Update zenodo link

Author: hannahbaumann

abfe_tutorial/abfe_analysis.ipynb

@@ -25,13 +25,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "8365a5cd-81f2-45ad-9b7b-9225f972da09",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "--2025-10-14 13:42:30--  https://zenodo.org/records/17348229/files/abfe_results.zip\n",
+      "Resolving zenodo.org (zenodo.org)... 2001:1458:d00:25::100:372, 2001:1458:d00:24::100:f6, 2001:1458:d00:61::100:2f3, ...\n",
+      "Connecting to zenodo.org (zenodo.org)|2001:1458:d00:25::100:372|:443... connected.\n",
+      "HTTP request sent, awaiting response... 200 OK\n",
+      "Length: 1005319 (982K) [application/octet-stream]\n",
+      "Saving to: ‘abfe_results.zip’\n",
+      "\n",
+      "abfe_results.zip    100%[===================>] 981.76K  1.61MB/s    in 0.6s    \n",
+      "\n",
+      "2025-10-14 13:42:31 (1.61 MB/s) - ‘abfe_results.zip’ saved [1005319/1005319]\n",
+      "\n",
+      "Archive:  abfe_results.zip\n",
+      "   creating: abfe_results\n",
+      "   creating: abfe_results/results_2\n",
+      "  inflating: abfe_results/toluene_results.json  \n",
+      "   creating: abfe_results/results_1\n",
+      "   creating: abfe_results/results_0\n",
+      "  inflating: abfe_results/results_2/1.json  \n",
+      "  inflating: abfe_results/results_1/1.json  \n",
+      "  inflating: abfe_results/results_0/1.json  \n"
+     ]
+    }
+   ],
    "source": [
-    "# ToDo: Update this!!!\n",
-    "!wget https://zenodo.org/records/17019064/files/abfe_results.zip\n",
+    "!wget https://zenodo.org/records/17348229/files/abfe_results.zip\n",
     "!unzip abfe_results.zip"
    ]
   },
@@ -46,7 +72,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "7fbf1482-25ca-427b-a881-af88a983461c",
    "metadata": {},
    "outputs": [],
@@ -61,13 +87,11 @@
     "from gufe.tokenization import JSON_HANDLER\n",
     "import pandas as pd\n",
     "from openff.units import unit\n",
-    "import math\n",
     "from openfecli.commands.gather import (\n",
     "    format_estimate_uncertainty,\n",
     "    _collect_result_jsons,\n",
     "    load_json,\n",
-    ")\n",
-    "from cinnabar import Measurement, FEMap"
+    ")"
    ]
   },
   {
@@ -83,7 +107,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "04ccdedd-84e3-4ccc-ae42-4f3772acb115",
    "metadata": {},
    "outputs": [],
@@ -129,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "3733c540-de62-45a0-ba66-268397a38b49",
    "metadata": {},
    "outputs": [],
@@ -187,7 +211,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "id": "08afcbcf-34a8-4450-a967-eb4ed5800ee1",
    "metadata": {},
    "outputs": [],
@@ -221,7 +245,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "id": "a5d4aef3-1fab-40b4-848c-d59df8ee1441",
    "metadata": {},
    "outputs": [],
@@ -235,7 +259,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "id": "0621e3a2-7906-4661-a640-c414456f8869",
    "metadata": {},
    "outputs": [],
@@ -339,7 +363,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 10,
    "id": "b077c4e2-373a-4314-a527-186bb4683262",
    "metadata": {},
    "outputs": [],
@@ -382,7 +406,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 11,
    "id": "5e026eaf-2a95-4d4a-873d-b0d6e8d622c8",
    "metadata": {},
    "outputs": [],
@@ -430,10 +454,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 12,
    "id": "7bc49c0e-6fec-409c-a01c-42c35f57dcc6",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/hannahbaumann/miniforge3/envs/openfe_dev/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
+      "\n",
+      "Due to the on going maintenance burden of keeping command line application\n",
+      "wrappers up to date, we have decided to deprecate and eventually remove these\n",
+      "modules.\n",
+      "\n",
+      "We instead now recommend building your command line and invoking it directly\n",
+      "with the subprocess module.\n",
+      "  warnings.warn(\n"
+     ]
+    }
+   ],
    "source": [
     "# Specify paths to result directories\n",
     "results_dir = [\n",
@@ -457,7 +497,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 13,
    "id": "46996a74-709c-41f2-ac39-0f77fb33371e",
    "metadata": {},
    "outputs": [],
@@ -468,7 +508,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 14,
    "id": "d1a6ad61-1e5a-4d8a-9067-9ed428ef145c",
    "metadata": {},
    "outputs": [
@@ -514,7 +554,7 @@
        "0      1        -18.36                   0.98"
       ]
      },
-     "execution_count": 32,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -534,7 +574,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 15,
    "id": "8b2c1dd8-ffa3-4585-94a7-4a1ed1454f30",
    "metadata": {},
    "outputs": [],
@@ -545,7 +585,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 16,
    "id": "08b72901-9c71-460b-b5da-9fb4a35e07f7",
    "metadata": {},
    "outputs": [
@@ -657,7 +697,7 @@
        "8  standard_state_correction      1          -9.0                    0.0"
       ]
      },
-     "execution_count": 34,
+     "execution_count": 16,
      "metadata": {},
      "output_type": "execute_result"
     }