Make use of PACKAGE_MANAGER_URL env variable

[phlg]

Linked to a couple of PRs on the helm charts :

• https://github.com/InseeFrLab/helm-charts-interactive-services/pull/76
• https://github.com/InseeFrLab/helm-charts-interactive-services/pull/77

This PR changes a couple changes a couple of things related to repository configuration :

• First, as the PR title implies, it makes use of the PACKAGE_MANAGER_URL that we can manage through Onyxia region and the interactive services helm charts. This way, it's possible to configure both a local instance for Posit Package Manager, and another repository, for instance for in-house packages that need to stay away from the PPM instance for whatever reason.
• Second, all the stuff related to repository configuration (for R/CRAN, pip and conda) was moved to a dedicated onyxia-set-repositories.sh file, which in turn is now called in onyxia-init.sh. The main purpose for this was to ease "private" rebuilding of these images. As might be common for other users rebuilding their own custom images, we needed to run the repository configuration at build time, and not only runtime. Because of this, we managed a script ripped from onyxia-init.sh containing all the pertaining commands. By having a dedicated file "upstream", we can just call the file which will have been baked in the image already.

⚠️ There are a fair number of points I'm not sure about though, please take them into account when reviewing :

• I couldn't be sure of what exactly was related to repository management. I made a couple of assumptions (stated below), and if case some are wrong, please let me know so I can move the related parts back in onyxia-init.sh :
  • Managing custom certificate authority (PATH_TO_CA_BUNDLE and certifi_ca.py)
  • Setting the R repositories for renv (the renv.config.repos.override) - I don't know if this should be done only when we set R_REPOSITORY and/or PACKAGE_MANAGER_URL, or all the time.
• The shebang for onyxia-init.sh is #!/usr/bin/env bash, but I naively went for a "basic" #!/bin/bash in onyxia-set-repositories.sh. Is that fine, or should I align with onyxia-init.sh ? I'm not sure what this implies.
• This is not actually related to the changes of this PR, but I was wondering why in the Dockerfile, onyxia-init.sh was explicitly chmodded even though its containing directory was recursively chmodded just a few lines prior (see the first and last lines in this excerpt : https://github.com/InseeFrLab/images-datascience/blob/main/base/Dockerfile#L31-L77)

[alexisdondon]

For a first step seems good to me we will see later if we should split certificates and repos for the moment let just move the code as it is.

For renv, the code seems to do something only if one variable at least is injected by onyxia that what i would have do too.

For the shebang, let's align to avoid some problems, https://www.baeldung.com/linux/bash-shebang-lines it seems that the existing shebang is more portable.

[phlg]

Thanks for the review, I fixed the shebang and marked the PR to be ready.

[fcomte]

I think we should set repo before executing user scripts.

[phlg]

I think we should set repo before executing user scripts.

(Hopefully) fixed with 44df6f9, thank you very much !