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Backport PR #2566 on branch 1.9.x (Switch to igraph name) #2568

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Jul 21, 2023
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Backport PR #2566 on branch 1.9.x (Switch to igraph name) #2568

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6419aee
Backport PR #2566: Switch to `igraph` name
flying-sheep Jul 21, 2023
c4b5760
Merge branch '1.9.x' into auto-backport-of-pr-2566-on-1.9.x
flying-sheep Jul 21, 2023
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6 changes: 3 additions & 3 deletions docs/installation.md
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Expand Up @@ -24,7 +24,7 @@ pip install 'scanpy[leiden]'
```

The extra `[leiden]` installs two packages that are needed for popular
parts of scanpy but aren't requirements: [python-igraph] [^cite_csardi06] and [leiden] [^cite_traag18].
parts of scanpy but aren't requirements: [igraph] [^cite_csardi06] and [leiden] [^cite_traag18].

(dev-install-instructions)=

Expand Down Expand Up @@ -83,7 +83,7 @@ pip install --user scanpy

- `brew install igraph`

- If python-igraph still fails to install, see the question on [compiling igraph].
- If igraph still fails to install, see the question on [compiling igraph].
Alternatively consider installing gcc via `brew install gcc --without-multilib`
and exporting the required variables:

Expand Down Expand Up @@ -125,5 +125,5 @@ The whole process takes just a couple of minutes.
[leiden]: https://leidenalg.readthedocs.io
[miniconda]: http://conda.pydata.org/miniconda.html
[on github]: https://github.com/scverse/scanpy
[python-igraph]: http://igraph.org/python/
[igraph]: https://python.igraph.org/en/stable/
[unofficial binaries]: https://www.lfd.uci.edu/~gohlke/pythonlibs/
6 changes: 3 additions & 3 deletions pyproject.toml
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Expand Up @@ -121,9 +121,9 @@ dev = [
"docutils",
]
# Algorithms
paga = ["python-igraph"]
louvain = ["python-igraph", "louvain>=0.6,!=0.6.2"] # Louvain community detection
leiden = ["python-igraph", "leidenalg"] # Leiden community detection
paga = ["igraph"]
louvain = ["igraph", "louvain>=0.6,!=0.6.2"] # Louvain community detection
leiden = ["igraph>=0.10", "leidenalg>=0.9"] # Leiden community detection
bbknn = ["bbknn"] # Batch balanced KNN (batch correction)
magic = ["magic-impute>=2.0"] # MAGIC imputation method
skmisc = ["scikit-misc>=0.1.3"] # highly_variable_genes method 'seurat_v3'
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2 changes: 1 addition & 1 deletion scanpy/logging.py
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Expand Up @@ -127,7 +127,7 @@ def format(self, record: logging.LogRecord):
'pandas',
('sklearn', 'scikit-learn'),
'statsmodels',
('igraph', 'python-igraph'),
'igraph',
'louvain',
'leidenalg',
'pynndescent',
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2 changes: 1 addition & 1 deletion scanpy/testing/_pytest/marks.py
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Expand Up @@ -10,7 +10,7 @@
louvain="louvain",
skmisc="scikit-misc",
fa2="fa2",
igraph="python-igraph",
igraph="igraph",
dask="dask",
zarr="zarr",
zappy="zappy",
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