Leiden consistently unable to correctly identify installed dependencies

[ollieeknight]

Heya Tom,

Many thanks for this package, it really great and I've been using it loads.

Something I've had to do for a while is manually tell the package 'no' to installing dependencies, even though they're all installed. I want to fix this so I can run markdown files with the package, and to streamline it.

1. I think that it is currently trying to import umap-learn when in fact the folder in site-packages is called umap. Am I mistaken or has this maybe been updated?
2. Even though I have all the packages installed, it's still telling me they're not

> library(reticulate)
> use_condaenv("r-reticulate", required = TRUE)
> library(leiden)
using environment: r-reticulate
conda environment r-reticulate installed
install dependencies (yes/no)?no
no
Unable to install python modules igraph and leidenalg
run in terminal:
conda install -n r-reticulate -c conda-forge leidenalg python-igraph pandas umap-learn
python modules igraph and leidenalg installed

> modules <- list(
+   numpy = py_module_available("numpy"),
+   pandas = py_module_available("pandas"),
+   igraph = py_module_available("igraph"),
+   umap = py_module_available("umap"),
+   leidenalg = py_module_available("leidenalg")
+ )
> print(modules)
$numpy
[1] TRUE

$pandas
[1] TRUE

$igraph
[1] TRUE

$umap
[1] TRUE

$leidenalg
[1] TRUE

and by contrast

> py_module_available("umap-learn")
[1] FALSE

when in bash

(r-reticulate) ~$ conda list umap-learn
# packages in environment at /data/gpfs-1/users/knighto_c/work/bin/miniconda3/envs/r-reticulate:
#
# Name                    Version                   Build  Channel
umap-learn                0.5.6            py38h578d9bd_0    conda-forge

and the final few packages of ~/work/bin/miniconda3/envs/r-reticulate/lib/python3.8/site-packages

tzdata
tzdata-2024.1.dist-info
umap
umap_learn-0.5.6.dist-info
unicodedata2-15.1.0.dist-info
unicodedata2.cpython-38-x86_64-linux-gnu.so
urllib3
urllib3-2.2.2.dist-info
wcwidth
wcwidth-0.2.13.dist-info
werkzeug
werkzeug-3.0.3.dist-info
wheel
wheel-0.43.0.dist-info
widgetsnbextension
widgetsnbextension-4.0.11.dist-info
_yaml
yaml
yamlordereddictloader-0.4.2.dist-info
yamlordereddictloader.py
yarl
yarl-1.9.4.dist-info
zipp
zipp-3.19.2.dist-info
zstandard
zstandard-0.22.0-py3.8.egg-info

Do you have any suggestions of how we can fix this together? I've already got a fork of this great packages with the 'umap' name fixed, if that seems to be the issue there.