Merge pull request #255 from Exabyte-io/feature/SOF-7779

update: fix formats + mol

Author: VsevolodX

config.yml

@@ -31,7 +31,7 @@ default:
     - uncertainties==3.1.6
     - jinja2
     - pymatgen-analysis-defects<=2024.4.23
-    - mat3ra-made==2025.11.24.post0
+    - mat3ra-made==2025.12.16.post0
 # packages below are used when made is installed from GH wheel (made should be installed from below)
 #    - https://exabyte-io.github.io/made/mat3ra_made-0.1.dev1+ge64d360b8-py3-none-any.whl
 #    - mat3ra-code
@@ -66,3 +66,4 @@ notebooks:
     packages_common:
       - mat3ra-standata
       - exabyte-api-client
+      - requests

other/generate_gifs/gif_processing.ipynb

@@ -184,7 +184,7 @@
    "metadata": {},
    "cell_type": "code",
    "source": [
-    "from other.media_generation.utils.font_manager import FontManager\n",
+    "from other.generate_gifs.utils.font_manager import FontManager\n",
     "\n",
     "# Initialize font manager and list available fonts\n",
     "font_manager = FontManager()\n",
@@ -243,7 +243,7 @@
    "metadata": {},
    "cell_type": "code",
    "source": [
-    "from other.media_generation.utils.gif_processor import GIFProcessor\n",
+    "from other.generate_gifs.utils.gif_processor import GIFProcessor\n",
     "\n",
     "\n",
     "def process_all_gifs():\n",

other/materials_designer/import_materials_from_files.ipynb

@@ -46,8 +46,8 @@
     "FOLDER_PATH = \"./uploads\"\n",
     "\n",
     "# By default, format will be guessed from file extension\n",
-    "# If set to specific format, notebook will only read that format\n",
-    "ENFORCED_FORMATS = None # e.g. [\"cif\", \"espresso-in\"]\n",
+    "# If set to specific format, or array of formats, notebook will only read that format\n",
+    "ENFORCED_FORMATS = None  # e.g. \"cif\" or [\"cif\", \"espresso-in\"]\n",
     "\n",
     "# If set to true, the file extension will be included in the resulting material name\n",
     "USE_FILE_NAME_NO_EXTENSION = False\n",
@@ -72,11 +72,14 @@
    "outputs": [],
    "source": [
     "import sys\n",
+    "\n",
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\n",
+    "\n",
     "    await micropip.install(\"mat3ra-api-examples\", deps=False)\n",
     "    await micropip.install('mat3ra-utils')\n",
     "    from mat3ra.utils.jupyterlite.packages import install_packages\n",
+    "\n",
     "    await install_packages(\"import_materials_from_files.ipynb\")"
    ]
   },
@@ -101,18 +104,18 @@
     "from pathlib import Path\n",
     "from ase.io import read\n",
     "\n",
-    "ase_atoms, readable_file_names, unreadable_file_names = [], [], []\n",
+    "ase_atoms_list, readable_file_names, unreadable_file_names = [], [], []\n",
     "file_names = os.listdir(FOLDER_PATH)\n",
     "\n",
     "for file_name in file_names:\n",
     "    file_path = os.path.join(FOLDER_PATH, file_name)\n",
-    "    formats = ENFORCED_FORMATS or [None]\n",
+    "    formats = [ENFORCED_FORMATS] if isinstance(ENFORCED_FORMATS, str) else ENFORCED_FORMATS or [None]\n",
     "\n",
     "    for fmt in formats:\n",
     "        try:\n",
     "            atoms = read(file_path, format=fmt)\n",
     "            atoms.info[\"file_name\"] = Path(file_name).stem if USE_FILE_NAME_NO_EXTENSION else file_name\n",
-    "            ase_atoms.append(atoms)\n",
+    "            ase_atoms_list.append(atoms)\n",
     "            readable_file_names.append(file_name)\n",
     "            print(\"Successfully read:\", atoms.info[\"file_name\"], \"using format:\", fmt)\n",
     "            break\n",
@@ -138,7 +141,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f\"Successfully read {len(ase_atoms)} files: {readable_file_names}. \")\n",
+    "print(f\"Successfully read {len(ase_atoms_list)} files: {readable_file_names}. \")\n",
     "print(f\"Unreadable files: {unreadable_file_names}. \")"
    ]
   },
@@ -182,46 +185,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import io\n",
-    "from ase import Atoms\n",
-    "from ase.io import write\n",
-    "from express import ExPrESS\n",
-    "\n",
-    "def ase_to_poscar(atoms: Atoms):\n",
-    "    output = io.StringIO()\n",
-    "    try:\n",
-    "        write(output, atoms, format=\"vasp\")\n",
-    "        content = output.getvalue()\n",
-    "    except Exception as e:\n",
-    "        print(f\"Error converting ASE atoms to POSCAR: {e}\")\n",
-    "        content = None\n",
-    "    finally:\n",
-    "        output.close()\n",
-    "\n",
-    "    return content\n",
-    "\n",
-    "def convert_ase_entry_to_esse(ase_entry):\n",
-    "    try:\n",
-    "        poscar = ase_to_poscar(ase_entry)\n",
-    "        if poscar is None:\n",
-    "            raise ValueError(\"Failed to generate POSCAR string\")\n",
-    "\n",
-    "        kwargs = {\n",
-    "            \"structure_string\": poscar,\n",
-    "            \"structure_format\": \"poscar\"\n",
-    "        }\n",
-    "\n",
-    "        handler = ExPrESS(\"structure\", **kwargs)\n",
-    "        esse = handler.property(\"material\", **kwargs)\n",
-    "\n",
-    "        esse[\"name\"] = ase_entry.info.get(\"file_name\", \"Unknown\")\n",
-    "\n",
-    "        return esse\n",
-    "    except Exception as e:\n",
-    "        print(f\"Error processing ASE entry: {e}\")\n",
-    "        return None\n",
+    "from mat3ra.made.tools.convert import from_ase\n",
     "\n",
-    "esse_entries = [entry for entry in map(convert_ase_entry_to_esse, ase_atoms) if entry is not None]"
+    "esse_entries = [from_ase(ase_atoms) for ase_atoms in ase_atoms_list]"
    ]
   },
   {