arviz-devs/community

General questions and discussion

Oriol Abril

@OriolAbril

Am I suppose to give some test or something in order to apply for gsoc or preproposals?

Anybody within the GSoC eligibility criteria can submit a proposal via GSoC website, we do not ask for any extra requirement if this is what you were asking

Smit Sanghavi

@smit-s

@OriolAbril Thanks, for the reply. That's all I wanted to know.

Smit Sanghavi

@smit-s

While trying to build docs I am constantly getting following error in spite of installing all requirements in virtual environment. Also tried setting it up without virtual env. Still getting same error

Build docs with sphinx
Running Sphinx v2.4.4

Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
File "/usr/local/envs/testenv_3.6_PYSTAN_latest_PYRO_latest_EMCEE_latest_TF_latest/lib/python3.6/site-packages/sphinx/config.py", line 348, in eval_configfile
execfile(filename, namespace)
File "/usr/local/envs/testenv_3.6_PYSTAN_latest_PYRO_latest_EMCEE_latest_TFlatest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 81, in execfile
exec(code, _globals)
File "/opt/arviz/doc/conf.py", line 24, in <module>
import sphinx_bootstrap_theme
ModuleNotFoundError: No module named 'sphinx_bootstrap_theme'

Ari Hartikainen

@ahartikainen

Is that in docker or you local workspace?

Smit Sanghavi

@smit-s

It happens with docker

Smit Sanghavi

@smit-s

To be precise , I followed the steps in contributing.md guide for building documentation . I just ran the command given there after building docker image. Please correct me if I missed any step.

Oriol Abril

@OriolAbril

It could be due to docker instructions (and or code) not updated after reorganizing requirements.txt files, I'll try to have a look

Smit Sanghavi

@smit-s

when I tried building docs locally after downloading dependencies and requirements i got following error-

Exception occurred:
File "/home/smit/.local/lib/python3.6/site-packages/bokeh/io/webdriver.py", line 140, in _create
raise RuntimeError("Neither firefox and geckodriver nor a variant of chromium browser and " \
RuntimeError: Neither firefox and geckodriver nor a variant of chromium browser and chromedriver are available on system PATH. You can install the former with 'conda install -c conda-forge firefox geckodriver'.
The full traceback has been saved in /tmp/sphinx-err-iioboned.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at https://github.com/sphinx-doc/sphinx/issues. Thanks!

i tried running 'conda install -c conda-forge firefox geckodriver'. as well and this command ran successfully but still while building i got same error

Ravin Kumar

@canyon289

Can you try building the docs inside of a docker container?

in ./scripts we have the Dockerfile and .sh scripts to create a container

This blog post explains why containerization helps if interested http://canyon289.github.io/DockerforDS.html#DockerforDS

Smit Sanghavi

@smit-s

Actually I tried building docs locally because I was getting error while building docs using docker as mentioned earlier

While trying to build docs I am constantly getting following error in spite of installing all requirements in virtual environment. Also tried setting it up without virtual env. Still getting same error
Build docs with sphinx
Running Sphinx v2.4.4
Configuration error:
There is a programmable error in your configuration file:
Traceback (most recent call last):
File "/usr/local/envs/testenv_3.6_PYSTAN_latest_PYRO_latest_EMCEE_latest_TF_latest/lib/python3.6/site-packages/sphinx/config.py", line 348, in eval_configfile
execfile(filename, namespace)
File "/usr/local/envs/testenv_3.6_PYSTAN_latest_PYRO_latest_EMCEE_latest_TFlatest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 81, in execfile
exec(code, _globals)
File "/opt/arviz/doc/conf.py", line 24, in <module>
import sphinx_bootstrap_theme
ModuleNotFoundError: No module named 'sphinx_bootstrap_theme'

btw great blog

This blog post explains why containerization helps if interested http://canyon289.github.io/DockerforDS.html#DockerforDS

Ravin Kumar

@canyon289

oh man thats not good

ill give it a run right now, sorry about that

Ravin Kumar

@canyon289

ok yea the docs build process from the straight container is pretty broken

ill add an issue to update and get around to it sometime

basically it seems like you need to run pip install -r requirements-docs.txt to get all the docs requirements

then also install bokeh

then run conda install -c conda-forge firefox geckodriver to get the selenium package going

even then though theres issues :(

Ravin Kumar

@canyon289

So here's how its built in CI, but its not working for me our local dev container https://github.com/arviz-devs/arviz/blob/master/.azure-pipelines/azure-pipelines-docs.yml#L39

I'm still getting errors about the webdriver. Will keeping digging in. Sorry about the trouble

Ravin Kumar

@canyon289

Alright seems like @ahartikainen is way ahead of me and has a PR open. I have not checked it yet but will do so later after I get some sleep https://github.com/arviz-devs/arviz/pull/1127/files

Michael Nowotny

@michaelnowotny

Dear ArviZ developers, I have added Arviz support to PyJAGS, the JAGS interface for Python (The project can be found here: https://pypi.org/project/pyjags/ and https://github.com/michaelnowotny/pyjags). Do you want to feature JAGS support on the ArviZ project page? Would you prefer to include the code to convert PyJAGS dictionaries into ArviZ inference data objects in the ArviZ project directly?

Ravin Kumar

@canyon289

Hey Michael, I would suggest adding the converter into the ArviZ code base. By doing so it makes it easy to discover, and more importantly with tests ensures that it is less likely to break

A number of other ppls have done so, as shown above. I will be upfront and say that adding into arviz is perhaps the "safer" solution but will require adding some tests and wrangling with python dependency stuff which can be annoying

alternatively if you would like to keep your code separate we could find a place to mention it on the docs somewhere. But do know that releases might break the integration

Were happy to help either way! Let us know what works for you

matrixbot

@matrixbot

Dominik Stańczak Hello everyone! (test message for matrix-gitter bridge... 🙂 )

Dominik Stańczak Nice, that worked! Hope you don't mind, I didn't want to keep yet another chat client installed :)

Dominik Stańczak Anyway, I have a question to you all wonderful folk. This line of arviz code plots a nice clean 2D KDE:

arviz.plot_kde(trace['T_e'], trace['n_e'], contour=False)

Dominik Stańczak But trying to do the same thing with an InferenceData object created from this same trace and PyMC3 model like this:

arviz.plot_kde(data, var_names = ["T_e", "n_e"])

results only in a ValueError: Inference Data object detected. Use plot_posterior instead of plot_kde.

Dominik Stańczak However, trying the following:

arviz.plot_posterior(data, var_names=["T_e", "n_e"])

results in only marginalized 1D KDEs. Is there any way to create a 2D KDE out of InferenceData?

Oriol Abril

@OriolAbril

Yep, we should probably update the error message. To plot 2D kde plot_pair has to be used

matrixbot

@matrixbot

Dominik Stańczak Nice, that works well! I'll send in a PR for the error message :0

Dominik Stańczak * Nice, that works well! I'll send in a PR for the error message :)

Dominik Stańczak Thanks!

Michael Nowotny

@michaelnowotny

@canyon289 Hi Ravin, sorry for the late response. I had not checked back on gitter for a while and then received an email from them today. I think that your suggestion of adding the code to Arviz makes the most sense. I am wondering what unit tests would make sense for this. The obvious one I can think of is constructing a deterministic dictionary of posterior samples, converting it to ArviZ and then checking if the samples are the same.

Michael Nowotny

@michaelnowotny

@canyon289 I have created a fork of ArviZ and added two modules: https://github.com/michaelnowotny/arviz/blob/master/arviz/data/io_pyjags.py and https://github.com/michaelnowotny/arviz/blob/master/arviz/tests/external_tests/test_data_pyjags.py.

Please let me know if the code is ok

Michael Nowotny

@michaelnowotny

I have added an example at the end of the inference data cookbook -> https://github.com/michaelnowotny/arviz/blob/master/doc/notebooks/InferenceDataCookbook.ipynb

matrixbot

@matrixbot

Dominik Stańczak It probably makes the most sense to start a pull request with those changes! They'll be easier to review then

Michael Nowotny

@michaelnowotny

I created a pull request on GitHub to facilitate code review.

Michael Nowotny

@michaelnowotny

I have addressed some of the pylint warnings in my pull request but don't know how to best resolve the issues surrounding pytest fixtures. Pylint complains that using a fixture in a test function is redefining a name from the outer scope (which it is). Can we safely ignore this or should we find a work-around?

matrixbot

@matrixbot

Dominik Stańczak Haven't looked at the pr itself but you probably need to add the fixture to the arguments of your test function? I'll try to take a closer look later

matrixbot

@matrixbot

Dominik Stańczak Hey, I added a note on the PR 🙂 basically just disable that particular linting

Michael Nowotny

@michaelnowotny

Thank you for your suggestion @matrixbot! I have added the first solution from the stack overflow article and will see if the linter passes.

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