x64"
+      CONDA_PY: "35"
+      CONDA_NPY: "1.10"
+
+install:
+  - set PATH=%PYDIR%;%PYDIR%\\Scripts;%PATH%
+  - conda config --add channels omnia
+  - conda update -yq --all
+  - conda install -yq conda-build jinja2
+
+build: false
+
+test_script:
+  - conda build -q devtools\conda-recipe