Fix documentation requiring download of PKSI-AT.hmm2 from antiSMASH

Author: althonos

docs/examples/.gitignore

@@ -1,3 +1,4 @@
 LuxC.hmm
 LuxC.domtbl
 rhodopsin.hmm
+PKSI-AT.hmm2

docs/examples/active_site.ipynb

@@ -45,6 +45,27 @@
     "## Loading the HMM"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let's start by downloading the PSKI-AT HMM from the AntiSMASH repository. We can use `urllib.request` to do that from within our Python script:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import shutil\n",
+    "from urllib.request import urlopen\n",
+    "\n",
+    "with urlopen('https://raw.githubusercontent.com/antismash/antismash/refs/heads/8-0-stable/antismash/modules/active_site_finder/data/PKSI-AT.hmm2') as src:\n",
+    "    with open(\"PKSI-AT.hmm2\", \"wb\") as dst:\n",
+    "        shutil.copyfileobj(src, dst)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -58,7 +79,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with pyhmmer.plan7.HMMFile(\"data/hmms/txt/PKSI-AT.hmm\") as hmm_file:\n",
+    "with pyhmmer.plan7.HMMFile(\"PKSI-AT.hmm2\") as hmm_file:\n",
     "    hmm = hmm_file.read()"
    ]
   },
@@ -271,7 +292,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -285,7 +306,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.13.11"
   }
  },
  "nbformat": 4,