Julia project specific environments (Project.toml)

[tbeason]

There is some discussion on the Quarto guide about how to use various environments from R or Python. Right now, it seems that in order to use Julia code blocks I must keep any packages that I want to use in my global/default environment, rather than project specific ones. In Julia, this done by having a Project.toml file for the project (and perhaps a Manifest.toml also but not always needed).

When starting Julia you can call julia --project=Project.toml if it is in the current directory or you can start Julia normally and from the REPL type ] and then activate .

] activate .

or you can write

using Pkg
Pkg.activate(".")

I know that the last option would work if I added it to a (each?) code block, but is there a way to just add something to the quarto.yml file instead to use a Project.toml file for the whole project?

[cscheid]

Thanks for the question! I don't believe we have such an option right now. I'm going to transfer this to a github issue and we'll take it from there.

[dpo]

One could add

    ```{julia}
    #| echo: false
    #| output: false
    using Pkg
    Pkg.activate("demo")
    Pkg.add("Plots")
    ```

to the top of the document. Is there a disadvantage to this solution?

[dmbates]

@tbeason In my experience the evaluation of the Julia code blocks does use the local Project.toml specification. The sequence is that the .qmd file is converted to a Jupyter notebook (.ipynb) which is then evaluated. I always use

execute-dir: project

in my _quarto.yml file which, I think, means that jupyter will be started in the project directory and the underlying Julia process will use the local Project.toml configuration.

(BTW, the option --project usually is given a directory name rather than a specific file and --project is sufficient to have it use the local Project.toml file.)

[svilupp]

Yeah, I have noticed that it magically works 90% of the time.

But earlier today I got stuck and couldn't get my IJulia to load the right environment (I kept getting import errors), which is why I asked this question separately (#1696)

My solution was to:

1. Add explicit environment initiation cell, eg, using Pkg; Pkg.activate(".",io=devnull)
2. Restart the daemon process (and print the debugging info to see where the problems are):
   quarto render hello.qmd --to html --execute-daemon-restart --execute-debug

One of those has helped. Hopefully, it helps others who will run into the same issue

[jjallaire]

I think I could use some help determining how the current behavior deviates from what would be ideal. In my current testing it looks like IJulia is automatically activating the environment associated with a .qmd or .ipynb (even to the point of scanning up the directory hierarchy to look for a Project.toml).

This is what I am seeing with Julia 1.7 and a recently installed version of IJulia.

Pls advise whether others are observing this same behavior and whether this is how things ought to work.

[dmbates]

I think I could use some help determining how the current behavior deviates from what would be ideal. In my current testing it looks like IJulia is automatically activating the environment associated with a .qmd or .ipynb (even to the point of scanning up the directory hierarchy to look for a Project.toml).

That is my understanding, and my experience, too.

[MHellmund]

The Julia project path may be specified by the environment variable JULIA_PROJECT, see https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_PROJECT.

Environment variables available at code block execution can be set in an _environment file, see
https://quarto.org/docs/projects/environment.html

[cderv]

Thanks I added your useful comment in the issue thread #1483