-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'main' into gvegayon/documentation/58-ci-for-rendering-q…
…uarto-files
- Loading branch information
Showing
31 changed files
with
1,385 additions
and
395 deletions.
There are no files selected for viewing
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,46 @@ | ||
name: model | ||
|
||
on: | ||
pull_request: | ||
push: | ||
branches: [main] | ||
|
||
jobs: | ||
install-and-test: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v4 | ||
|
||
- uses: actions/setup-python@v5 | ||
with: | ||
python-version: "3.12" | ||
|
||
- name: cache poetry | ||
uses: actions/cache@v4 | ||
with: | ||
path: ~/.local | ||
key: ${{ runner.os }}-poetry | ||
- name: install poetry | ||
run: pip install poetry | ||
|
||
- name: install package | ||
run: poetry install -C model | ||
|
||
- name: install pytest-cov | ||
run: poetry run -C model pip install pytest-cov | ||
|
||
- name: run tests | ||
run: | | ||
poetry run -C model pytest \ | ||
--cov=pyrenew --cov-report term --cov-report xml model | ||
- name: Upload coverage to Codecov | ||
uses: codecov/codecov-action@v4 | ||
with: | ||
env_vars: OS,PYTHON | ||
fail_ci_if_error: true | ||
flags: unittests | ||
file: coverage.xml | ||
plugin: pycoverage | ||
token: ${{ secrets.CODECOV_TOKEN }} | ||
verbose: true |
2 changes: 1 addition & 1 deletion
2
.github/workflows/test_pipeline.yaml → .github/workflows/test_pipeline.yml
100755 → 100644
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,4 +1,4 @@ | ||
name: installation and testing pipeline | ||
name: pipeline | ||
|
||
on: | ||
pull_request: | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,12 +1,15 @@ | ||
# PyRenew | ||
# PyRenew: A Package for Bayesian Renewal Modeling with JAX and Numpyro. | ||
|
||
A package for Bayesian renewal modeling with JAX and Numpyro. | ||
`pyrenew` is a flexible tool for simulating and statistical inference of epidemiological models, emphasizing renewal models. Built on top of the [`numpyro`](https://num.pyro.ai/) Python library, `pyrenew` provides core components for model building, including pre-defined models for processing various types of observational processes. | ||
|
||
## Installation | ||
|
||
Install via pip with | ||
|
||
```bash | ||
pip install git+https://github.com/cdcent/cfa-pyrenew.git | ||
``` | ||
|
||
## Demo | ||
The `docs` folder contains a Jupyter notebook with an interactive demo to get you started. It simulates observed hospitalizations using a simple renewal process model and then fits to it using a No-U-Turn Sampler. | ||
|
||
The [`docs`](docs) folder contains quarto documents to get you started. It simulates observed hospitalizations using a simple renewal process model and then fits it using a No-U-Turn Sampler. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1 +1,2 @@ | ||
!*png | ||
*_files/libs |
Oops, something went wrong.