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MatthewRalston / kmerdb

Python bioinformatics CLI for k-mer counts and de Bruijn graphs
https://matthewralston.github.io/kmerdb
Apache License 2.0
12 stars 1 forks source link

New issue 'appmap' (stderr, logger, plain-txt stdout, file outputs, rich formatting if/when necessary) #133

Closed MatthewRalston closed 5 months ago

MatthewRalston commented 6 months ago

The application needs stderr/logging capture, sigterm/exit intercept, distinct stdout and stderr (and logfile) interfaces [metadata]. With relevant preceding or following information about the program, stats/schema definitions, and relevant online information about command issues.

I'm calling this the 'app-map' for ambiguities sake.

And the stdout/stderr components will follow.

Edit 6/1/24:

Very old issue as far as style is concerned, I'm managing this category of interface issue less, so I made necessary interface tweaks, and the interface for the application is still driven by logger.

I'm not concerned, I just have a taste issue.

The interface is still really clunky. Usage examples sparingly, interface not fleshed out, as far as printing end-run usability post-doc to cli. Like, I can see it better, I'm just reorienting still about the graph approach. Trying to skip D2 metrics, focus on tractable biological problems instead of just methodology, calculation, and reproducibility.

I'm young and unconfident with my introduction to physiology, mol bio, disease pathology, and so I buy time by procrastinating on deciding on disease area specifics so I can improve me secondary skillsets of computation and statistics. If such skills become the primary skillset, I'll adapt with the economy. If not, then this "simple" python style, so long as it is functional and reproducible, is just accessory to other faculties ive been developing after my first engineering job and entry to the field.

MatthewRalston commented 5 months ago

Okay. Maintenance pre-release 0.7.9 has been "pre-released" on gh. Okay, so now, the branch 'interface' will lead from here.

The new interface changes will be described in commit message only. That said, README.md (#137 ) should contain a .gif by now of the usage patterns by now.

MatthewRalston commented 5 months ago

Released v0.8.0 today. Greatly simplifies the interface, tests most (shuf and index still on backlog... but unchanged and independent from logging overhaul...so) subcommands (acceptance testing). Usage command, logger/stderr overhaul, no rich text formatting included.

I like rich.py but its an extra dependency i dont need. Biggest features to close this ticket are appmap, the logging overhaul logger and the usage subcommands. Changes to the 'interface' branch have been merged to master.

Marking this closed.