Are you also providing the --extra-index-url on the command-line in CI? So in CI, do you have both the command-line argumnet and the uv.toml file present?

Correct, in CI I have both the command line argument and the uv.toml present

Ah, ok. Command-line arguments always take precedence over configuration files, so yes, this is the expected behavior. I think you'll need to find a way to avoid passing the command-line argument in CI.

is there any reason to implement that behavior? That is not the behavior of pip when there are configurations specified as global in pip.conf

It's standard for the command line to override environment variables, and for environment variables to override configuration files. Even pip implements this (at least as-written here): https://pip.pypa.io/en/stable/topics/configuration/#precedence-override-order.

Ok, I looked into it and the difference in behavior is that in the case of pip, for the concrete case of the extra-index-url (since it can take multiple values), the value passed in the command line is merged with the value specified in the config file (i.e., if you have 1 extra index url specified in pip.conf and another in the command line, in the end, the two are used).

Oh, you want both index URLs to be respected? I assumed from the original issue that you were trying to disable the index URL from the command-line given extra-index-url = [].

Sorry If I was not explicit enough in the original issue, but yes, I would like to have both to be respected.

I think it's reasonable to merge here when the type is a vector? We at least merge when we discover multiple configuration files. What do you think @zanieb?

I think merging seems reasonable, we have --isolated to stop reading the configuration file.

Out now in v0.1.45. Let me know if you continue to see issues.

Everything works as expected from my side, thank you!