Add dependencies to recommend so more notebooks run properly

This commit adds some additional dependencies so that more notebooks
under `docs/tutorials` can run properly when installing with
`pip install snapatac2[recommend]`.

In future work, it may make sense to remove dependencies like
`scanorama` and `harmonypy` from `extra`
`[project.optional-dependencies]` as `scanpy` already shares the
exact same dependencies and it may be easier for future maintenance
for `scanpy` to deal with versioning and pinning.

snapatac2-python/pyproject.toml

@@ -57,6 +57,6 @@ Changelog = "https://kzhang.org/SnapATAC2/version/dev/changelog.html"
 
 [project.optional-dependencies]
 extra = ["scanorama>=1.7.3", "harmonypy>=0.0.9", "xgboost>=1.4", "umap-learn>=0.5.0"]
-recommend = ["scanpy[skmisc]>=1.9", "scvi-tools>=1.0"]
+recommend = ["scanpy[scanorama, skmisc, magic, harmony]>=1.9", "scvi-tools>=1.0"]
 all = ["snapatac2[extra]", "snapatac2[recommend]"]
 test = ["pytest", "hypothesis==6.72.4"]