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3 | 3 | Quickstart with PyMC3 |
4 | 4 | ===================== |
5 | 5 |
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6 | | -Official conda packages are not yet available in conda-forge. You can either |
7 | | -build your own conda package or install the master version from github. |
| 6 | +sunode is available on conda-forge. You can setup an environmet to use conda-forge |
| 7 | +package if you don't have that already, and install sunode::: |
8 | 8 |
|
9 | | -To use the development version, we create a new conda environment with the requirements |
10 | | -and install using pip:: |
| 9 | + conda create -n sunode-env |
| 10 | + conda activate sunode-env |
| 11 | + conda config --add channels conda-forge |
| 12 | + conda config --set channel_priority strict |
| 13 | + |
| 14 | + conda install sunode |
| 15 | + |
| 16 | +You can also checkout the development version and install that::: |
11 | 17 |
|
12 | 18 | git clone [email protected]:aseyboldt/sunode |
13 | 19 | # Or if no ssh key is configured: |
14 | 20 | git clone https://github.com/aseyboldt/sunode |
15 | 21 |
|
16 | 22 | cd sunode |
17 | | - conda create -n sunode -c conda-forge python numba pymc3 sympy pandas xarray sundials |
18 | | - conda activate sunode |
| 23 | + conda install --only-deps sunode |
19 | 24 | pip install -e . |
20 | 25 |
|
21 | | -To build and install a conda package locally, we clone the repo as above, and then run:: |
22 | | - |
23 | | - cd sunode |
24 | | - conda build ./conda |
25 | | - |
26 | | - conda install -c local sunode |
27 | | - # Install it into a new environment: |
28 | | - conda create -n sunode -c local -c conda-forge sunode |
29 | | - |
30 | | -Instructions for installation on Windows can be found |
31 | | -`here <https://gist.github.com/michaelosthege/5bd75c99cd5e806ee049b02ed528bab3>`_ |
| 26 | +Installing the development version on Windows requires a compatible visual studio |
| 27 | +version. |
32 | 28 |
|
33 | 29 | Sampling Bayesian models with Hamiltonian MCMC involving an ODE is where the |
34 | 30 | features of sunode shine. We need to solve the ODE (ofter rather small ODEs) a |
35 | 31 | large number of times, so Python overhead will hurt us a lot, and we need to |
36 | 32 | compute gradients as well. Sunode provides some utility functions that make it |
37 | 33 | easy to include an ODE into a PyMC3 model. If you want to use it in a |
38 | 34 | different context, see :ref:`usage-basic`. |
39 | | - |
40 | | - |
41 | 35 | We will use the Lotka-Volterra equations as example: |
42 | 36 |
|
43 | 37 | .. math:: |
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