Readme makes references to ecotaxa/cyz2json. There may be other ecotaxa references

[JoeRibeiro]

You will find result in : https://github.com/ecotaxa/cyz2json/actions and release in : https://github.com/ecotaxa/cyz2json/releases

[LucindaLanoy]

I tried to look at the history of the repo, if I'm not mistaken, Seb forked the repo at some point in january 2025, made a lot of changes with github actions etc, then a few days later merged the changes back to the original repo, I wouldn't be surprised if this is why the Readme references the ecotaxa version.

[LucindaLanoy]

I would like to know what you think about the github action + docker addition, do you feel like it improved the process ? I guess it was made to work with CytoProcess, but I can't say for sure, and while its purpose was to facilitate the installation of cyz2json, I can't help but feel like it actually had the opposite effect, but that might just be me and my limited knowledge about all of this.

[JoeRibeiro]

I suspect it was added to help reproducibility, though that might seem odd. By spinning up 3 new clean operating systems it forces you to explicitly list all the build dependencies in your dockerfile. So when the next person goes to build it, you don't have a case of "oh I forgot I installed that".

[LucindaLanoy]

Yes, I guess it makes sense then.

[LucindaLanoy]

This does make me wonder though, what are the purpose of the shell.nix and Makefile ? I tried compiling without them in the repo and it worked fine so I guess their purpose isn't for compilation. By the comments, I feel like the Makefile purpose was to build the initial release (zip file) and the shell.nix seems to have the purpose of making a reproducible .NET environment (don't know how it's used though...). I'm currently trying to figure out what each file in the repo does because I fear some things are actually not used at all and they just make everything seems even more clutered.

[JoeRibeiro]

I'm not certain but I think Rob Blackwell used the .nix

[LucindaLanoy]

Two ecotaxa references remain in the README, the first is in the Build with GitHub actions/OnMacOSX section on the security bypass, I don't really know what the code does so it is a bit difficult to change. The second mention is in Running the program/Linux section on running the executable loaded from github, once again a code I don't really understand and can't easily change.