Merge pull request #195 from rstudio/custom-docs

Author: isabelizimm

.github/workflows/docs.yml

@@ -23,6 +23,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[docs]
+          python -m pip install griffe==0.32.3
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
       - name: build docs

docs/_quarto.yml

@@ -24,7 +24,7 @@ website:
         file: reference/index.qmd
       - text: "Advanced Usage"
         menu:
-          - custom_handler.md
+          - custom_elements.qmd
       - text: "Changelog"
         file: changelog.md
       - text: "Learn more"

docs/custom_code.qmd

@@ -0,0 +1,199 @@
+# Creating and deploying custom code
+
+In some cases, you may need to create and deploy custom code as part of your MLOps workflow using vetiver. This could be necessary when you need to:
+
+- deploy custom models in vetiver
+- deploy unsupported models in vetiver
+- include custom code in vetiver
+- deploy a vetiver model with a custom pipeline
+
+ You may also have custom code in a known framework, such as a column transformer for a scikit-learn model.
+
+In these cases, extra steps will be required to successfully create and deploy a `VetiverModel` object.
+
+# Making a custom model
+
+Vetiver supports basic [scikit-learn](https://scikit-learn.org/), [torch](https://pytorch.org/), [statsmodels](https://www.statsmodels.org/stable/index.html), [xgboost](https://xgboost.readthedocs.io/en/stable/), and [spacy](https://spacy.io/) models. If you need to alter the usage of these models, or deploy a different type of model, you will likely need to create a new model handler.
+
+To create a model handler, you should create a subclass of vetiver's `BaseHandler` class. This handler should include the following:
+
+- `model_type`:  A static method that declares the type of your model.
+- `handler_predict()`: A method that defines how predictions should be made for your model. This method is used at the /predict endpoint in the VetiverAPI.
+
+Here's an example of a handler for a model of `newmodeltype` type. Once you have defined your handler, you can initialize it with your model and pass it to the `VetiverModel` class.
+
+```python
+from vetiver.handlers.base import BaseHandler
+
+class CustomHandler(BaseHandler):
+    def __init__(self, model, prototype_data):
+        super().__init__(model, prototype_data)
+
+    model_type = staticmethod(lambda: newmodeltype)
+    pip_name = "scikit-learn" # package's installation name on pip
+
+    def handler_predict(self, input_data, check_prototype: bool):
+        """
+        Your code for making predictions using the custom model
+
+        Parameters
+        ----------
+        input_data:
+            Data POSTed to API endpoint
+        check_prototype: bool
+            Whether the prototype should be enforced
+        """
+        prediction = model.fancy_new_predict(input_data)
+
+        return prediction
+
+new_model = CustomHandler(model, prototype_data)
+
+VetiverModel(new_model, "custom_model")
+```
+
+If your model is a common type, please consider [submitting a pull request](https://github.com/rstudio/vetiver-python/pulls).
+
+To deploy custom code, you need to include the necessary source code in your deployment files. If your model or other elements can be imported from a Python package, you can include the relevant packages in a `requirements.txt` file for deployment. However, if you have custom source code in local files, you will need to include those files in the deployment process.
+
+# Deploying custom elements
+
+If your `VetiverModel` includes custom source code, you need to include that code in your deployment files to build an API in another location. The example below shows a user-created `FeatureSelector`, which is part of a scikit-learn pipeline.
+
+```{.python filename="model.py"}
+from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.tree import DecisionTreeClassifier
+from sklearn.pipeline import Pipeline
+
+# create custom data preprocessing
+class FeatureSelector(BaseEstimator, TransformerMixin):
+    def __init__(self, columns):
+        self.columns = columns
+
+    def fit(self, X, y=None):
+        return self
+
+    def transform(self, X, y=None):
+        return X[self.columns]
+
+# create model
+model = Pipeline(steps=[
+    ('feature_selector', FeatureSelector(features)),
+    ('decision_tree', DecisionTreeClassifier())
+])
+
+# create deployable model object
+from vetiver import VetiverModel, vetiver_pin_write
+
+v = VetiverModel(model, "selected_decision_tree", protoype_data = X)
+
+# pin model to some location, eg, Posit Connect
+import pins
+
+board = pins.board_connect(allow_pickle_read=True)
+vetiver_pin_write(board, v)
+```
+
+::: {.panel-tabset}
+## Docker
+
+To generate files needed to start a Docker container, you can use the command `vetiver.prepare_docker`.
+
+```{.python}
+vetiver.prepare_docker(board, "selected_decision_tree")
+```
+
+When you run this line, 3 files are generated: a Dockerfile, an `app.py` file, and a `vetiver_requirements.txt`. In the `app.py` file, you'll need to add an import statement that is formatted `from {name of file, excluding .py, that has custom element} import {name of custom element}`.
+
+```{.python filename="app.py"}
+from vetiver import VetiverModel
+import vetiver
+import pins
+from model import FeatureSelector # add this line to import your custom feature engineering
+
+
+b = pins.board_connect(allow_pickle_read=True)
+v = VetiverModel.from_pin(b, 'selected_decision_tree')
+
+vetiver_api = vetiver.VetiverAPI(v)
+api = vetiver_api.app
+```
+
+Add a line to your Dockerfile to copy your source file(s) into your Docker container. The format will be `COPY path/to/your/filename.py /vetiver/app/filename.py`, where the destination is always in the `/vetiver/app/` directory.
+
+```{.bash filename="Dockerfile"}
+# # Generated by the vetiver package; edit with care
+# start with python base image
+FROM python:3.10
+
+# create directory in container for vetiver files
+WORKDIR /vetiver
+
+# copy  and install requirements
+COPY vetiver_requirements.txt /vetiver/requirements.txt
+
+#
+RUN pip install --no-cache-dir --upgrade -r /vetiver/requirements.txt
+
+# copy app file
+COPY app.py /vetiver/app/app.py
+
+# ADD THIS LINE to copy model source code
+COPY model.py /vetiver/app/model.py
+
+# expose port
+EXPOSE 8080
+
+# run vetiver API
+CMD ["uvicorn", "app.app:api", "--host", "0.0.0.0", "--port", "8080"]
+```
+
+## Posit Connect
+
+To deploy custom code to Posit Connect, you'll first start with the command `vetiver.write_app`.
+
+```{.python}
+vetiver.write_app(board, 'selected_decision_tree')
+```
+
+This will generate an `app.py` file, where you'll need to add an import statement that is formatted `from {name of file, excluding .py, that has custom element} import {name of custom element}`.
+
+```{.python filename=="app.py"}
+from vetiver import VetiverModel
+import vetiver
+import pins
+from model import FeatureSelector # add this line to import your custom feature engineering
+
+
+b = pins.board_connect(allow_pickle_read=True)
+v = VetiverModel.from_pin(b, 'selected_decision_tree')
+
+vetiver_api = vetiver.VetiverAPI(v)
+api = vetiver_api.app
+```
+
+After editing the `app.py` file, you can deploy it to Posit Connect using the `rsconnect` package. Use the `rsconnect.api.actions.deploy_python_fastapi()` function to deploy the API, specifying the Connect server URL, API key, directory containing the `app.py` and `model.py` files, and the entry point of the API.
+
+```{.python}
+from rsconnect.api.actions import deploy_python_fastapi
+import rsconnect
+
+url = "example.connect.com" # your Posit Connect server url
+api_key = os.environ(CONNECT_API_KEY) # your Posit Connect API key
+
+connect_server = rsconnect.api.RSConnectServer(
+    url = url,
+    api_key = api_key
+)
+
+rsconnect.actions.deploy_python_fastapi(
+        connect_server = connect_server,
+        directory = "./", # path to the directory containing the app.py and model.py files
+        entry_point = "app:api" # the API is the app.py file, in a variable named api
+    )
+
+```
+
+:::
+
+Please note that the above steps are a general guide, and you may need to adapt them to your specific use case and deployment environment. If you have any questions, please consider [opening an issue](https://github.com/rstudio/vetiver-python/issues/new).

docs/custom_handler.md

@@ -46,12 +46,15 @@ class VetiverAPI:
 
     Notes
     -----
-    This generates an API with either 2 or 3 GET endpoints and 1 POST endpoint.
+    This generates an API with either 3 or 4 GET endpoints and 1 POST endpoint.
 
+    ```
     ├──/ping (GET)
     ├──/metadata (GET)
+    ├──/prototype (GET)
     ├──/pin-url (GET, if VetiverModel metadata `url` field is not None)
     └──/predict (POST)
+    ```
 
     Parameter `check_ptype` was changed to `check_prototype`. Handling of `check_ptype`
     will be removed in a future version.