From 05068c347ac176d664ada3b0d5979255d35ce686 Mon Sep 17 00:00:00 2001
From: Philipp A <flying-sheep@web.de>
Date: Fri, 21 Jul 2023 12:53:30 +0200
Subject: [PATCH] Switch to `igraph` name (#2566)

---
 .gitignore                      | 1 +
 docs/installation.md            | 6 +++---
 pyproject.toml                  | 6 +++---
 scanpy/logging.py               | 2 +-
 scanpy/testing/_pytest/marks.py | 2 +-
 5 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index ed60829903..74a7fdcc33 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,6 +21,7 @@
 /scanpy/tests/notebooks/figures/
 
 # Environment management
+/hatch.toml
 /Pipfile
 /Pipfile.lock
 /requirements*.lock
diff --git a/docs/installation.md b/docs/installation.md
index b8b75e1a9d..c94883946b 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -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)=
 
@@ -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:
 
@@ -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/
diff --git a/pyproject.toml b/pyproject.toml
index 1a0d3abdac..076155e867 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -131,9 +131,9 @@ 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'
diff --git a/scanpy/logging.py b/scanpy/logging.py
index 712a187961..086c559593 100644
--- a/scanpy/logging.py
+++ b/scanpy/logging.py
@@ -127,7 +127,7 @@ def format(self, record: logging.LogRecord):
     'pandas',
     ('sklearn', 'scikit-learn'),
     'statsmodels',
-    ('igraph', 'python-igraph'),
+    'igraph',
     'louvain',
     'leidenalg',
     'pynndescent',
diff --git a/scanpy/testing/_pytest/marks.py b/scanpy/testing/_pytest/marks.py
index 64ef05d24e..6ea633bf17 100644
--- a/scanpy/testing/_pytest/marks.py
+++ b/scanpy/testing/_pytest/marks.py
@@ -10,7 +10,7 @@
     louvain="louvain",
     skmisc="scikit-misc",
     fa2="fa2",
-    igraph="python-igraph",
+    igraph="igraph",
     dask="dask",
     zarr="zarr",
     zappy="zappy",