Minor doc updates: Update overview figure; refer to ms2rescore.rescor…

…e in Python API tutorial; remove v3.0 warning in readme

README.md

@@ -10,11 +10,6 @@
 
 Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
 
-> ⚠️ Note: This is the documentation for the fully redeveloped version 3.0 of MS²Rescore. While
-> MS²Rescore 3.0 has been drastically improved over the previous version, you might run into some
-> unforeseen issues. Please report any issues you encounter on the [issue tracker][issues] or post
-> your questions on the [GitHub Discussions][discussions] forum.
-
 ## About MS²Rescore
 
 MS²Rescore performs ultra-sensitive peptide identification rescoring with LC-MS predictors such as

docs/source/tutorials/in-depth-python-api.ipynb

@@ -7,6 +7,18 @@
     "# Using the Python API "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This tutorial shows how to use the MS²Rescore Python API for each step of the rescoring process\n",
+    "individually. This is useful if you want to customize rescoring for your own Python\n",
+    "workflow or if you want to understand how MS²Rescore works.\n",
+    "\n",
+    "Note that the full MS²Rescore workflow is also available from Python with the single function call\n",
+    "`ms2rescore.rescore()`."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,