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    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
    image.png
    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 StaƄczak Hello everyone! (test message for matrix-gitter bridge... 🙂 )
    Dominik StaƄczak Nice, that worked! Hope you don't mind, I didn't want to keep yet another chat client installed :)
    Dominik StaƄczak 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 StaƄczak 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 StaƄczak 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 StaƄczak Nice, that works well! I'll send in a PR for the error message :0
    Dominik StaƄczak * Nice, that works well! I'll send in a PR for the error message :)
    Dominik StaƄczak 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.
    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 StaƄczak 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 StaƄczak 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 StaƄczak 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.