Init setup

.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 +1,14 @@
-# reichlab-python-template
+# iddata
 
-[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.
+This is a Python module for accessing infectious disease data.
 
 
 ## 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/iddata.git
 ```
 
 ## Setup for local development
@@ -58,7 +31,7 @@ Developers will be using a Python virtual environment that:
 2. Change to the repo's root directory:
 
     ```bash
-    cd reichlab-python-template
+    cd iddata
     ```
 
 3. Make sure the correct version of Python is currently active, and create a Python virtual environment:
@@ -134,20 +107,3 @@ 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 = "iddata"
+description = "Python module for accessing infectious disease data"
 license = {text = "MIT License"}
 readme = "README.md"
 requires-python = ">=3.9"
@@ -11,27 +11,25 @@ classifiers = [
 dynamic = ["version"]
 
 dependencies = [
-    "structlog",
+    "numpy",
+    "pandas",
+    "pymmwr",
     "rich",
+    "s3fs",
     "toml"
 ]
 
 [project.optional-dependencies]
 dev = [
     "coverage",
-    "freezegun",
-    "mypy",
     "pre-commit",
     "pytest",
     "ruff",
     "types-toml",
 ]
 
 [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/iddata.git"
 
 [build-system]
 # Minimum requirements for the build system to execute.
@@ -44,11 +42,7 @@ 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 = ["iddata"]
 
 [tool.ruff]
 line-length = 120
@@ -61,4 +55,4 @@ inline-quotes = "double"
 quote-style = "double"
 
 [tool.setuptools.dynamic]
-version = {attr = "reichlab_python_template.__version__"}
+version = {attr = "iddata.__version__"}

requirements/requirements-dev.txt

@@ -1,65 +1,106 @@
-#
-# This file is autogenerated by pip-compile with Python 3.11
-# by the following command:
-#
-#    pip-compile --extra=dev --output-file=requirements/requirements-dev.txt
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml --extra dev -o requirements/requirements-dev.txt
+aiobotocore==2.15.2
+    # via s3fs
+aiohappyeyeballs==2.4.3
+    # via aiohttp
+aiohttp==3.10.10
+    # via
+    #   aiobotocore
+    #   s3fs
+aioitertools==0.12.0
+    # via aiobotocore
+aiosignal==1.3.1
+    # via aiohttp
+attrs==24.2.0
+    # via
+    #   aiohttp
+    #   pymmwr
+botocore==1.35.36
+    # via aiobotocore
 cfgv==3.4.0
     # via pre-commit
 coverage==7.5.1
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
 distlib==0.3.8
     # via virtualenv
 filelock==3.14.0
     # via virtualenv
-freezegun==1.5.0
-    # via python-app (pyproject.toml)
+frozenlist==1.5.0
+    # via
+    #   aiohttp
+    #   aiosignal
+fsspec==2024.10.0
+    # via s3fs
 identify==2.5.36
     # via pre-commit
+idna==3.10
+    # via yarl
 iniconfig==2.0.0
     # via pytest
+jmespath==1.0.1
+    # via botocore
 markdown-it-py==3.0.0
     # via rich
 mdurl==0.1.2
     # via markdown-it-py
-mypy==1.10.0
-    # via python-app (pyproject.toml)
-mypy-extensions==1.0.0
-    # via mypy
+multidict==6.1.0
+    # via
+    #   aiohttp
+    #   yarl
 nodeenv==1.8.0
     # via pre-commit
+numpy==2.1.3
+    # via
+    #   iddata (pyproject.toml)
+    #   pandas
 packaging==24.0
     # via pytest
+pandas==2.2.3
+    # via iddata (pyproject.toml)
 platformdirs==4.2.1
     # via virtualenv
 pluggy==1.5.0
     # via pytest
 pre-commit==3.7.0
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
+propcache==0.2.0
+    # via yarl
 pygments==2.18.0
     # via rich
+pymmwr==0.2.2
+    # via iddata (pyproject.toml)
 pytest==8.2.0
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
 python-dateutil==2.9.0.post0
-    # via freezegun
+    # via
+    #   botocore
+    #   pandas
+pytz==2024.2
+    # via pandas
 pyyaml==6.0.1
     # via pre-commit
 rich==13.7.1
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
 ruff==0.4.3
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
+s3fs==2024.10.0
+    # via iddata (pyproject.toml)
+setuptools==75.3.0
+    # via nodeenv
 six==1.16.0
     # via python-dateutil
-structlog==24.1.0
-    # via python-app (pyproject.toml)
 toml==0.10.2
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
 types-toml==0.10.8.20240310
-    # via python-app (pyproject.toml)
-typing-extensions==4.11.0
-    # via mypy
+    # via iddata (pyproject.toml)
+tzdata==2024.2
+    # via pandas
+urllib3==2.2.3
+    # via botocore
 virtualenv==20.26.1
     # via pre-commit
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools
+wrapt==1.16.0
+    # via aiobotocore
+yarl==1.17.1
+    # via aiohttp

requirements/requirements.txt

@@ -1,18 +1,72 @@
-#
-# This file is autogenerated by pip-compile with Python 3.11
-# by the following command:
-#
-#    pip-compile --output-file=requirements/requirements.txt
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -o requirements/requirements.txt
+aiobotocore==2.15.2
+    # via s3fs
+aiohappyeyeballs==2.4.3
+    # via aiohttp
+aiohttp==3.10.10
+    # via
+    #   aiobotocore
+    #   s3fs
+aioitertools==0.12.0
+    # via aiobotocore
+aiosignal==1.3.1
+    # via aiohttp
+attrs==24.2.0
+    # via
+    #   aiohttp
+    #   pymmwr
+botocore==1.35.36
+    # via aiobotocore
+frozenlist==1.5.0
+    # via
+    #   aiohttp
+    #   aiosignal
+fsspec==2024.10.0
+    # via s3fs
+idna==3.10
+    # via yarl
+jmespath==1.0.1
+    # via botocore
 markdown-it-py==3.0.0
     # via rich
 mdurl==0.1.2
     # via markdown-it-py
+multidict==6.1.0
+    # via
+    #   aiohttp
+    #   yarl
+numpy==2.1.3
+    # via
+    #   iddata (pyproject.toml)
+    #   pandas
+pandas==2.2.3
+    # via iddata (pyproject.toml)
+propcache==0.2.0
+    # via yarl
 pygments==2.18.0
     # via rich
+pymmwr==0.2.2
+    # via iddata (pyproject.toml)
+python-dateutil==2.9.0.post0
+    # via
+    #   botocore
+    #   pandas
+pytz==2024.2
+    # via pandas
 rich==13.7.1
-    # via python-app (pyproject.toml)
-structlog==24.1.0
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
+s3fs==2024.10.0
+    # via iddata (pyproject.toml)
+six==1.16.0
+    # via python-dateutil
 toml==0.10.2
-    # via python-app (pyproject.toml)
+    # via iddata (pyproject.toml)
+tzdata==2024.2
+    # via pandas
+urllib3==2.2.3
+    # via botocore
+wrapt==1.16.0
+    # via aiobotocore
+yarl==1.17.1
+    # via aiohttp