Revamp CI

[abretaud]

No description provided.

[abretaud]

• Yep, let's pin the version of protobuf
• Yep, let's use a more recent debian version! bookworm maybe?

[mboudet]

Might not need to do both (3.20.3 is the breaking point, should be compatible after).

However, we should pin all deps anyway..

[rsiminel]

I just created a PR, here is what it does and does not do:

Yep, let's pin the version of protobuf

• Looking at the requirements.txt of each repo, it seems that only biomaj-process and biomaj-download require protobuf and conveniently, @mboudet has an open branch to fix protobuf in each of those repos. Shall we pin the version there ?

Yep, let's use a more recent debian version!

• Done using bullseye. Looking through the file history, it seems that Oliver's Dockerfile-deb11 was just a copy-paste of the Dockerfile as it was two years ago with FROM debian:buster changed to FROM debian:bullseye. Ok to remove now ?

The 'publish' job should be restricted to tags / pushs to the master.

• Done. I just added an if: github.ref == 'refs/heads/master' to the publish job.

We should use this quicker way: pip install git+https://github.com/genouest/biomaj-core.git (for all of these modules)

• Done but I'm surprised at how easy that was, can you guys make sure I didn't get rid of anything important ?

[rsiminel]

So now this PR closes #5
Thanks for making it possible to get rid of those pesky git clones mboudet!

[mboudet]

Added changes:

• Add #!/bin/env python3 to the various CLI files in the modules

The CLI files are properly installed with the pip install, just not in /root/module/cli.
#!/bin/env python3 is required since we can't directly call 'python3' on a file in the PATH. (We could try to use an absolute path to the file, but not sure if that's reliable).
Another issue is that #!/bin/env python3 works as expected, but #!/bin/env python uses the conda python instead, so there is a module not found error.

Not really fond of this solution to be honest, but it works... for now.

• Updated prometheus

Not much of a choice here. I tried rebuilding the 1.8.2 image, but it doesn't work anymore. At most, people will lose the last 720 hours data, which is not that much I feel like. Not sure if anyone actually use the prometheus to be honest.
There might be a 'proper' upgrade procedure, but it's out of the scope of this repo.