Merge 1b15255 into 70d9a64

Author: swo

.github/actions/mkdocs-build/action.yaml

@@ -0,0 +1,14 @@
+name: mkdocs-build
+description: Build mkdocs
+runs:
+  using: composite
+  steps:
+    - run: pipx install poetry
+      shell: bash
+    - uses: actions/setup-python@v5
+      with:
+        python-version: 3.10.12
+    - run: poetry install --only mkdocs
+      shell: bash
+    - run: poetry run mkdocs build
+      shell: bash

.github/workflows/mkdocs.yaml

@@ -0,0 +1,47 @@
+name: mkdocs
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+env:
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/mkdocs-build
+
+  deploy:
+    if: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+
+    runs-on: ubuntu-latest
+    needs: build
+
+    permissions:
+      contents: read
+      id-token: write
+      pages: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/mkdocs-build
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          name: github-pages
+          path: site
+          retention-days: "3"
+      - name: deploy to gh pages
+        uses: actions/deploy-pages@v4
+        with:
+          artifact_name: github-pages
+          preview: false

.gitignore

@@ -113,9 +113,6 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 .pybuilder/
 target/
@@ -367,10 +364,6 @@ deps/downloads/
 deps/usr/
 deps/src/
 
-# Build artifacts for creating documentation generated by the Documenter package
-docs/build/
-docs/site/
-
 # File generated by Pkg, the package manager, based on a corresponding
 # Project.toml It records a fixed state of all packages used by the project. As
 # such, it should not be committed for packages, but should be committed for
@@ -382,3 +375,6 @@ docs/site/
 tmp/
 */logs/
 logs/
+
+# mkdocs local build
+site/

README.md

@@ -14,86 +14,39 @@ This project provides data tools and low friction access to versioned datasets w
 - Utilities for time-stamping and template loading
 - Data validation and quality checks
 - Custom workflows
-- Tooling for easy access to Socrata Open Data API (e.i., data.cdc.gov)
-  (copied and modified from [here](https://github.com/CDCgov/cfasodapy))
+- Tooling for easy access to Socrata Open Data API (e.i., data.cdc.gov) (copied and modified from [here](https://github.com/CDCgov/cfasodapy))
 
 ## Getting started
 
-To use this repository:
-
-1. Clone the repository
-2. Install dependencies (**requires: `poetry >= 2.0`**):
-   ```
-   poetry install
-   ```
-3. Example: run the COVID-19 vaccination trends ETL pipeline, with extraction, raw data schema validation (-v) and transformed data validation (-t).
-   ```
-   python -m cfa.dataops.etl.covid19vax_trends --extract -v -t
+1. Clone the repository and install dependencies with `poetry install` (**requires `poetry >= 2.0`**)
+2. Ensure your have access to the relevant resources (e.g., `az login --identity`)
+3. See which datasets are available:
+   ```python
+   import cfa.dataops
+   print(cfa.dataops.list_datasets())
    ```
-4. [Optional] installing developer dependencies:
+4. See which versions of a dataset are available:
+   ```python
+   print(cfa.dataops.datacat.scenarios.seroprevalence.load.get_versions())
    ```
-   poetry install --with dev
+5. Get a specific version of a dataset:
+   ```python
+   df = cfa.dataops.get_data(name="scenarios.seroprevalence", version="latest", output="polars")
+   df.glimpse()
    ```
 
-To add a new dataset:
-1. Create a new TOML configuration file in `cfa/dataops/datasets/{team_dir}/`
-2. Create a new ETL script in `cfa/dataops/etl/{team_dir}/`
-3. Add SQL transformation templates in `cfa/dataops/etl/transform_templates/{team_dir}/` (is using SQL for transforms). These are [Mako templates](https://www.makotemplates.org/)
-
-## Deep Dive Documentation
-
-- [Dataset Developer Guide](docs/dataset_developer.md)
-- [Dataset User Guide](docs/dataset_user.md)
-
-## Accessing Datasets
-
-When the ETL pipelines are run, the data sources (raw and/or transformed) are stored into Azure Blob Storage. There will be times when we want to access these datasets directly. The function `get_data()` found in `cfa.dataops.datasets.catalog` helps retrieve that data, compile into a single dataframe, and return that dataframe. The parameters for `get_data()` are as follows:
-- name: the name of the data source
-- version: either 'latest' or string containing the datetime of required version. Default is 'latest'.
-- type: either 'raw' or 'transformed'. Default is 'transformed'.
-- output: the type of dataframe to output, either 'pandas' or 'polars'. Default is 'pandas'.
-
-The available datasets can be found by running `list_datasets()`, which can be found in the `cfa.dataops.catalog` submodule.
-
-An example for getting the polars dataframes for the latest raw versions of the covid19vax_trends and seroprevalence datasets is below:
-```python
-from cfa.dataops import get_data
-vax_df = get_data("scenarios.covid19vax_trends", type = "transformed", output = "polars")
-sero_df = get_data("scenarios.seroprevalence", type = "transformed", output = "polars")
-```
-
-## Running Workflows
-
-This `cfa.dataops` repository contains a `workflows` module. The following workflows are currently available:
-- covid
-
-Workflows can be run in a python virtual environment terminal where `cfa.dataops` is installed with the following format:
-```bash
-python3 -m cfa.dataops.workflows.<name>.<module> --<args>
-```
-
-### Covid Workflow
-There are two modules to the covid workflow with the following optional command line arguments:
-- generate_data (this must be run before the next module)
-   - -p, --path: path to store generated data; default is covid/data. Not needed if -b flag is used.
-   - -b, --blob: whether to store generated data to Blob Storage (flag)
-- run:
-   - -c, --config: path to intialization config
-   - -b, --blob: whether to pull from and push prepped data to Blob Storage (flag)
-
-Ex:
-```bash
-python3 -m cfa.dataops.workflows.covid.generate_data -b
-python3 -m cfa.dataops.workflows.covid.run -b
-```
+Read the [Dataset User Guide](docs/dataset_user.md) for more information about accessing datasets.
 
+Read the [Dataset Developer Guide](docs/dataset_developer.md) for information about how to run ETL to add new versions of an existing datasets and about how to create new datasets.
 
 ## Project admins
 
 - Thomas Hladish <utx5@cdc.gov> (CDC/OD/ORR/CFA)
 - Phillip Rogers <ap66@cdc.gov> (CDC/OD/ORR/CFA)(CTR)
 - Ryan Raasch <xng3@cdc.gov> (CDC/OD/ORR/CFA)(CTR)
 
+---
+
 ## Disclaimers
 
 ### General Disclaimer
@@ -102,54 +55,30 @@ This repository was created for use by CDC programs to collaborate on public hea
 
 ### Public Domain Standard Notice
 
-This repository constitutes a work of the United States Government and is not
-subject to domestic copyright protection under 17 USC § 105. This repository is in
-the public domain within the United States, and copyright and related rights in
-the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).
-All contributions to this repository will be released under the CC0 dedication. By
-submitting a pull request you are agreeing to comply with this waiver of
-copyright interest.
+This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/). All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
 
 ### License Standard Notice
 
 This repository is licensed under ASL v2 or later.
 
-This source code in this repository is free: you can redistribute it and/or modify it under
-the terms of the Apache Software License version 2, or (at your option) any
-later version.
+This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
 
-This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the Apache Software License for more details.
+This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.
 
-You should have received a copy of the Apache Software License along with this
-program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
+You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
 
 The source code forked from other open source projects will inherit its license.
 
 ### Privacy Standard Notice
 
-This repository contains only non-sensitive, publicly available data and
-information. All material and community participation is covered by the
-[Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
-and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
-For more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).
+This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the [Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md) and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md). For more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).
 
 ### Contributing Standard Notice
 
-Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)
-and submitting a pull request. (If you are new to GitHub, you might start with a
-[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing
-to this project, you grant a world-wide, royalty-free, perpetual, irrevocable,
-non-exclusive, transferable license to all users under the terms of the
-[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or
-later.
+Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo) and submitting a pull request. (If you are new to GitHub, you might start with a [basic tutorial](https://help.github.com/articles/set-up-git).) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the [Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or later.
 
-All comments, messages, pull requests, and other submissions received through
-CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).
+All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).
 
 ### Records Management Standard Notice
 
-This repository is not a source of government records but is a copy to increase
-collaboration and collaborative potential. All government records will be
-published through the [CDC web site](http://www.cdc.gov).
+This repository is not a source of government records but is a copy to increase collaboration and collaborative potential. All government records will be published through the [CDC web site](http://www.cdc.gov).

docs/api.md

@@ -0,0 +1,5 @@
+# API reference
+
+::: cfa.dataops.catalog.get_data
+
+::: cfa.dataops.catalog.list_datasets