Merge pull request #137 from Exabyte-io/hotfix/pmg-defects

chore: limit pmg defects package that is not using latest pmg

Author: VsevolodX

config.yml

@@ -23,7 +23,7 @@ default:
     - sympy==1.12
     - uncertainties==3.1.6
     - jinja2
-    - pymatgen-analysis-defects
+    - pymatgen-analysis-defects<=2024.4.23
 notebooks:
   - name: create_interface_with_min_strain_zsl.ipynb
     packages_common:

other/materials_designer/create_interface_with_min_strain_zsl.ipynb

@@ -207,8 +207,8 @@
     "film_slabs = [create_slab(film_slab_configuration, termination) for termination in film_slab_terminations]\n",
     "substrate_slabs = [create_slab(substrate_slab_configuration, termination) for termination in substrate_slab_terminations]\n",
     "\n",
-    "visualize([{\"material\":slab, \"title\": slab.metadata[\"termination\"]} for slab in film_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")\n",
-    "visualize([{\"material\":slab, \"title\": slab.metadata[\"termination\"]} for slab in substrate_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")  "
+    "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in film_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")\n",
+    "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in substrate_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")  "
    ],
    "metadata": {
     "collapsed": false

utils/jupyterlite.py

@@ -189,12 +189,14 @@ def get_data_python(key: str, globals_dict: Optional[Dict] = None):
     """
     try:
         data_from_host = []
+        index = 0
         for filename in sorted(os.listdir(UPLOADS_FOLDER)):
             if filename.endswith(".json"):
                 with open(os.path.join(UPLOADS_FOLDER, filename), "r") as file:
                     data = json.load(file)
                 name = os.path.splitext(filename)[0]
-                print(f"Data from {name} has been read successfully.")
+                print(f"{index}: Data from {name} has been read successfully.")
+                index += 1
                 data_from_host.append(data)
         if globals_dict is not None:
             globals_dict[key] = data_from_host