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exoplanet-dev / jaxoplanet

Astronomical time series analysis with JAX
https://jax.exoplanet.codes
MIT License
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docs: synthetic radial velocities #107

Closed lgrcia closed 9 months ago

lgrcia commented 9 months ago

A simple tutorial to compute and fit the radial velocities of a star hosting an exoplanet

dfm commented 9 months ago

Thanks! Take a look at the rendered version here: https://jaxoplanet--107.org.readthedocs.build/en/107/tutorials/rv/

Some thoughts:

  1. I don't love that we see _body_stack in the printed system - I will open a separate PR about that! Done by @dfm in #117
  2. Could you add a semicolon at the end of plotting cells so that we don't get output like: 
    <ErrorbarContainer object of 3 artists>
  3. The progress bar output from sampling is pretty unwieldy - perhaps it would be enough to install ipywidgets as part of the docs extra in pyproject.toml? Done by @soichiro-hattori already!
dfm commented 9 months ago

@soichiro-hattori: it looks like the progress bar is still getting muddled on this one. Do you know what's going on? Maybe it's because we need to run parallel sampling to get the notebook-style progress bars?

soichiro-hattori commented 9 months ago

That's interesting! I don't have a good idea but I imagine it has to do with what you mentioned about running a single chain vs multiple chains! I "think" that there are different calls to the tqdm package based on the number of chains from what's written here https://github.com/pyro-ppl/numpyro/pull/900.

@lgrcia could you try adding this line to the top of your notebook from tqdm import tqdm.notebook as tqdm

soichiro-hattori commented 9 months ago

@lgrcia: I guess that didn't make a difference :( If you add numpyro.set_host_device_count(2) right after import numpyro you should be able to force the chains to run in parallel and get rid of this progress bar issue.

dfm commented 9 months ago

I'm going to merge this now and we can tweak the formatting in a new PR.

Thanks @lgrcia!!

lgrcia commented 9 months ago

Thanks 🙏🏼