Emcee reader support

[OriolAbril]

To this date, there are 3 possible cases to be taken into account in from_emcee:

• emcee2
• emcee3
• emcee3 "reader", which is using emcee.backend to store the posterior in file and reading it afterwards. It is different from the "regular" emcee3 sampler because the observed data is not stored.

The first two cases already work, this adds support to the 3rd case. I have run some tests manually in my computer to check they work, but I don't know how to update the tests to include different emcee versions.

[canyon289]

@OriolAbril Can you write the test suite in pytest for the new emcee "reader" and check it works in your local environment?

After that I can make the changes in TravisCI to test the emcee reader as well

[OriolAbril]

I added a test for the emcee reader in its own file inside the tests folder. However I am not sure about how to implement it directly in test_data.py, because it should only executed when emcee version is >=3 but without stopping to test the regular emcee3 sampler.

Here, all tests will probably fail because I think actually none of them uses emcee3, but in my local environment pytest test_emceereader.py is passed.

[ColCarroll]

This would be a great use for a pytest.skipif fixture:

needs_emcee3 = pytest.mark.skipif(emcee.__version__ < '3', reason="emcee3 required")

...

@needs_emcee3
def test_emcee3_stuff(...):
    ...

https://docs.pytest.org/en/latest/skipping.html

[ahartikainen]

I think having individual test files for each library a good idea. Let's still use skip fixture to handle different versions.

Good work!

[canyon289]

What @ColCarroll and @ahartikainen said about skipif :)

@OriolAbril Let us know if you need help with any of this.

And thank you for adding tests

[OriolAbril]

I used skipif to implement an extra test inside the class for emcee. Now the test should pass, but it may not mean I have implemented them properly because they will be skipped. What sould be changed to include emcee3 in the tests?

I did not run them locally because I do not have all libraries installed (i.e. stan). Splitting them as @ahartikainen proposed would ease running them locally, at least for me.

[canyon289]

@OriolAbril
Youre able to select tests to run using the -k parameter in pytest. I can provide an example if needed

https://docs.pytest.org/en/latest/usage.html#specifying-tests-selecting-tests

[OriolAbril]

Will the -k flag avoid importing the libraries at the start of helpers.py? It is my first time using pytest, I hope I don't take too much of your time.

[canyon289]

@OriolAbril You're definitely not taking up too much of my time! I'll speak for everyone and say we really appreciate YOUR time :)

If you'd like we can chat on gitter as well for faster collaboration.

https://gitter.im/arviz-devs/community

You are correct though. -k won't help here. I'll make a note of this, that we should make it easier to test if not all libraries are installed

[canyon289]

@OriolAbril Two more things I can mention
We have a docker image for testing if you'd like to check that tests work locally without messing with your host operating system.

Also annoying, youre welcome to push tests to TravisCI and see if they pass there.

[OriolAbril]

For now I'd rather push the changes here, but I will start looking into docker. Can you recommend me some tutorials?

Now only the lint check is failing, I disabled all no-member and invalid-arguments in the emcee3 code. Also an invalid-name for needs_emcee3, but I wasn't really sure about disabling it or using uppercase

[ahartikainen]

Is it for tests? Disable is fine.

[ahartikainen]

For now I'd rather push the changes here

TBH this is mostly how I do stuff. I just run black arviz and pylint arviz (or usually specific file I have changed) (I ignore all import errors) and then push to travis.

This is because I do dev work on different machines / phone, so I only need git tools and vim.

[canyon289]

ThIs LGTM. The rest of the work is on us to add emcee3 reader testing to TravisCI

If no one has any problems I'll open an issue for emcee3 reader testing and will merge in 24 hours.

[ahartikainen]

Sounds fine.

LGTM

[canyon289]

Thanks @OriolAbril