From b41272dcb3390207c3ebed2558906351540c035c Mon Sep 17 00:00:00 2001
From: Florian Frantzen <florian.frantzen@rwth-aachen.de>
Date: Fri, 18 Oct 2024 14:58:01 +0200
Subject: [PATCH] Refactor `pygsp` dependency

---
 README.md      | 9 ++++++---
 docs/index.rst | 6 ++++--
 pyproject.toml | 8 ++++----
 3 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 3214e30..baaf071 100644
--- a/README.md
+++ b/README.md
@@ -51,12 +51,14 @@ for the topological domains supported in [TopoNetX](https://github.com/pyt-team/
 `TopoEmbedX` is available on PyPI and can be installed using `pip`.
 
 ```bash
+pip install "pygsp @ git+https://github.com/epfl-lts2/pygsp@a3412ce7696c02c8a55439e89d0c9ab8ae863269"
 pip install "karateclub @ git+https://github.com/benedekrozemberczki/karateclub@cb46a91df8dcbeb2570debcf6a9d0c518107a2de"
 pip install topoembedx
 ```
 
-The library depends on `karateclub`, which did not receive updates on PyPI for a long time.
-You have to manually install the latest version from GitHub for up-to-date NetworkX compatibility.
+The library depends on `pygsp` and `karateclub`, which did not receive updates
+on PyPI for a long time. You have to manually install the latest versions from
+GitHub for up-to-date Python and NetworkX compatibility.
 
 ## 🦾 Getting Started
 
@@ -100,9 +102,10 @@ cd TopoEmbedX
 git pull
 ```
 
-3. Install a recent version of `karateclub`:
+3. Install a recent version of `pygsp` and `karateclub`:
 
 ```bash
+pip install "pygsp @ git+https://github.com/epfl-lts2/pygsp@a3412ce7696c02c8a55439e89d0c9ab8ae863269"
 pip install "karateclub @ git+https://github.com/benedekrozemberczki/karateclub@cb46a91df8dcbeb2570debcf6a9d0c518107a2de"
 ```
 
diff --git a/docs/index.rst b/docs/index.rst
index 27e2a36..7e267ee 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -30,11 +30,13 @@ for the topological domains supported in `TopoNetX <https://github.com/pyt-team/
 
 .. code-block:: bash
 
+   pip install "pygsp @ git+https://github.com/epfl-lts2/pygsp@a3412ce7696c02c8a55439e89d0c9ab8ae863269"
    pip install "karateclub @ git+https://github.com/benedekrozemberczki/karateclub@cb46a91df8dcbeb2570debcf6a9d0c518107a2de"
    pip install topoembedx
 
-The library depends on ``karateclub``, which did not receive updates on PyPI for a long time.
-You have to manually install the latest version from GitHub for up-to-date NetworkX compatibility.
+The library depends on ``pygsp`` and ``karateclub``, which did not receive
+updates on PyPI for a long time. You have to manually install the latest
+versions from GitHub for up-to-date Python and NetworkX compatibility.
 
 🔍 References
 -------------
diff --git a/pyproject.toml b/pyproject.toml
index ac5a2e7..a998cdc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,10 +39,10 @@ dependencies=[
     "scipy",
     "toponetx",
 
-    # We don't have a direct dependency on pygsp, but it is required by karateclub.
-    # The version on PyPI is severely outdated and does not work on Python 3.12.
-    # At least using the latest version from GitHub works for now.
-    "pygsp @ git+https://github.com/epfl-lts2/pygsp@a3412ce7696c02c8a55439e89d0c9ab8ae863269"
+    # These dependencies did not receive a new release on PyPI for a long time.
+    # We ask the user to manually install the latest version from GitHub separately.
+    "karateclub",
+    "pygsp"
 ]
 
 [project.optional-dependencies]