Devlog: Documentation and v0.1.0

Date: 2026-07-22

Instead of jumping right into code — like I normally do — I decided to instead write documentation on how the project would be handled from a development standpoint. This included deciding on things such as Semantic Versioning, Conventional Commits, short-lived branches, and squash merges. None of it was particularly original, but the point was to remove any ambiguity regarding the actual developm from the actual work. I no longer need to wonder whether a feature belongs directly on main, what a release branch will be named, or whether generated binaries should be comitted.

I also decided that CHANGELOG.md would remain at the root similar to the README, and other policy documents / actual project-facing documentation would live under docs/.

The first code

The original CLI I wrote walked over every argument and then tried to interpret options and commands inside that very same loop. This causes conflicts and issues, especially relating to reading a filepath that might not exist in argv.

I replaced it with the rule that one invocation has one command, and everything after it belongs to that command.

The accepted shape thus is now:

    bioflo <command> [arguments]

Commands may officially be written with zero, one, or two leading dashes — though any amount of dashes is current accepted. Dash removal is bounded rather than handled by an open-ended pointer loop, so inputs such as - and -- cannot be walked beyond the end of the string.

Testing this produced a strange error where for whatever reason my system got stuck on a kernel write request, which froze all other kernel requests and muddied any other programs from running in my terminal. I restarted my computer and that was that. Really annoying because for like 20 minutes I thought the issue was me. It was not.

Sequence decisions

The first actual library module handles basic DNA sequences.

Currently, a valid sequence can contain A, C, G, T, and N. I chose to accept N because unknown bases are common in real sequence data — from personal experience. Lowercase input is rejected rather than normalized implicitly purely just because I haven’t gotten to it yet. Empty strings are invalid sequences, but I did make it so that GC content for an empty string returns 0.0 to avoid division by zero.

GC content is returned as a fraction between 0.0 and 1.0, not as a percentage. This is to keep the value reusable rather than prioritize presentability.

I deliberately kept the public API small for now as to avoid overextending the first release:

is_valid_dna
count_nucleotide
gc_count
gc_content

The base-checking helper I have kept private. This is my first attempt at treating prop as an explicit public-facing endpoint rather than using it for everything.

What v0.1.0 means

Version 0.1.0 is by no means a feature-complete release (obviously). It’s my first steps at not only making a specific library for bioinformatics, but also testing Flower’s ability to even create usable libraries.

The CLI still does not read files, FASTA parsing does not yet exist, and case normalization / additional ambiguity codes are also deferred.

In the coming planned work, I intend for Bio-Flow to reach a somewhat usable state in the hopes of utilizing it for some of my own personal projects :)