Upgraded conda environment to include updated packages due to availab…

…ility issues
NegarJanani · Aug 28, 2024 · ae04e74 · ae04e74
1 parent d57fd93
commit ae04e74
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Showing 2 changed files with 16 additions and 15 deletions.
diff --git a/code/process.ipynb b/code/process.ipynb
@@ -12,7 +12,8 @@
     "import pandas\n",
     "import networkx\n",
     "\n",
-    "import utilities"
+    "import utilities\n",
+    "from math import gcd\n"
    ]
   },
   {
@@ -387,7 +388,7 @@
     "        key = 'direct_not_annotations' if utilities.is_NOT_qaulifier(row.Qualifier) else 'direct_annotations'\n",
     "\n",
     "        gene = row['GeneID']\n",
-    "        graph.node[go_id][key].add(gene)\n",
+    "        graph.nodes[go_id][key].add(gene)\n",
     "    \n",
     "    return graph"
    ]
@@ -401,12 +402,12 @@
     "def propagate_annotations(graph):\n",
     "    \"\"\"Infer annotations through propagations\"\"\"\n",
     "    for node in networkx.topological_sort(graph):\n",
-    "        data = graph.node[node]\n",
+    "        data = graph.nodes[node]\n",
     "        inferred = data['inferred_annotations']\n",
     "        inferred -= data['direct_not_annotations']\n",
     "        inferred |= data['direct_annotations']\n",
     "        for subsuming_node in graph.successors(node):\n",
-    "            subsuming_data = graph.node[subsuming_node]\n",
+    "            subsuming_data = graph.nodes[subsuming_node]\n",
     "            subsuming_data['inferred_annotations'] |= inferred"
    ]
   },
@@ -628,7 +629,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -642,7 +643,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,

diff --git a/environment.yml b/environment.yml
@@ -2,13 +2,13 @@ name: gene-ontology
 channels:
   - conda-forge
 dependencies:
-  - conda-forge::networkx=2.2
-  - conda-forge::numpy=1.15.3
-  - conda-forge::pandas=0.23.4
-  - conda-forge::python=3.6.7
-  - conda-forge::requests=2.20.0
-  - conda-forge::notebook=5.7.0
-  - conda-forge::nbconvert=5.4.0
-  - conda-forge::ipykernel=5.1.0
+  - conda-forge::networkx=2.6
+  - conda-forge::numpy=1.24.3
+  - conda-forge::pandas=2.0.3
+  - conda-forge::python=3.8.19
+  - conda-forge::requests=2.32.3
+  - conda-forge::notebook=7.2.1
+  - conda-forge::nbconvert=7.16.4
+  - conda-forge::ipykernel=6.29.5
   - pip:
-    - obonet==0.2.3
+    - obonet==1.1.0