Merge branch 'dev' of github.com:Exabyte-io/api-examples into dev

.github/workflows/cicd.yml

@@ -28,6 +28,31 @@ jobs:
           python -m pip install pre-commit
           pre-commit run --all-files --show-diff-on-failure
 
+  publish-py-package:
+    needs: [run-linter]
+    runs-on: ubuntu-latest
+    if: github.ref_name == 'dev'
+
+    steps:
+      - name: Checkout this repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout actions repository
+        uses: actions/checkout@v4
+        with:
+          repository: Exabyte-io/actions
+          token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          path: actions
+
+      - name: Publish python release
+        uses: ./actions/py/publish
+        with:
+          python-version: 3.8.x
+          github-token: ${{ secrets.BOT_GITHUB_TOKEN }}
+          pypi-api-token: ${{ secrets.PYPI_API_TOKEN }}
+
 # TODO: Add back when when fixed.
 #  build-and-deploy-docs:
 #    runs-on: ubuntu-20.04

other/jupyterlite/utils.py

@@ -69,22 +69,28 @@ async def install_packages(notebook_name, requirements_path="config.yml", verbos
     requirements_hash = str(hash(json.dumps(requirements)))
     if os.environ.get("requirements_hash") != requirements_hash:
         packages_default_common = requirements.get("default", {}).get("packages_common", []) or []
-        packages_default_environment_specific = requirements.get("default", {}).get(f"packages_{ENVIRONMENT.value}", []) or []
+        packages_default_environment_specific = (
+            requirements.get("default", {}).get(f"packages_{ENVIRONMENT.value}", []) or []
+        )
 
         notebook_requirements = next(
             (cfg for cfg in requirements.get("notebooks", []) if cfg.get("name") == notebook_name), None
         )
         if notebook_requirements:
             packages_notebook_common = notebook_requirements.get("packages_common", []) or []
-            packages_notebook_environment_specific= notebook_requirements.get(f"packages_{ENVIRONMENT.value}", []) or []
+            packages_notebook_environment_specific = (
+                notebook_requirements.get(f"packages_{ENVIRONMENT.value}", []) or []
+            )
         else:
             raise ValueError(f"No packages found for notebook {notebook_name}")
 
+        # Note: environment specific packages have to be installed first,
+        # because in Pyodide common packages might depend on them
         packages = [
-            *packages_default_common,
             *packages_default_environment_specific,
-            *packages_notebook_common,
             *packages_notebook_environment_specific,
+            *packages_default_common,
+            *packages_notebook_common,
         ]
 
         for pkg in packages:

other/materials_designer/create_interface_with_min_strain_zsl.ipynb

@@ -10,8 +10,7 @@
     "\n",
     "<h2 style=\"color:green\">Usage</h2>\n",
     "\n",
-    "0. Make sure to select Input Materials\n",
-    "1. Execute \"Run first: ...\" cell below to load Input Materials into the current kernel\n",
+    "1. Make sure to select Input Materials\n",
     "2. Set Input Parameters (e.g. `MILLER_INDICES`, `THICKNESS`, `MAX_AREA`) below or use the default values\n",
     "3. Click \"Run\" > \"Run All Cells\" to run all cells\n",
     "4. Wait for the run to complete (depending on the area, it can take 1-2 min or more). Scroll down to view cell results.\n",
@@ -31,25 +30,6 @@
     "3. When the strain matching is finished, the interface with the lowest strain (and the smallest number of atoms) is selected. We create the corresponding supercells and place them at a specified distance from each other (note no shift is performed currently).\n"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<h2 style=\"color:red\">Run first: load input materials in current kernel</h2>\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from jupyterlite.utils import get_data\n",
-    "\n",
-    "# Get the list of input materials and load them into `materials_in` variable\n",
-    "get_data(\"materials_in\", globals())"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -75,7 +55,9 @@
     "    \"MATERIAL_INDEX\": 1,  # the index of the material in the materials_in list\n",
     "    \"MILLER_INDICES\": (0, 0, 1),  # the miller indices of the interfacial plane\n",
     "    \"THICKNESS\": 1,  # in layers\n",
-    "}"
+    "}\n",
+    "\n",
+    "USE_CONVENTIONAL_CELL = True  # if True, the surface plane is constructed using miller indices of the conventional cell"
    ]
   },
   {
@@ -143,12 +125,45 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 3. Create interfaces\n",
+    "## 3. Load and prepare input Materials\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from jupyterlite.utils import get_data\n",
+    "from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer\n",
+    "from src.utils import to_pymatgen\n",
+    "\n",
+    "# Get the list of input materials and load them into `materials_in` variable\n",
+    "get_data(\"materials_in\", globals())\n",
+    "\n",
+    "if \"materials_in\" in globals():\n",
+    "    pymatgen_materials = [to_pymatgen(item) for item in materials_in]\n",
+    "    if USE_CONVENTIONAL_CELL: pymatgen_materials = [SpacegroupAnalyzer(item).get_conventional_standard_structure() for\n",
+    "                                                    item in pymatgen_materials]\n",
+    "\n",
+    "    for material in pymatgen_materials:\n",
+    "        print(material, \"\\n\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 4. Create interfaces\n",
     "\n",
-    "### 3.1. Extract Interfaces and Terminations\n",
+    "### 4.1. Extract Interfaces and Terminations\n",
     "\n",
     "Extract all possible layer/substrate supercell combinations within the maximum area including different terminations."
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "code",
@@ -160,14 +175,11 @@
    "outputs": [],
    "source": [
     "from src.pymatgen_coherent_interface_builder import CoherentInterfaceBuilder, ZSLGenerator\n",
-    "from src.utils import to_pymatgen\n",
-    "\n",
-    "if \"materials_in\" in globals():\n",
-    "    pymatgen_materials = [to_pymatgen(item) for item in materials_in]\n",
-    "for material in pymatgen_materials:\n",
-    "    print(material, \"\\n\")\n",
-    "\n",
+    "from src.utils import translate_to_bottom\n",
     "\n",
+    "# Translate the materials to the bottom of the cell to allow for multilayer heterostructures creation\n",
+    "pymatgen_materials = [translate_to_bottom(item) for item in pymatgen_materials]\n",
+    "    \n",
     "def create_interfaces(settings):\n",
     "    print(\"Creating interfaces...\")\n",
     "    zsl = ZSLGenerator(\n",
@@ -221,7 +233,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 3.2. Print out the interfaces and terminations"
+    "### 5.2. Print out the interfaces and terminations"
    ]
   },
   {
@@ -239,9 +251,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 4. Sort interfaces by strain\n",
+    "## 5. Sort interfaces by strain\n",
     "\n",
-    "### 4.1. Sort all interfaces"
+    "### 5.1. Sort all interfaces"
    ]
   },
   {
@@ -271,7 +283,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 4.2. Print out interfaces with lowest strain for each termination"
+    "### 5.2. Print out interfaces with lowest strain for each termination"
    ]
   },
   {
@@ -291,7 +303,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 5. Plot the results\n",
+    "## 6. Plot the results\n",
     "\n",
     "Plot the number of atoms vs strain. Adjust the parameters as needed.\n"
    ]
@@ -367,9 +379,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 6. Select the interface to pass outside this kernel\n",
+    "## 7. Select the interface to pass outside this kernel\n",
     "\n",
-    "### 6.1. Select the interface with the desired termination and strain\n",
+    "### 7.1. Select the interface with the desired termination and strain\n",
     "\n",
     "The data in `sorted_interfaces` now contains an object with the following structure:\n",
     "\n",
@@ -409,7 +421,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 6.2. Pass data to the outside runtime\n"
+    "### 7.2. Pass data to the outside runtime\n"
    ]
   },
   {