Running sample notebook fails with error "Permission Denied"

[nluetts]

Describe the bug
Running OpticSim.NotebooksUtils.run_sample("EmittersIntro.jl") fails with error "Permission Denied"

To Reproduce
Steps to reproduce the behavior:

mkdir myproject && cd myproject
julia

julia> ]activate .
julia> ]add OpticSim
julia> using OpticSim
julia> OpticSim.NotebooksUtils.run_sample("EmittersIntro.jl")
┌ Info: Copying the sample notebook [EmittersIntro.jl] from the samples directory to the current one
│ /home/nluetts/.julia/packages/OpticSim/gelEh/samples/notebooks/EmittersIntro.jl ->
└ /tmp/myproject/EmittersIntro.jl
[ Info: Running sample notebook from [/tmp/myproject/EmittersIntro.jl]
[ Info: Launching Notebook [/tmp/myproject/EmittersIntro.jl]
ERROR: SystemError: opening file "/tmp/myproject/EmittersIntro.jl": Permission denied

Expected behavior
Running OpticSim.NotebooksUtils.run_sample("EmittersIntro.jl") opens Pluto and let's you play with the example

Desktop (please complete the following information):

• OS: Fedora 40
• Julia version 1.10.6
• OpticSim.jl version 0.6.0

Additional context

The problem is that the created file has no write permissions:

[nluetts@fedora myproject]$ ll
total 292
-rw-r--r--. 1 nluetts nluetts 95212 Nov 15 10:21 'EmittersIntro backup 1.jl'
-r--r--r--. 1 nluetts nluetts 95212 Nov 15 10:21  EmittersIntro.jl
-rw-r--r--. 1 nluetts nluetts 94886 Nov 15 10:13  Manifest.toml
-rw-r--r--. 1 nluetts nluetts    57 Nov 15 10:13  Project.toml

Manually setting chmod +w EmittersIntro.jl fixes the problem.

I guess you could add a call to Base.Filesystem.chmod after this line:

OpticSim.jl/src/NotebooksUtils/NotebooksUtils.jl

Line 139 in c15efe4

cp(src_fn, dst_fn)

but I am not sure if that would be cross-platform.

[brianguenter]

Have you tried that fix? If it works submit a PR and I'll test it on my machine. Then we'll know it works on Fedora and Windows.

[nluetts]

Yes, it fixes the error, but the notebook does not run through, it errors out when loading PlutoUI.jl and DataFrames.jl, because those are not part of my test project. So I guess you should opt into the Pluto package management or create a folder including a Project.toml/Manifest.toml + the sample notebook instead of merely copying the notebook file.

[brianguenter]

Sorry for the delayed response, we had a bomb cyclone hit our state. Power and internet went out for 500,000 people.

Last time I checked Pluto package management could be extremely slow, since it didn't cache anything from previous runs of Pluto. Has this changed with the release of 1.11?

[nluetts]

I am not sure, since I am not a regular user of Pluto. In that case, however, you could change the mere copy of the notebook to creation of a dedicated directory, see my previous comment. Either way, project management should be added somehow, or you could add a note to the docs of run_sample() saying that the user has to create the project themself.