Merge pull request #1 from reichlab/init_setup

Initial setup, porting/adapting model code from flusion-experiments

.github/workflows/pythonapp-workflow.yml

@@ -16,9 +16,6 @@ jobs:
       - name: lint
         run: |
            ruff check .
-      - name: type check
-        run: |
-           mypy .
       - name: run tests
         run: |
            pytest

README.md

@@ -1,41 +1,16 @@
-# reichlab-python-template
+# idmodels
 
-[REPLACE WITH A DESCRIPTION OF YOUR PROJECT]
-
-A Python template for Reich Lab projects.
-
-This repo contains a Python package with minimal functionality. It serves as a starting point for new projects (it can be selected as the template when creating a new repo in the Reich Lab org).
-
-There as some opinionated choices here (explained below) which people should override as needed. The main goal is to have a consistent starting point to get up and running with a new Python code base.
-
-## Getting started
-
-[REMOVE THIS SECTION AFTER FOLLOWING THE INSTRUCTIONS BELOW]
-
-If you're using this repo as a template for a new project, make the following changes:
-
-1. Rename the `reichlab_python_template` directory (under `src`) to the name of your package (no hyphens!).
-
-2. Replace all instances of `reichlab-python-template` with the name of your repo/project.
-
-3. Replace all instances of `reichlab_python_template` with the name of your package (remember that Python module names cannot contain hyphens).
-
-4. Update [`pyproject.toml`](pyproject.toml). This file is required and will describe several aspects of your project. `pyproject.toml` replaces `setup.py` and is described in detail on [Python's packaging website](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/).
-
-5. Follow the _Setup for local development_ instructions below to ensure that everything works as expected.
+A Python module for modeling infectious disease.  Currently supports two classes of models:
 
+ - gradient boosting quantile regression (`gbqr`)
+ - seasonal autoregressive integrated models with exogenous covariates (`sarix`)
 
 ## Installing and running the package (no development)
 
 To install this package via pip:
 
 ```bash
-pip install git+[GITHUB LINK TO YOUR REPO]
-```
-
-To run it:
-```bash
-reichlab_python_template
+pip install git+https://github.com/reichlab/idmodels.git
 ```
 
 ## Setup for local development
@@ -58,7 +33,7 @@ Developers will be using a Python virtual environment that:
 2. Change to the repo's root directory:
 
     ```bash
-    cd reichlab-python-template
+    cd idmodels
     ```
 
 3. Make sure the correct version of Python is currently active, and create a Python virtual environment:
@@ -106,10 +81,6 @@ Prerequisites:
 The "lockfile" for this project is simply an annotated requirements.txt that is generated by [uv](https://github.com/astral-sh/uv) (uv is a replacement for [pip-compile](https://pypi.org/project/pip-tools/), which
 could also be used). There's also a requirements-dev.txt file that contains dependencies needed for development (_e.g._, pytest).
 
-While it's possible to use `pip freeze` to generate a detailed lockfile without a third-party tool like `uv`, the output of `pip freeze` doesn't distinguish between direct and indirect dependencies. This distinction probably doesn't matter for a small project, but on a large project, understanding the dependency graph is critical for resolving conflicts.
-
-Additionally, `uv` (and `pip-compile`) are able to use the list of high-level dependencies in `pyproject.toml` to generate a detailed requirements.txt file, which is a good workflow for keeping everything in sync.
-
 To add or remove a project dependency:
 
 1. Add or remove the dependency in the `[dependencies]` section of `pyproject.toml` (or in the `dev` section of `[project.optional-dependencies]`, if it's a development dependency). Don't pin a specific version, since that will make it harder for users to install the package.
@@ -134,20 +105,3 @@ To add or remove a project dependency:
     # a handy sync option that will cleanup unused dependencies
     uv pip sync requirements/requirements-dev.txt && python -m pip install -e .
     ```
-
-## Opinionated notes on Python tooling
-
-[REMOVE THIS SECTION]
-
-The Python ecosystem is overwhelming! Current opinionated preferences, subject to change:
-
-- To install and manage various versions of Python: [pyenv](https://github.com/pyenv/pyenv) + a local .python-version file
-- To install Python packages that are available from anywhere on the machine, regardless of which Python environment is activated: [pipx](https://pipx.pypa.io/stable/)
-- To create and manage Python virtual environments: [venv](https://docs.python.org/3/library/venv.html).
-    - It's handy having the environment packages right there in the project directory
-    - Most third-party tools for managing virtual environments (_e.g._, poetry, PDM, pipenv) do _too much_ and get in the way
-- To generate requirements files from `pyproject.toml`: ['uv'](https://github.com/astral-sh/uv?tab=readme-ov-file#getting-started). It's new, but it's orders of magnitude faster than `pip-compile`.
-- To install dependencies: uv again (again, mostly due to speed; good old pip is another fine option)
-- Logging: [structlog](https://www.structlog.org/en/stable/). Python's built-in logging module is tedious.
-- Linting and formatting: [ruff](https://github.com/astral-sh/ruff) because it does both and is fast.
-- Pre-commit hooks: [pre-commit](https://pre-commit.com/).

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
-name = "reichlab-python-template"
-description = "Python template for Reich Lab projects"
+name = "idmodels"
+description = "A Python module for modeling infectious disease."
 license = {text = "MIT License"}
 readme = "README.md"
 requires-python = ">=3.9"
@@ -11,27 +11,26 @@ classifiers = [
 dynamic = ["version"]
 
 dependencies = [
-    "structlog",
-    "rich",
-    "toml"
+    "iddata @ git+https://github.com/reichlab/iddata",
+    "lightgbm",
+    "numpy",
+    "pandas",
+    "sarix @ git+https://github.com/elray1/sarix",
+    "scikit-learn",
+    "tqdm",
+    "timeseriesutils @ git+https://github.com/reichlab/timeseriesutils"
 ]
 
 [project.optional-dependencies]
 dev = [
     "coverage",
-    "freezegun",
-    "mypy",
     "pre-commit",
     "pytest",
-    "ruff",
-    "types-toml",
+    "ruff"
 ]
 
 [project.urls]
-Repository = "https://github.com/reichlab/reichlab-python-template.git"
-
-[project.entry-points."console_scripts"]
-reichlab_python_template = "reichlab_python_template.app:main"
+Repository = "https://github.com/reichlab/idmodels.git"
 
 [build-system]
 # Minimum requirements for the build system to execute.
@@ -44,11 +43,7 @@ testpaths = [
 ]
 
 [tools.setuptools]
-packages = ["reichlab_python_template"]
-
-[tool.reichlab_python_template]
-# to write json-formatted logs to disk, uncomment the following line specify the file location
-# log_file = "/path/to/log/files/rechlab_python_template.log"
+packages = ["idmodels"]
 
 [tool.ruff]
 line-length = 120
@@ -61,4 +56,4 @@ inline-quotes = "double"
 quote-style = "double"
 
 [tool.setuptools.dynamic]
-version = {attr = "reichlab_python_template.__version__"}
+version = {attr = "idmodels.__version__"}