NEW: Add tensorboard hparams to CLI

biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis

BSD 3-Clause "New" or "Revised" License

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NEW: Add tensorboard hparams to CLI #95

Closed gwarmstrong closed 4 years ago

gwarmstrong commented 4 years ago

This adds the ability to log hyperparameters for tensorboard. A sample visualization of this functionality is included below:

Screen Shot 2019-11-07 at 1 23 06 PM

Summary of changes to code:

Logged hparams using tensorboard in the songbird.multinomial click CLI
Added flake8 and pep8 for the songbird script
Added tests for songbird CLI in scripts/test_songbird_cli.py (to verify that hparams doesn't break CLI)

Closes #93

mortonjt commented 4 years ago

@gwarmstrong , this is a great contribution. I've tested it out and can verify that the hparams works as expected.

One thing that would add icing to the cake to this PR is to link a screenshot of the new hparams functionality to the readme along with a brief explanation of the proposed functionality.

Also, we'll want to update the changelog with the new changes. Thanks!

gwarmstrong commented 4 years ago

@mortonjt sounds good, can do.

re readme: Does it seem reasonable to append the brief explanation to the "5. Adjusting parameters to get reasonable fitting " section?

mortonjt commented 4 years ago

Yes, that should work fine.

On Mon, Nov 11, 2019, 3:38 PM George Armstrong notifications@github.com wrote:

@mortonjt https://github.com/mortonjt sounds good, can do.

re readme: Does it seem reasonable to append the brief explanation to the "5. Adjusting parameters to get reasonable fitting " section?

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gwarmstrong commented 4 years ago

@mortonjt I've added a blurb to the readme, including an image, shown below:

Questions/comments:

What should I do about relative vs. http link for the moment? I noticed all pictures in the README have links to the git, presumably so they do not have to be shipped with the package.
I left the version string in changlog ambiguous for the moment. Since I wasn't sure how I should update it. Let me know if there is something specific I should change it to.