Merge pull request #133 from Exabyte-io/update/SOF-7390-lfs-1

update/SOF 7390 lfs 1

.gitattributes

@@ -15,3 +15,4 @@ examples/workflow/get_workflows.ipynb !filter !diff !merge text
 images/*.png filter=lfs diff=lfs merge=lfs -text
 *.upf filter=lfs diff=lfs merge=lfs -text
 examples/assets/bash_workflow_template.json filter=lfs diff=lfs merge=lfs -text
+*.whl filter=lfs diff=lfs merge=lfs -text

config.yml

@@ -13,9 +13,9 @@ default:
   packages_pyodide:
     - lzma
     - sqlite3
-    - https://files.mat3ra.com/uploads/pymatgen-2024.4.13-py3-none-any.whl
-    - https://files.mat3ra.com:44318/web/pyodide/spglib-2.0.2-py3-none-any.whl
-    - https://files.pythonhosted.org/packages/d9/0e/2a05efa11ea33513fbdf4a2e2576fe94fd8fa5ad226dbb9c660886390974/ruamel.yaml-0.17.32-py3-none-any.whl
+    - emfs:/drive/api-examples/packages/pymatgen-2024.4.13-py3-none-any.whl
+    - emfs:/drive/api-examples/packages/spglib-2.0.2-py3-none-any.whl
+    - emfs:/drive/api-examples/packages/ruamel.yaml-0.17.32-py3-none-any.whl
     - networkx==3.2.1
     - monty==2023.11.3
     - scipy==1.11.2
@@ -32,8 +32,8 @@ notebooks:
     packages_python:
     packages_pyodide:
       - annotated_types>=0.6.0
-      - https://files.mat3ra.com/uploads/pydantic_core-2.18.2-py3-none-any.whl
-      - https://files.mat3ra.com/uploads/pydantic-2.7.1-py3-none-any.whl
+      - emfs:/drive/api-examples/packages/pydantic_core-2.18.2-py3-none-any.whl
+      - emfs:/drive/api-examples/packages/pydantic-2.7.1-py3-none-any.whl
       - mat3ra-esse
       - mat3ra-made
   - name: import_material_from_jarvis_db_entry.ipynb
@@ -45,8 +45,8 @@ notebooks:
       - setuptools
     packages_python:
     packages_pyodide:
-      - https://files.mat3ra.com:44318/uploads/paginate-0.5.6-py3-none-any.whl
-      - https://files.mat3ra.com:44318/uploads/watchdog-2.3.1-py3-none-any.whl
+      - emfs:/drive/api-examples/packages/paginate-0.5.6-py3-none-any.whl
+      - emfs:/drive/api-examples/packages/watchdog-2.3.1-py3-none-any.whl
   - name: import_materials_from_files.ipynb
     packages_common:
       - express-py==2024.2.2.post2
@@ -55,5 +55,16 @@ notebooks:
       - setuptools
     packages_python:
     packages_pyodide:
-      - https://files.mat3ra.com:44318/uploads/paginate-0.5.6-py3-none-any.whl
-      - https://files.mat3ra.com:44318/uploads/watchdog-2.3.1-py3-none-any.whl
+      - emfs:/drive/api-examples/packages/paginate-0.5.6-py3-none-any.whl
+      - emfs:/drive/api-examples/packages/watchdog-2.3.1-py3-none-any.whl
+  - name: create_point_defect.ipynb
+    packages_common:
+      - ipywidgets
+    packages_python:
+    packages_pyodide:
+      - annotated_types>=0.6.0
+      - emfs:/drive/api-examples/packages/pydantic_core-2.18.2-py3-none-any.whl
+      - emfs:/drive/api-examples/packages/pydantic-2.7.1-py3-none-any.whl
+      - pymatgen-analysis-defects
+      - mat3ra-esse
+      - mat3ra-made

other/materials_designer/create_point_defect.ipynb

@@ -79,7 +79,7 @@
     "    import micropip\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
     "    from utils.jupyterlite import install_packages\n",
-    "    await install_packages(\"create_interface_with_min_strain_zsl.ipynb\", \"../../config.yml\")"
+    "    await install_packages(\"create_point_defect.ipynb\", \"../../config.yml\")"
    ],
    "metadata": {
     "collapsed": false

utils/jupyterlite.py

@@ -1,6 +1,7 @@
 import json
 import os
 from enum import Enum
+from typing import Any, Dict, Optional
 
 from IPython.display import Javascript, display
 
@@ -24,22 +25,22 @@ class EnvironmentEnum(Enum):
     import sys
 
 
-async def install_package_pyodide(pkg, verbose=True):
+async def install_package_pyodide(pkg: str, verbose=True):
     """
     Install a package in a Pyodide environment.
     Args:
         pkg (string): The name of the package to install.
         verbose (bool): Whether to print the name of the installed package.
     """
-    is_url = pkg.startswith("http://") or pkg.startswith("https://")
+    is_url = pkg.startswith("http://") or pkg.startswith("https://") or pkg.startswith("emfs:/")
     are_dependencies_installed = not is_url
     await micropip.install(pkg, deps=are_dependencies_installed)
     pkg_name = pkg.split("/")[-1].split("-")[0] if is_url else pkg.split("==")[0]
     if verbose:
         print(f"Installed {pkg_name}")
 
 
-def install_package_python(pkg, verbose=True):
+def install_package_python(pkg: str, verbose=True):
     """
     Install a package in a standard Python environment.
     Args:
@@ -51,7 +52,7 @@ def install_package_python(pkg, verbose=True):
         print(f"Installed {pkg}")
 
 
-async def install_packages(notebook_name, requirements_path="config.yml", verbose=True):
+async def install_packages(notebook_name: str, requirements_path="config.yml", verbose=True):
     """
     Install the packages listed in the requirements file for the notebook with the given name.
     Args:
@@ -113,7 +114,7 @@ async def install_packages(notebook_name, requirements_path="config.yml", verbos
         os.environ["requirements_hash"] = requirements_hash
 
 
-def set_data_pyodide(key, value):
+def set_data_pyodide(key: str, value: Any):
     """
     Take a Python object, serialize it to JSON, and send it to the host environment
     through a JavaScript function defined in the JupyterLite extension `data_bridge`.
@@ -138,7 +139,7 @@ def set_data_pyodide(key, value):
     set_data_python(key, value)
 
 
-def set_data_python(key, value):
+def set_data_python(key: str, value: Any):
     """
     Write data to the `uploads` folder in a JupyterLab environment.
     Args:
@@ -154,7 +155,7 @@ def set_data_python(key, value):
         print(f"Data for {key} written to {file_path}")
 
 
-def set_data(key, value):
+def set_data(key: str, value: Any):
     """
     Switch between the two functions `set_data_pyodide` and `set_data_python` based on the environment.
     Args:
@@ -167,7 +168,7 @@ def set_data(key, value):
         set_data_python(key, value)
 
 
-def get_data_pyodide(key, globals_dict=None):
+def get_data_pyodide(key: str, globals_dict: Optional[Dict] = None):
     """
     Load data from the host environment into globals()[key] variable.
     Args:
@@ -178,7 +179,7 @@ def get_data_pyodide(key, globals_dict=None):
         globals_dict[key] = globals_dict["data_from_host"]
 
 
-def get_data_python(key, globals_dict=None):
+def get_data_python(key: str, globals_dict: Optional[Dict] = None):
     """
     Read data from the `uploads` folder in a JupyterLab environment.
     Args:
@@ -200,7 +201,7 @@ def get_data_python(key, globals_dict=None):
         print("No data found in the 'uploads' folder.")
 
 
-def get_data(key, globals_dict=None):
+def get_data(key: str, globals_dict: Optional[Dict] = None):
     """
     Switch between the two functions `get_data_pyodide` and `get_data_python` based on the environment.
     Args: