add jupyter notebook support in documentation (#109)

* add jupyter notebook support in documentation

* add ruff linting and formatting for jupyter notebooks

* add the capability for notebook testing

.devcontainer/devcontainer.json

@@ -26,7 +26,8 @@
 				"streetsidesoftware.code-spell-checker",
 				"ms-azuretools.vscode-docker",
 				"charliermarsh.ruff",
-				"njpwerner.autodocstring"
+				"njpwerner.autodocstring",
+				"ms-toolsai.jupyter"
 			],
 			"settings": {
 				"python.analysis.extraPaths": [

.github/workflows/pre-commit.yml

@@ -19,7 +19,7 @@ jobs:
         python-version: '3.10'
     - uses: pre-commit/[email protected]
     - run: pip install -r requirements-dev.txt
-    - run: ruff check scripts/ sub-packages/
+    - run: ruff check scripts/ sub-packages/ docs/
     - run: tach check
     - uses: trufflesecurity/trufflehog@main
       with:

.secrets.baseline

@@ -90,6 +90,10 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -122,6 +126,16 @@
       "path": "detect_secrets.filters.heuristic.is_templated_secret"
     }
   ],
-  "results": {},
-  "generated_at": "2024-07-16T22:20:55Z"
+  "results": {
+    "docs/docs/developer-guide/jupyter-notebooks.ipynb": [
+      {
+        "type": "Base64 High Entropy String",
+        "filename": "docs/docs/developer-guide/jupyter-notebooks.ipynb",
+        "hashed_secret": "9a4fdd92fe53aa1f5be34f8faf864679dfd36481",
+        "is_verified": true,
+        "line_number": 83
+      }
+    ]
+  },
+  "generated_at": "2024-08-20T19:17:56Z"
 }

.vscode/settings.json

@@ -3,6 +3,7 @@
         "allclose",
         "bionemo",
         "dtype",
+        "NBVAL",
         "nemo",
         "pretraining",
         "rampup",

docs/Dockerfile

@@ -2,4 +2,5 @@ FROM squidfunk/mkdocs-material:latest
 
 # Install plugins.
 COPY docs/requirements.txt /tmp/
-RUN pip install -r /tmp/requirements.txt
+RUN apk add gcc python3-dev musl-dev linux-headers
+RUN pip install --disable-pip-version-check --no-cache-dir -r /tmp/requirements.txt

docs/mkdocs.yml

@@ -51,6 +51,7 @@ plugins:
         python:
           paths:
             - ../sub-packages/*/src
+  - mkdocs-jupyter
 
 markdown_extensions:
   - pymdownx.snippets:

docs/requirements.txt

@@ -3,3 +3,4 @@ mkdocs-minify-plugin
 mkdocstrings[python]
 mkdocs-gen-files
 pymdown-extensions
+mkdocs-jupyter

requirements-test.txt

@@ -5,3 +5,4 @@ testbook==0.4.2
 requests_mock==1.11.0
 # For SwiftStack access
 awscli==1.33.33
+nbval==0.11.0