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If you are wondering where the data of this site comes from, please visit https://api.github.com/users/swansonk14/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.

swansonk14/p_tqdm 242

Parallel processing with progress bars

swansonk14/IntroML 22

A hands-on introduction to machine learning

swansonk14/chemprop-intro 11

An introduction to machine learning for chemical property prediction

swansonk14/chemprop-factor 7

Matrix factorization and deep learning for molecular property prediction

cryptovoting/shuffle-sum 4

An implementation of the Shuffle-Sum protocol for homomorphic ranked-choice voting

blakeelias/homer 2

A crowdsourced flashcard repository for remembering everything you learn, using the magic of spaced repetition learning!

swansonk14/mcmc-decrypt 2

Markov Chain Monte Carlo for decryption

swansonk14/random_pairs 2

Randomly pairs people

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Kyle Swanson

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Updating readme

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Plot improvements

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Changing plots from PNG to PDF and increasing fontsize

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Kyle Swanson

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Experimenting with methylation memory

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Changing memory mechanism

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Name change

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Adding average drift and average ligand concentration

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Changing defaults and adding gaussian noise to some ligand-methylation relations

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Changing defaults

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Plot drift across bins

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Change figsize and add start and end points on cell paths

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Option to save plots

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Changing save_dir logic

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Kyle Swanson

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Fixing entropy units

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Adjusting plotting parameters

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Improved 3d plot saving

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Making linearize_params based on ints and altering figsize

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Kyle Swanson

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Changing defaults

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Adding units

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Changing arena size

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Changing exponential base from e to 2

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PublicEvent

issue commentswansonk14/typed-argument-parser

Bug in writing reproducibility section to file

Hi @hesther,

Thank you for letting us know about that issue! As of Tap version 1.7.1, the reproducibility information now comes from the git repo of the file that is run (in your case, Chemprop's <path_to_chemprop>/train.py) rather than the git repo that you are currently in. Hopefully this should fix your issue!

Best, Kyle and Jesse

hesther

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created tagswansonk14/typed-argument-parser

tagv_1.7.1

Typed argument parser for Python

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v_1.7.1

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Kyle Swanson

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Increment version to 1.7.1

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Kyle Swanson

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Changed reproducibility info to use path to Python file that is run

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issue commentswansonk14/typed-argument-parser

Empty metavar wreaks havoc on an `assert` statement

Hi @cardoso-neto,

Thank you for bringing up this very unusual bug! We were certainly confused for a while. We did some debugging, and we believe that the error is actually due to a bug in argparse and thus manifests itself in Tap. For example, consider the following code:

from argparse import ArgumentParser

parser = ArgumentParser()
subparsers = parser.add_subparsers()
subparser = subparsers.add_parser('a')
subparser.add_argument('--b', metavar='', required=True)
subparser.add_argument('--c')
args = parser.parse_args()

If you run this code (python file.py a) and make your terminal window very narrow, then you'll get the same error. The problem seems to derive from this line in argparse, which compares the length of the text of the arguments to the terminal window size and tries to wrap the text if the terminal window is too narrow. The code that does the text wrapping works incorrectly when metavar='' and results in the assertion error that you mentioned. Increasing the width of the terminal window, using either this argparse code or the Tap code that you posted, resolves the error.

Since this error appears to be a problem in argparse, I don't think we'll be able to fix it in Tap unfortunately. We will reach out to the argparse developers about this issue, and please feel free to contact them yourself as well to get this issue fixed!

Thanks again for bringing our attention to this very subtle bug!

Best, Kyle and Jesse

cardoso-neto

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Kyle Swanson

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Improve polynomial and step function

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Random initial position

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Kyle Swanson

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Maintaining randomly sampled methylation levels over time

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Cleaning up ligand-methylation relations and adding new ones

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