Install Python module leidenalg on the builders

[jwokaty]

Add leiden to the cran deps packages for scBubbletree if it is accepted into Bioconductor: Bioconductor/Contributions#2781. It also requires leidenalg.

[hpages]

I'm confused, isn't CRAN package leiden already on all the build machines?

Besides we don't need to do anything to manage dependencies on CRAN packages. Those will be automatically installed by the build system granted that Bioconductor package developers have them listed in the Depends, Imports, or Suggests field of their package.

What we need to manually install on the build machines are the external dependencies i.e. deps that are not R packages. Those are the deps that package developers should list in their SystemRequirements field.

In this case, I think it's Python module leidenalg (needed by CRAN package leiden), but let's wait confirmation from the scBubbletree submitter (also they will need to add a SystemRequirements field first).

[lshep]

They depend on Seurat , that depends on leiden, leiden has the python system dependencies and python module requirements.

[hpages]

Any chance you can install leidenalg on nebbiolo2 Jen? 😄

[hpages]

Maybe you did, maybe I'm not using the right command:

biocbuild@nebbiolo2:~$ python3
Python 3.8.10 (default, Jun 22 2022, 20:18:18) 
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import leidenalg
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'leidenalg'
>>> 

[jwokaty]

I pip3 installed it.

[hpages]

Any idea why I can't load the module?

[jwokaty]

I think you tried before it was installed. It loads now.

[hpages]

Still failing: Bioconductor/Contributions#2781 (comment)

Are you installing this system-wide, as documented? All system deps need to be installed system-wide.

You should be able to start python3 and import leidenalg from any account.

Please communicate with the scBubbletree submitter. Thanks!

[jwokaty]

Ok, that's probably what it is.

[snaketron]

Now that scBubbletree is accepted could you please install the Python module leidenalg
on the other machines.

It is currently failing on lconway with the same error:

Message: Cannot find Leiden algorithm, please install through pip (e.g. pip install leidenalg).

https://bioconductor.org/checkResults/3.16/bioc-LATEST/scBubbletree/

Thanks!

[jwokaty]

@snaketron Thanks for following up. It's installed on all devel machines. We should see how it fairs on the next build report this weekend.