Anthony Gitter

I found the initial proposal from last week fairly complex when I looked through the actual examples. The modified version from @vincerubinetti that listed prompts and then mapped prompts to...

Right, having to escape the dots in exact filenames could surprise a less experienced user. You may still decide regex is the best way to go, in which case I...

For the tests below, I'm now running with the example data to make sure I don't have an error in my edge or prize files ``` OmicsIntegrator -e interactomes/inbiomap.9.12.2016.exp.oi2 -p...

I believe this is happening because the costs are so huge. For example, ``` >>> a = np.array([1.0, 2.0]) >>> a array([1., 2.]) >>> a.dtype dtype('float64') >>> b = 10**20...

> Does this mean you're able to run OI2 successfully now? No, I'm still stuck with the same pcst_fast TypeError. Because the test cases pass in my conda environment, I...

I lowered the default g from 20 to 1, and the pcst_fast TypeError went away. Preventing this error could involve: - Updating `_check_validity_of_hyperparameters` to set a maximum value of g...

After more testing, the issue does not seem to be only due to the magnitude of g. I could reproduce the error with g = 20, but it works when...

I expanded the scope of this pull request to fix an error I encountered when trying to run the `OmicsIntegrator` command: ``` $ OmicsIntegrator Traceback (most recent call last): File...

I have a fork that fixes several of the command line-related issues I reported recently and adds basic GitHub Actions testing. I can expand the scope of this pull request...

This is the description I was following, which could also be updated https://github.com/fraenkel-lab/OmicsIntegrator2/blob/ea1092fe0053556338cf29c4840a1ff35e8a4f81/src/__main__.py#L43-L44