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cnapy-org / CNApy

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
https://cnapy-org.github.io/CNApy-guide/
Apache License 2.0
46 stars 7 forks source link

Version 122 #526

Closed Paulocracy closed 1 month ago

axelvonkamp commented 2 months ago

Is it necessary to always install openjdk in the installer scripts? The setup.py of efmtool_link should install a JDK if needed. At least for the CI tests it appears to work.

Paulocracy commented 2 months ago

At least on systems without Java it is necessary, the efmtool_link requirements don't seem to suffice. Some check whether or not a correct JDK version could also work to prevent unneccessary JDK installations, although I'm not sure if there's a robust cross-platform way to do it.

axelvonkamp commented 2 months ago

I just tried the Windows installer. It works but at the beginning I see warning messages that commercial Anaconda channels are being used. I am not sure whether they have actually been used, is it safe to ignore these warnings?

Paulocracy commented 2 months ago

Yes you can see the warning if your global Anaconda config (which micromamba seems to use if there is one) still includes the default channel, you can remove it with conda config --remove channels defaults. In any case, with the -c conda-forge argument in the bat's mamba command, I think that the default channel is not used anywhere.

Paulocracy commented 2 months ago

Some links weren't displayed correctly, and I added conda-forge and openjdk to the conda instructions to prevent licensing problems and Java errors for the conda users