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Mention conda-forge in Readme
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README.md

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@@ -14,16 +14,29 @@ sunode comes with a theano wrapper so that parameters of an ode can be estimated
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using pymc3.
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### Installation
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sunode is available on conda-forge. Set up a conda environment to use conda-forge
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and install sunode:
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```bash
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conda create -n sunode-env
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conda activate sunode-env
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conda config --add channels conda-forge
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conda config --set channel_priority strict
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conda install sunode
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```
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You can also install the development version. One windows you have to make
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sure the correct visual studio version is install and in the PATH.
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```
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git clone [email protected]:aseyboldt/sunode
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# Or if no ssh key is configured:
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git clone https://github.com/aseyboldt/sunode
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cd sunode
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conda create -n sunode -c conda-forge python numba pymc3 sympy pandas xarray sundials
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conda activate sunode
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conda install --only-deps sunode
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pip install -e .
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```
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Installation instructions for windows can be found [here](https://gist.github.com/michaelosthege/5bd75c99cd5e806ee049b02ed528bab3).
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### Solve an ode outside of a pymc3 model
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We will use the Lotka-Volterra equations as an example ODE:
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pm.Lognormal('lynx', mu=y_hat['lynx'], sd=sd, observed=lynx_data)
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```
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We can sample using pymc3 (I suspect you might need `cores=1` on windows for the moment):
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We can sample using pymc3 (You need `cores=1` on windows for the moment):
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```
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with model:
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trace = pm.sample(tune=1000, draws=1000, chains=6, cores=6)
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```
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Many solver options can not be specified with a nice interface at the moment,
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we can call the raw sundials functions however (this should change in the future):
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Many solver options can not be specified with a nice interface for now,
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we can call the raw sundials functions howeve:
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```
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lib = sunode._cvodes.lib

doc/source/quickstart_pymc3.rst

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Quickstart with PyMC3
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=====================
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Official conda packages are not yet available in conda-forge. You can either
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build your own conda package or install the master version from github.
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sunode is available on conda-forge. You can setup an environmet to use conda-forge
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package if you don't have that already, and install sunode:::
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To use the development version, we create a new conda environment with the requirements
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and install using pip::
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conda create -n sunode-env
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conda activate sunode-env
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conda config --add channels conda-forge
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conda config --set channel_priority strict
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conda install sunode
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You can also checkout the development version and install that:::
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git clone [email protected]:aseyboldt/sunode
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# Or if no ssh key is configured:
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git clone https://github.com/aseyboldt/sunode
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cd sunode
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conda create -n sunode -c conda-forge python numba pymc3 sympy pandas xarray sundials
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conda activate sunode
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conda install --only-deps sunode
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pip install -e .
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To build and install a conda package locally, we clone the repo as above, and then run::
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cd sunode
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conda build ./conda
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conda install -c local sunode
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# Install it into a new environment:
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conda create -n sunode -c local -c conda-forge sunode
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Instructions for installation on Windows can be found
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`here <https://gist.github.com/michaelosthege/5bd75c99cd5e806ee049b02ed528bab3>`_
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Installing the development version on Windows requires a compatible visual studio
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version.
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Sampling Bayesian models with Hamiltonian MCMC involving an ODE is where the
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features of sunode shine. We need to solve the ODE (ofter rather small ODEs) a
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large number of times, so Python overhead will hurt us a lot, and we need to
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compute gradients as well. Sunode provides some utility functions that make it
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easy to include an ODE into a PyMC3 model. If you want to use it in a
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different context, see :ref:`usage-basic`.
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We will use the Lotka-Volterra equations as example:
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.. math::

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