Convert Model In README To Notebook (#55)

* add notebook

* pre-commit action

* update pre-commit config

* minor edit to pyproject file

* small update to notebook

* update quarto notebook further

* verify notebook works; add docstrings to data

.github/workflows/pre-commit.yaml

@@ -19,4 +19,4 @@ jobs:
       run: pip install poetry
     - name: Install packages
       run: poetry install --with dev
-    - uses: ./.github/actions/pre-commit
+    - uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -13,6 +13,48 @@ repos:
     -   id: end-of-file-fixer
     -   id: mixed-line-ending
     -   id: trailing-whitespace
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    # prevent giant files from being committed.
+    -   id: check-added-large-files
+        args: ["--maxkb=10000"]
+    # simply check whether files parse as valid
+    # python
+    -   id: check-ast
+    # check for files with names that would
+    # conflict on a case-insensitive filesystem
+    # like MacOS HFS+ or Windows FAT.
+    -   id: check-case-conflict
+    # checks for a common error of placing
+    # code before the docstring.
+    -   id: check-docstring-first
+    # attempts to load all yaml files to
+    # verify syntax.
+    -   id: check-yaml
+        # allow yaml files which use the
+        # multi-document syntax
+        args: ["--allow-multiple-documents"]
+    # attempts to load all TOML files to
+    # verify syntax.
+    -   id: check-toml
+    # makes sure files end in a newline and
+    # only a newline.
+    -   id: end-of-file-fixer
+    # replaces or checks mixed line ending.
+    -   id: mixed-line-ending
+    # verifies that test files are named
+    # correctly.
+    -   id: name-tests-test
+        # ensure tests match test_.*\.py
+        args: ["--pytest-test-first"]
+    # trims trailing whitespace.
+    -   id: trailing-whitespace
+    # checks that non-binary executables have
+    # a proper shebang.
+    -   id: check-executables-have-shebangs
+        files: \.sh$
 ################################################################################
 # QUARTO README RENDERING
 ################################################################################
@@ -39,7 +81,7 @@ repos:
     -   id: isort
         args: ["--profile", "black", "--line-length", "79"]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.8.3
     hooks:
       - id: ruff
         args: ["--ignore=E741", "--ignore=E731", "--fix"]
@@ -54,15 +96,19 @@ repos:
 # SPELLING
 ################################################################################
 -   repo: https://github.com/crate-ci/typos
-    rev: v1.27.0
+    rev: typos-dict-v0.11.37
     hooks:
     -   id: typos
         args: ["--force-exclude"]
 ################################################################################
 # COMMIT MESSAGES
 ################################################################################
 -   repo: https://github.com/commitizen-tools/commitizen
-    rev: v3.30.0
+    rev: v4.1.0
     hooks:
     -   id: commitizen
+-   repo: https://github.com/jorisroovers/gitlint
+    rev:  v0.19.1
+    hooks:
+    -   id: gitlint
 ################################################################################

README.md

@@ -78,6 +78,8 @@ Install `forecasttools-py` via:
   Submission](https://github.com/CDCgov/forecasttools-py/blob/main/notebooks/flusight_from_idata.qmd)
 - [Community Meeting Utilities Demonstration
   (2024-11-19)](https://github.com/CDCgov/forecasttools-py/blob/main/notebooks/forecasttools_community_demo_2024-11-19.qmd)
+- [Creating InferenceData Objects and Using Forecasttools
+  Datasets](https://github.com/CDCgov/forecasttools-py/blob/main/notebooks/datasets_and_idata_creation.qmd)
 
 *Coming soon as webpages, once [Issue
 26](https://github.com/CDCgov/forecasttools-py/issues/26) is completed*.

README.qmd

@@ -78,6 +78,7 @@ pip3 install git+https://github.com/CDCgov/forecasttools-py@main
 
 * [Format Arviz Forecast Output For FluSight Submission](https://github.com/CDCgov/forecasttools-py/blob/main/notebooks/flusight_from_idata.qmd)
 * [Community Meeting Utilities Demonstration (2024-11-19)](https://github.com/CDCgov/forecasttools-py/blob/main/notebooks/forecasttools_community_demo_2024-11-19.qmd)
+* [Creating InferenceData Objects and Using Forecasttools Datasets](https://github.com/CDCgov/forecasttools-py/blob/main/notebooks/datasets_and_idata_creation.qmd)
 
 _Coming soon as webpages, once [Issue 26](https://github.com/CDCgov/forecasttools-py/issues/26) is completed_.
 

forecasttools/data.py

@@ -20,8 +20,15 @@ def check_url(url: str) -> bool:
     example FluSight submission and the
     US 2020 Census data.
 
-    url
+    Parameters
+    ----------
+    url : str
         The url to be checked.
+
+    Returns
+    -------
+    bool
+        Whether the URL is valid.
     """
     try:
         response = request.urlopen(url)
@@ -40,7 +47,9 @@ def check_file_save_path(
     """
     Checks whether a file path is valid.
 
-    file_save_path
+    Parameters
+    ----------
+    file_save_path : str
         The file path to be checked.
     """
     directory = os.path.dirname(file_save_path)
@@ -61,7 +70,9 @@ def make_census_dataset(
     saves the dataset as a csv in a given
     directory, if it does not already exist.
 
-    file_save_path
+    Parameters
+    ----------
+    file_save_path : str
         The path for where to save the output file.
     """
     # check that file and directory paths are valid
@@ -103,12 +114,14 @@ def make_nshn_fitting_dataset(
     NOT use the API endpoint, and instead expects
     a CSV.
 
-    dataset
+    Parameters
+    ----------
+    dataset : str
         Name of the dataset to create. Either
         "COVID" or "flu".
-    nhsn_dataset_path
+    nhsn_dataset_path : str
         Path to the NHSN dataset (csv file).
-    file_save_path
+    file_save_path : str
         The path for where to save the output file.
     """
     # check that dataset parameter is possible
@@ -178,7 +191,9 @@ def get_and_save_flusight_submission(
     """
     Saves an example FluSight submission as a csv.
 
-    file_save_path
+    Parameters
+    ----------
+    file_save_path : str
         The path for where to save the output file.
     """
     # check if the save file exists