As an amateur who reads journal papers (maybe not the audience you're most concerned about), the two most important things to helping my understanding of the paper's results are, in order:
1. a program that I can run against the data in the paper (where I can modify the data to see how that changes the results the program generates); and
2. the source code to that program, that I can read to understand what it does.
For #1, I'd encourage you to publish something like a Docker image of your built binary, to a permanent public Docker image host; to use that Docker image version of your program to do the actual experiment/data processing for your paper; and then to cite, in your paper, the specific fully-qualified Docker image ID (e.g. hub.docker.com/foo/bar@sha256:abcdef0123...6789) that was used to create the results.
I would also encourage you to, if possible, publish your data in some repository, e.g. GitHub; and to cite the data using a fixed hash (e.g. Git commit hash) as well.
With these two pieces of information, anyone can easily do the simplest possible kind of "reproduction" of your results: namely, they can fetch the same Docker image used in the paper, and then run it against the same data used in the paper, to — hopefully — produce the same results shown in the paper.
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As for #2...
If you're really worried about "trade secrets", you can just solve #2 by making the code itself only "available upon request."
But don't underestimate the number of people in your field who say they're hoarding their code for reasons of "competitive advantage", but who are really doing so out of personal shame at the state the code is in, and fear that a bug might be found there that will invalidate their result.
These people are, IMHO, not embracing the spirit that led them to become scientists. You should want any bugs in your papers — including in the code — to be found! That's what the pursuit of (academic) science is about — everyone checking each-other's work so that we can all believe more strongly in the results!
You don't need to clean up your code. Maybe get an "alpha reader" to go over it first, like self-published authors do, if you're worried about nitpickers. But the only thing code really "needs" to be valuable, is to compile and run and do something useful.
Personally, all I'd want from your repo is for there to be a Dockerfile in there that will, within its fiddly little internal build environment, manage to output the exact Docker image cited in the paper.
If I cared about modifying the code, I could take the rest from there.