Rename instances of Multisignal Renewal to PyRenew (#399)

* rename all instances of multisignal-epi-inference to PyRenew * one more change * add deptry config to pyrpoject.toml * remove args from deptry action
CDCgov · Aug 20, 2024 · f891cb7 · f891cb7
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diff --git a/.github/workflows/deptry.yml b/.github/workflows/deptry.yml
@@ -29,4 +29,4 @@ jobs:
 
       - name: run deptry
         run: |
-          poetry run deptry . --per-rule-ignores "DEP001=pyrenew,DEP001=pytest,DEP003=pytest,DEP001=test"
+          poetry run deptry .
diff --git a/Dockerfile b/Dockerfile
@@ -1,7 +1,7 @@
 FROM ubuntu:24.04
 
 LABEL org.opencontainers.image.description="Image of PyRenew python package"
-LABEL org.opencontainers.image.source="https://github.com/CDCgov/multisignal-epi-inference"
+LABEL org.opencontainers.image.source="https://github.com/CDCgov/PyRenew"
 LABEL org.opencontainers.image.authors="CDC's Center for Forecasting Analytics"
 LABEL org.opencontainers.image.license="Apache-2.0"
 

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 ⚠️ This is a work in progress ⚠️
 
-`pyrenew` is a flexible tool for simulation 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. To start, visit the tutorials section on the project's website [here](https://cdcgov.github.io/multisignal-epi-inference/tutorials/index.html).
+`pyrenew` is a flexible tool for simulation 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. To start, visit the tutorials section on the project's website [here](https://cdcgov.github.io/PyRenew/tutorials/index.html).
 
 The following diagram illustrates the composition of the `HospitalAdmissionsModel` class. Notably, all components are modular and can be replaced with custom implementations.
 
@@ -43,7 +43,7 @@ flowchart LR
 Install via pip with
 
 ```bash
-pip install git+https://github.com/CDCgov/multisignal-epi-inference@main
+pip install git+https://github.com/CDCgov/PyRenew@main
 ```
 
 ## Container image
@@ -56,8 +56,8 @@ docker pull ghcr.io/CDCgov/pyrenew:latest
 
 ## Resources
 
-* [The MSR Website](https://cdcgov.github.io/multisignal-epi-inference/tutorials/index.html) provides general documentation and tutorials on using MSR.
-* [The Model Equations Sheet](https://github.com/CDCgov/multisignal-epi-inference/blob/main/equations.md) describe the mathematics of the renewal processes and models MSR supports.
+* [The MSR Website](https://cdcgov.github.io/PyRenew/tutorials/index.html) provides general documentation and tutorials on using MSR.
+* [The Model Equations Sheet](https://github.com/CDCgov/PyRenew/blob/main/equations.md) describe the mathematics of the renewal processes and models MSR supports.
 * Additional reading on renewal processes in epidemiology
   * [_Semi-mechanistic Bayesian modelling of COVID-19 with renewal processes_](https://academic.oup.com/jrsssa/article-pdf/186/4/601/54770289/qnad030.pdf)
   * [_Unifying incidence and prevalence under a time-varying general branching process_](https://link.springer.com/content/pdf/10.1007/s00285-023-01958-w.pdf)

diff --git a/docs/README.md b/docs/README.md
@@ -1,3 +1,3 @@
 # Sphinx website source code
 
-The files under this folder contain the source code for the project's Sphinx website. The website is automatically built and published by GitHub Actions. The website is hosted at <https://cdcgov.github.io/multisignal-epi-inference/>.
+The files under this folder contain the source code for the project's Sphinx website. The website is automatically built and published by GitHub Actions. The website is hosted at <https://cdcgov.github.io/PyRenew/>.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -61,7 +61,7 @@
 
 html_theme = "sphinx_book_theme"
 html_theme_options = {
-    "repository_url": "https://github.com/CDCgov/multisignal-epi-inference",
+    "repository_url": "https://github.com/CDCgov/PyRenew",
     "use_edit_page_button": True,
     "use_issues_button": True,
     "use_repository_button": True,

diff --git a/docs/source/developer_documentation.rst b/docs/source/developer_documentation.rst
@@ -5,8 +5,8 @@ Developer Documentation
 Github Workflow
 ---------------
 
--  You should request reviews for pull requests from ``multisignal-epi-inference-devs``, unless you have a good reason to request reviews from a smaller group.
--  Reviews from all of ``multisignal-epi-inference-devs`` are  encouraged, but an approving review from a `codeowner <https://github.com/CDCgov/multisignal-epi-inference/blob/main/.github/CODEOWNERS>`_ (@dylanhmorris, @damonbayer, or @gvegayon) is required before a pull request can be merged to ``main``.
+-  You should request reviews for pull requests from ``PyRenew-devs``, unless you have a good reason to request reviews from a smaller group.
+-  Reviews from all of ``PyRenew-devs`` are  encouraged, but an approving review from a `codeowner <https://github.com/CDCgov/PyRenew/blob/main/.github/CODEOWNERS>`_ (@dylanhmorris, @damonbayer, or @gvegayon) is required before a pull request can be merged to ``main``.
 -  For CDC contributors, If your pull request has not received a review at the time of the next standup, use standup to find a reviewer.
 -  External contributors should expect to receive a review within a few days of creating a pull request.
 -  If you create a draft pull request, indicate what, if anything, about the current pull request should be reviewed.
@@ -67,7 +67,7 @@ This entry tells Sphinx to generate documentation for the ``HospitalAdmissions``
 New tutorials
 ~~~~~~~~~~~~~
 
-``PyRenew`` tutorials are `quarto documents <https://quarto.org>`__ located under `./docs/source/tutorials <https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials>`__. Tutorials are automatically rendered using GitHub actions (see the Workflow file `here <https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml>`__).
+``PyRenew`` tutorials are `quarto documents <https://quarto.org>`__ located under `./docs/source/tutorials <https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials>`__. Tutorials are automatically rendered using GitHub actions (see the Workflow file `here <https://github.com/CDCgov/PyRenew/actions/workflows/website.yaml>`__).
 
 To make the new tutorial available in the website, developers should follow these steps:
 
@@ -82,7 +82,7 @@ To make the new tutorial available in the website, developers should follow thes
           getting_started
           example_with_datasets
 
-3. Add an rst entry with the same basename as the ``quarto`` file in the ``./docs/source/tutorials`` directory. For instance, the `example_with_datasets.rst` file was added to the repository. This last step can be done running the bash script `./hook_scripts/pre-commit-rst-placeholder.sh <https://github.com/CDCgov/multisignal-epi-inference/blob/main/hook_scripts/pre-commit-rst-placeholder.sh>`__. Note the script should be executed by ``pre-commit``.
+3. Add an rst entry with the same basename as the ``quarto`` file in the ``./docs/source/tutorials`` directory. For instance, the `example_with_datasets.rst` file was added to the repository. This last step can be done running the bash script `./hook_scripts/pre-commit-rst-placeholder.sh <https://github.com/CDCgov/PyRenew/blob/main/hook_scripts/pre-commit-rst-placeholder.sh>`__. Note the script should be executed by ``pre-commit``.
 
 
 Adding new pages

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -2,8 +2,8 @@
 .. This `index.rst` file is only a placeholder. Do not edit this file. The final
 .. `index.rst` document is automatically generated via GitHub Actions using the
 .. root level `README.md` file:
-..   https://github.com/CDCgov/multisignal-epi-inference/tree/main/README.md
+..   https://github.com/CDCgov/PyRenew/tree/main/README.md
 ..
 .. Any changes made to this file will be discarted during the next build. The
 .. GitHub action building this is in:
-.. https://github.com/CDCgov/multisignal-epi-inference/tree/main/.github/workflows/website.yaml`
+.. https://github.com/CDCgov/PyRenew/tree/main/.github/workflows/website.yaml`
diff --git a/docs/source/tutorials/basic_renewal_model.rst b/docs/source/tutorials/basic_renewal_model.rst
@@ -2,4 +2,4 @@
 .. Please do not edit this file directly.
 .. This file is just a placeholder.
 .. For the source file, see:
-.. <https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials/basic_renewal_model.qmd>
+.. <https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials/basic_renewal_model.qmd>
diff --git a/docs/source/tutorials/extending_pyrenew.rst b/docs/source/tutorials/extending_pyrenew.rst
@@ -2,4 +2,4 @@
 .. Please do not edit this file directly.
 .. This file is just a placeholder.
 .. For the source file, see:
-.. <https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials/extending_pyrenew.qmd>
+.. <https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials/extending_pyrenew.qmd>
diff --git a/docs/source/tutorials/getting_started.qmd b/docs/source/tutorials/getting_started.qmd
@@ -26,7 +26,7 @@ poetry install
 To install `pyrenew` using pip, run the following command:
 
 ```bash
-pip install git+https://github.com/CDCgov/multisignal-epi-inference@main
+pip install git+https://github.com/CDCgov/PyRenew@main
 ```
 
 

diff --git a/docs/source/tutorials/getting_started.rst b/docs/source/tutorials/getting_started.rst
@@ -2,4 +2,4 @@
 .. Please do not edit this file directly.
 .. This file is just a placeholder.
 .. For the source file, see:
-.. <https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials/getting_started.qmd>
+.. <https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials/getting_started.qmd>
diff --git a/docs/source/tutorials/hospital_admissions_model.rst b/docs/source/tutorials/hospital_admissions_model.rst
@@ -2,4 +2,4 @@
 .. Please do not edit this file directly.
 .. This file is just a placeholder.
 .. For the source file, see:
-.. <https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials/hospital_admissions_model.qmd>
+.. <https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials/hospital_admissions_model.qmd>
diff --git a/docs/source/tutorials/index.rst b/docs/source/tutorials/index.rst
@@ -1,7 +1,7 @@
 Tutorials
 =========
 
-This section contains tutorials that demonstrate how to use the `pyrenew` package. The source code for the tutorials can be found in the project repository: https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials.
+This section contains tutorials that demonstrate how to use the `pyrenew` package. The source code for the tutorials can be found in the project repository: https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials.
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/source/tutorials/periodic_effects.rst b/docs/source/tutorials/periodic_effects.rst
@@ -2,4 +2,4 @@
 .. Please do not edit this file directly.
 .. This file is just a placeholder.
 .. For the source file, see:
-.. <https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials/periodic_effects.qmd>
+.. <https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials/periodic_effects.qmd>
diff --git a/docs/source/tutorials/time.rst b/docs/source/tutorials/time.rst
@@ -2,4 +2,4 @@
 .. Please do not edit this file directly.
 .. This file is just a placeholder.
 .. For the source file, see:
-.. <https://github.com/CDCgov/multisignal-epi-inference/tree/main/docs/source/tutorials/time.qmd>
+.. <https://github.com/CDCgov/PyRenew/tree/main/docs/source/tutorials/time.qmd>
diff --git a/hook_scripts/pre-commit-rst-placeholder.sh b/hook_scripts/pre-commit-rst-placeholder.sh
@@ -44,7 +44,7 @@ for qmd in ${TUTORIALS_DIR}/*.qmd; do
     echo ".. Please do not edit this file directly." >> $rst
     echo ".. This file is just a placeholder." >> $rst
     echo ".. For the source file, see:" >> $rst
-    echo ".. <https://github.com/CDCgov/multisignal-epi-inference/tree/main/${TUTORIALS_DIR}/${bname}.qmd>" >> $rst
+    echo ".. <https://github.com/CDCgov/PyRenew/tree/main/${TUTORIALS_DIR}/${bname}.qmd>" >> $rst
 
 done
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
-name = "multisignal-epi-inference"
+name = "PyRenew"
 version = "0.1.0"
-description = "The CFA Multisignal Renewal project contains Pyrenew, a Python package for multi-signal Bayesian renewal modeling with NumPyro."
+description = "PyRenew, a Python package for multi-signal Bayesian renewal modeling with JAX and NumPyro."
 authors = ["CFA"]
 license = "Apache 2.0"
 readme = "README.md"
@@ -46,6 +46,7 @@ ipywidgets = "^8.1.3"
 optional = true
 
 [tool.poetry.group.test.dependencies]
+pytest = "^8.3.2"
 pytest-cov = "^5.0.0"
 pytest-mpl = "^0.17.0"
 
@@ -72,8 +73,12 @@ exclude = [  # don't report on objects that match any of these regex
     '\.__call__$'
 ]
 
-
-
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.deptry]
+known_first_party = ["pyrenew", "test"]
+
+[tool.deptry.per_rule_ignores]
+DEP004 = ["pytest"]
-Original file line number
+Diff line change
@@ Expand Up / @@ -26,7 +26,7 @@ poetry install @@
     To install `pyrenew` using pip, run the following command:
     ```bash
-    pip install git+https://github.com/CDCgov/multisignal-epi-inference@main
+    pip install git+https://github.com/CDCgov/PyRenew@main
     ```
@@ Expand Down @@