Keep getting Manifest.toml not found error

[biona001]

Hello,

For some reason JLSO.jl keeps trying to update my package's Manifest.toml file when I save my custom type. The line that throws this error is:

endswith(outfile, ".jlso") && JLSO.save(outfile, :compressed_Hunique => compressed_Hunique, format=:julia_serialize, compression=:gzip)

and the error message is:

SystemError: opening file "/Users/biona001/.julia/dev/MendelImpute/Manifest.toml": No such file or directory

Unfortunately, my custom type is pretty complicated to generate and simpler examples don't lead to this error. As far as I understand, this should be happening only when I try to read in an old JLSO format? Is there some way to bypass this?

Alternatively, if there's some tutorial on how to generate and manage a Manifest.toml file for my own package, that would be very helpful as well.

[rofinn]

Is there a full traceback? Can you confirm that the Manifest.toml file exists? JLSO will also read the active project manifest when saving files, this is how we retain a record of the software state when you saved your data. If for whatever reason the Manifest.toml location is incorrect then we need to fix that.

https://github.com/invenia/JLSO.jl/blob/master/src/metadata.jl#L39

[biona001]

I see. The path it checks is correct. So basically I need to generate a Manifest.toml file for my package? Most of my packages don't have one and for the few that do, I don't remember how they were generated. I guess I can figure that out. Thanks!

[rofinn]

Typically, if you start Julia with julia --project=. it'll activate a local environment in your current working directory. You can then add only the packages you need for the project and they should be saved in a local Manifest.toml file by default. This is generally recommended as it'll provide a cleaner environment for tracking software dependencies for you data files. I suppose we could include that suggestion the docs.

[oxinabox]

I don't see why we are not picking up the global Manifest in this case?
Seems like a bug.

[rofinn]

Would it be a bug with JLSO though? This is all we're doing joinpath(dirname(Base.active_project()), "Manifest.toml").

[oxinabox]

Unclear, but something weird is going on, because that should work on the global enviroment, and in packages without a Manifest.toml.
Like I don't know how it is possible to have this happen when JLSO is loaded.
Since a Manifest needs to be created to install it.

All I cna thing is one could be via loading JLSO, then doing ] activate DirectoryThatDoesNotExist.
Or maybe doing something like manipulating the LOAD_PATH directly rather than using Pkg to activate projects