I've got some good news. This is still janky as heck, but I've got a python tool which parses the saf file, converts it into a pandas dataframe, and allows me to spit out some histograms.
The janky part is that the histograms are still essentially a proof-of-pipeline, matplotlib has turned out to be very different (not bad, just different) from the plotting language (ggplot2) I am used to.
This image will get better between now and Friday. My plan to is push my local repo to a fork of ma5 on my github account, then send you a pull request on Friday. Based on how that goes and your feedback, then write up a post.
The downside is that I probably won't have time for 1c, but I can deal with that. It's been very informative using pandas and matplotlib on non-toy data.
Super! This looks very nice. Just two comments:
I can give one more week for 1c, as I still haven't found the time to start writing 1d ^^
I can certainly make it multiple figures, i was actually pondering that over morning coffee.
The code exists as a standalone thing, but utopian would like your github ma5 to be the main repo, so I am developing it in a new directory under tools. This also helps with the criterion that a task is accepted by an author by incorporating a pull request.
I am not sure to understand the utopian request. This addon was supposed to stay independent of madanalysis, as it is only useful once the working directory has been created. I will see with utopian.
One thing that' been consistently an issue is that the utopian workflow is based on largely monolithic projects. Frameworks which generate code or tiny tools complicate the idea of what the main repo should be.
If you want a standalone tool, it might be easier to write this as an idea post, and have me write it up as a developer, rather than as a task request on an existing project.
This is actually what I have in mind but this project being such a large scale thing, this renders everything complicated. I am still discussinng things with utopian.
You can for instance check the comment of the utopian moderator here. It goes along what I have in mind :)