remove checkm2 github link in main deps to be able to deploy in Pypi and update doc

Author: JeanMainguy

docs/installation.md

@@ -68,8 +68,14 @@ Binette is available on [PyPI](https://pypi.org/project/Binette/) and can be ins
 pip install binette
 ```
 
-In addition to Python dependencies, Binette requires [Diamond](https://github.com/bbuchfink/diamond) to be installed and executable.
+In addition to Python dependencies, Binette requires a few external tools:
 
+* **[DIAMOND](https://github.com/bbuchfink/diamond)** must be installed and available in your system’s `PATH`.
+* **[CheckM2](https://github.com/chklovski/CheckM2)** (version `1.1.0`) is also required but not distributed on PyPI. You can install it directly from GitHub:
+
+```bash
+pip install git+https://github.com/chklovski/CheckM2.git@1.1.0
+```
 
 ## Downloading the CheckM2 database
 

pyproject.toml

@@ -25,7 +25,6 @@ classifiers=[
 requires-python = ">=3.12"
 
 dependencies = [
-    "checkm2 @ git+https://github.com/chklovski/CheckM2.git@1.1.0",
     "joblib>=1.0,<2.0",
     "networkx>=3.0,<4.0",
     "numpy>1.24,<3.0",
@@ -39,6 +38,10 @@ dependencies = [
 
 [project.optional-dependencies]
 
+checkm2 = [
+    "checkm2 @ git+https://github.com/chklovski/CheckM2.git@1.1.0"
+]
+
 doc = [
     "sphinx==6.2.1",
     "sphinx_rtd_theme==1.2.2",