PyStan 3 Beta 4 Released

Announcements
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PyStan 3 Beta 4 is now available on PyPI for macOS and Linux users. Documentation: https://pystan-next.readthedocs.io/

Installation: python3 -m pip install --pre pystan

New in PyStan 3 Beta 4:

  • Stan 2.25.0

New in PyStan 3 Beta series:

  • Automatic caching of compiled Stan models
  • Automatic caching of samples from Stan models
  • Open source software: ISC License
  • CVODES support out-of-the-box.
  • Timely releases. PyStan 3 releases tend to arrive 30 hours after Stan releases (n = 1).

Requirements:

  • macOS or Linux.
  • Python 3.7 or higher.

Upgrading to PyStan 3 from PyStan 2:

There are many backwards-incompatible changes in PyStan 3.0.
Upgrading to Newer Releases summarizes the changes.

Known issues:

  • Only the recommended sampler (No-U-Turn Sampler) is currently supported.
  • Windows is not supported at this time.
  • Linux users with older operating systems may have problems using wheels from PyPI. Ubuntu 20.04 and Debian Bullseye should work. Users with an older version of GCC or Clang need to install httpstan from source before installing pystan.
  • PyStan 3 does not work in a Jupyter Notebook due to a bug in Jupyter Notebook. A workaround exists, Using PyStan 3 with Jupyter Notebook and Jupyterlab
5 Likes
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I get an asyncio error when I try to run inside a Jupyter notebook – but it works fine from ipython3 on the console. I’m on macOS Catalina 10.5.7, Python 3.8 from python.org.

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-10-7b3b7768a627> in <module>
     25                 "sigma": [15, 10, 16, 11,  9, 11, 10, 18]}
     26 
---> 27 posterior = stan.build(schools_code, data=schools_data)
     28 fit = posterior.sample(num_chains=4, num_samples=1000)
     29 eta = fit["eta"]  # array with shape (8, 4000)

/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/stan/model.py in build(program_code, data, random_seed)
    300 
    301     try:
--> 302         return asyncio.run(go())
    303     except KeyboardInterrupt:
    304         pass

/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/asyncio/runners.py in run(main, debug)
     31     """
     32     if events._get_running_loop() is not None:
---> 33         raise RuntimeError(
     34             "asyncio.run() cannot be called from a running event loop")
     35 

RuntimeError: asyncio.run() cannot be called from a running event loop
1 Like
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This is a known problem.

I use nest_asyncio before import stan.

import nest_asyncio
nest_asyncio.apply()

There is also one option to install older jupyter.

2 Likes
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Here’s the documentation on the issue: Using PyStan 3 with Jupyter Notebook and Jupyterlab

1 Like
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Thanks/sorry for not finding it on my own — but it’s useful to have this here on the announcement page (and on readthdocs.io?). I suspect that a large fraction of potential users are also on Jupyter…

1 Like
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Thanks @ariddell @ahartikainen and anyone else who worked on this release!

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this seems to be working with jupyter but the spyder (version=4.2.1) gives the same asyinco error and when using the mentioned code before import stan in spyder it is giving the following error:

RuntimeError: Exception during call to services function: BrokenProcessPool('A process in the process pool was terminated abruptly while the future was running or pending.'), traceback: [' File "/opt/anaconda3/envs/stan3/lib/python3.8/asyncio/tasks.py", line 280, in __step\n result = coro.send(None)\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/site-packages/httpstan/services_stub.py", line 150, in call\n future.result()\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/asyncio/futures.py", line 178, in result\n raise self._exception\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/asyncio/tasks.py", line 280, in __step\n result = coro.send(None)\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/site-packages/httpstan/services_stub.py", line 150, in call\n future.result()\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/asyncio/futures.py", line 178, in result\n raise self._exception\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/asyncio/tasks.py", line 280, in __step\n result = coro.send(None)\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/site-packages/httpstan/services_stub.py", line 150, in call\n future.result()\n', ' File "/opt/anaconda3/envs/stan3/lib/python3.8/asyncio/futures.py", line 178, in result\n raise self._exception\n']

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Maybe this could work in spyder (it runs commands in a thread)