wytamma / beastiary Goto Github PK

If you add a trace via the modal and press enter the page refreshes. Need to block the default form submission.

Add a --host or --share cli arg that sill proxy beastiary through a server so the analysis is publicly available.

Add joint-marginal plots

Binary Serialization: binary formats can significantly reduce the payload size. Consider using formats such as Apache Arrow or custom binary payloads for trace data.

Add the ability to specific the amount of burnin

Add an option to drag and drop files into Beastiary. The files will not be able to be tracked, however, it would allow you to statically examine files. The file would just load into the browser so no data transfer is required.

calculateStats is the main blocker and should be moved to the worker. Also need better management of workers so you don't create 1 per calculation. E.g. create a worker pool.

When you use the ADD button to add a log file if the file doesn't exist beastiary should display an error.

Currently the byte of the last row read is used to keep track of the location in the log file. However, the byte could be tracked on the Trace model to save adding it to the last Sample read.

Replace polling with web sockets e.g.

from fastapi import FastAPI, WebSocket

app = FastAPI()

@app.websocket("/data")
async def data_websocket(websocket: WebSocket):
    await websocket.accept()
    while True:
        data = await generate_data()  # Your function to get real-time data
        await websocket.send_json(data)
        await asyncio.sleep(1)  # Adjust based on desired update frequency

Add an option to watch a folder. This will add files to beastiary when they are added to the folder. Might also need to handle patterns e.g. *.log

The trace is laggy with 100K points. Change to webGL

1. Convergence diagnostics
2. Easier selection of multiple traces across log files

Ess calculation for each parameter

Add the ability to pass beastiary a logfile path at start up, so that it is automatically added.

beastiary --logfile '/path/to/log'

The auto login fails the first time you open the webapp

I like the blue, but there is a lot of it...

SAWarning: Identity map already had an identity for (<class 'beastiary.models.sample.Sample'>, (116,), None), replacing it with newly flushed object. Are there load operations occurring inside of an event handler within the flush?
db.commit()

Mixing and convergence in tree space is an important requirement for effective Bayesian phylogenetic inference. The Beastiary backend should compute real-time convergence diagnostics (similar to RWTY) for assessing the adequacy with which the MCMC has sampled the phylogenetic tree topology space.

The custom domain for the docs is reverting to my blog url...

import pkg_resources
version = pkg_resources.get_distribution('beastiary').version

For security reasons browsers don't allow access to file paths. I think that means we can't have a drag and drop interface (although this wouldn't work on remote servers anyway). I think the best option would be to have a file explorer interface like the one in the vue ui.

Add the ability to select multiple traces

Add cumulative ESS plots and run time predictions based on target

Add CLI configurations to parse any type of delimited file.

Create the basic layout for the dashboard.

Using polling to automatically get new samples for the active trace

Add statistics for parameters (mean, 95% CI, etc)

Beastiary will freeze if the dataset being loaded is very large (100,000 samples). Is there a way to optimise the loading time of large datasets?

I found that if spaces are present in a parameter name, the name will be split and the additional words will be used to label the subsequent parameters.

In the attached log file and screenshot, the parameter "Current Tree" is split by Beastiary, with "Current" labelling the correct column and "Tree" labeling the adjacent column (which should be "Location.rates.California.NewYork"). All of the data in the log file is present, but the labels are incorrect from that point on.

sample.log