Merge branch 'master' into ardunn-master

# Conflicts:
#	requirements.txt
#	workshop/lessons/08_ml_matminer/matminer-notes.ipynb

Author: Shyam D

.github/run_notebooks.py

@@ -0,0 +1,52 @@
+""" Python script to run notebooks in the directory they exist in """
+import os
+
+import nbformat
+import yaml
+from nbclient import NotebookClient
+from nbclient.exceptions import CellExecutionError
+
+
+def recursive_get(items):
+    if isinstance(items, dict):
+        for v in items.values():
+            yield from recursive_get(v)
+    elif isinstance(items, list):
+        for v in items:
+            yield from recursive_get(v)
+    else:
+        yield items
+
+
+with open("mkdocs.yml") as f:
+    mkdocs_config = yaml.load(f)
+
+notebooks = [
+    item
+    for item in recursive_get(mkdocs_config.get("nav", {}))
+    if item.endswith(".ipynb")
+]
+
+os.chdir("workshop")
+for notebook in notebooks:
+    print(f"Loading {notebook}")
+    nb = nbformat.read(notebook, as_version=4)
+
+    for cell in nb.cells:
+        if cell.get("cell_type", "") == "code" and "no-execute" in cell.get(
+            "metadata", {}
+        ).get("tags", []):
+            cell["cell_type"] = "markdown"
+
+    client = NotebookClient(
+        nb,
+        timeout=600,
+        resources={"metadata": {"path": os.path.dirname(notebook)}},
+    )
+    try:
+        client.execute()
+        nbformat.write(nb, notebook)
+    except CellExecutionError:
+        msg = 'Error executing the notebook "%s".\n\n' % notebook
+        print(msg)
+        raise

.github/workflows/dependabot-merge.yml

@@ -1,9 +1,12 @@
 name: Merge me!
 
 on:
-  check_suite:
+  workflow_run:
     types:
       - completed
+    workflows:
+      # List all required workflow names here.
+      - 'testing'
 
 jobs:
   merge-me:
@@ -13,4 +16,4 @@ jobs:
       - name: Merge me!
         uses: ridedott/merge-me-action@v2
         with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/testing.yml

@@ -67,6 +67,14 @@ jobs:
     - name: Install workshop package
       run: pip install -e .
 
+    - name: Install workshop data
+      run: python ./binder/populate_nobel_database.py
+
+    - name: Run Notebooks
+      env:
+        PMG_MAPI_KEY: ${{ secrets.MAPI_KEY }}
+      run: python .github/run_notebooks.py
+
     - name: Build
       run: mkdocs build
 
@@ -105,6 +113,14 @@ jobs:
     - name: Install workshop package
       run: pip install -e .
 
+    - name: Install workshop data
+      run: python ./binder/populate_nobel_database.py
+
+    - name: Run Notebooks
+      env:
+        PMG_MAPI_KEY: ${{ secrets.MAPI_KEY }}
+      run: python .github/run_notebooks.py
+
     - name: Build
       run: mkdocs build
 

binder/apt.txt

@@ -2,4 +2,4 @@ vim
 graphviz
 mongodb
 gfortran
-zip
+zip

mkdocs.yml

@@ -4,7 +4,7 @@ copyright: Built by The Materials Project
 site_url: https://workshop.materialsproject.org
 repo_url: https://github.com/materialsproject/workshop
 docs_dir: workshop
-extra_css: 
+extra_css:
   - assets/workshop.css
 extra_javascript:
   - assets/config.js

python_module/mp_workshop/fireworks_config/__init__.py

@@ -32,7 +32,10 @@
 
 dumpfn(fw_config, fw_config_dir / "FW_config.yaml")
 dumpfn(
-    fworker, fw_config_dir / "my_fworker.yaml", indent=4, default_flow_style=False,
+    fworker,
+    fw_config_dir / "my_fworker.yaml",
+    indent=4,
+    default_flow_style=False,
 )
 
 

requirements.txt

@@ -7,6 +7,7 @@ pymongo==3.12.0
 robocrys==0.2.7
 crystal-toolkit==2021.4.29
 matminer==0.7.3
+ipywidgets==7.5.1
 mpcontribs-client==3.12.0
 graphviz==0.17
-mp-api==0.5.1
+mp-api==0.5.1

workshop/assets/config.js

@@ -9,4 +9,4 @@ window.MathJax = {
       ignoreHtmlClass: ".*|",
       processHtmlClass: "arithmatex"
     }
-  };
+  };