Releases · CDCgov/PyRenew

What's Changed

Clean up actions by @damonbayer in #411
Test convolve mode in hospitaladmissionspy by @sbidari in #398
create randomvariable module by @sbidari in #412
Fix README numpyro link formatting in RST version by @damonbayer in #416
Set find_heuristic_step_size Default To True by @AFg6K7h4fhy2 in #417
Use dev version of numpyro by @damonbayer in #421
Remove UTF-8 Encoding Headers by @AFg6K7h4fhy2 in #422
Remove redundant jnp.array in ar.py by @damonbayer in #424
Modify README With Instantiated Model Information by @AFg6K7h4fhy2 in #430
Reworks InitializeInfectionsExponentialGrowth to work with numpyro.plate by @damonbayer in #432
create a censored normal distribution by @sbidari in #428
Fix text in readme by @damonbayer in #436
Add default observation rate to compute_delay_ascertained_incidence by @damonbayer in #437
Remove duplicate test introduced in #437 by @damonbayer in #438
Remove SampledValue by @damonbayer in #441
Vectorize ARProcess() by @dylanhmorris in #439
multidimensional array convention by @sbidari in #445
update infectionswithfeedback process by @sbidari in #440
Document scan conventions in developer_documentation.rst by @dylanhmorris in #448
Remove gvegayon from CODEOWNERS by @gvegayon in #449
Vectorize differenced process by @dylanhmorris in #446
Require at least numpyro 0.15.3 by @damonbayer in #453
use init_to_sample as default init_strategy by @damonbayer in #454
231 write sphinx documentation using markdown via myst by @dylanhmorris in #457
Add and configure intersphinx by @dylanhmorris in #463
Remove black and isort in favor of ruff by @dylanhmorris in #467
Remove redundant tutorial build by @dylanhmorris in #469
Further Prune PostProcessing Code, Specifically plot_posterior And spread_draws by @AFg6K7h4fhy2 in #431
refactor infectionswithfeedback.py to allow shared infection feedback strength across sites by @sbidari in #470
Use ruff format for qmds by @damonbayer in #473
Adding the post-page-artifact job by @gvegayon in #456

Full Changelog: v0.1.0...v0.1.1

What's Changed

Re-implementation of the pyrenews basicrenewlmodel using the proposed modularization in #26
Missing pieces from #26 and closes #29 in #32
Added transform and test for scaled logit in #37
Renaming metaclasses to metaclass in #36
Create typos.yaml by @natemcintosh in #42
34 port notebooks under modeldocs to quarto in #35
Extra mathematical description of discrete delay distributions by @SamuelBrand1 in #44
Sphinx(it) deploy of doc by @gvegayon in #49
Porting changes from CDCent by @gvegayon in #51
Bump pillow from 10.2.0 to 10.3.0 in /model by @dependabot in #56
Do not attempt to deploy Sphinx site in PRs by @dylanhmorris in #62
Formally addresses implementing the observed hospitalizations module in #39
Adding code coverage workflow by @gvegayon in #64
Setup of quarto docs by @gvegayon in #59
change all ArrayLike imports to jax.typing.ArrayLike by @dylanhmorris in #66
Refactoring sample from dicts to named arguments + **kwargs by @gvegayon in #63
Minor issue in README.md (link to precommit workflow) by @gvegayon in #67
add code coverage CI to pipeline code by @natemcintosh in #71
Issue 47 - pyrenew_demo.qmd by @cshelley in #77
First Pass Documentation (docstrings) For Latent Folder by @AFg6K7h4fhy2 in #73
First Pass Documentation (docstrings) For Model Folder by @AFg6K7h4fhy2 in #74
First Pass Documentation (docstrings) For Observation Folder by @AFg6K7h4fhy2 in #76
Add .DS_Store to .gitignore by @damonbayer in #82
First Pass Documentation (docstrings) For Top Level Pyrenew Files by @AFg6K7h4fhy2 in #89
First Pass Documentation (docstrings) For Deterministic Folder by @AFg6K7h4fhy2 in #86
First Pass Documentation (docstrings) For Process Folder by @AFg6K7h4fhy2 in #87
~~Test~~ Demo using data from WW R package by @gvegayon in #55
Clean Model Documentation by @AFg6K7h4fhy2 in #94
47 thl2 first pass on documentation by @cshelley in #96
50 standardize language by @gvegayon in #90
Convert md tutorials to rst and copy them to the website by @gvegayon in #95
Removing files supposed to be removed! and fixing website by @gvegayon in #99
Bump tqdm from 4.66.2 to 4.66.3 in /model by @dependabot in #100
Bump tqdm from 4.66.2 to 4.66.3 in /docs by @dependabot in #101
Bump idna from 3.6 to 3.7 in /docs by @dependabot in #72
Bump jinja2 from 3.1.3 to 3.1.4 in /docs by @dependabot in #102
Bump jinja2 from 3.1.3 to 3.1.4 in /model by @dependabot in #103
Adding Null RVs by @gvegayon in #93
Changing the theme of sphinx by @gvegayon in #104
Add Validation Hooks For Docstrings (Numpydocs) And Spelling (Typos) by @AFg6K7h4fhy2 in #106
Removing prev deleted file and fixing pre-commit by @gvegayon in #109
Adding missing figures in demos. by @gvegayon in #110
Create a dockerfile for running the model code locally or in azure by @gvegayon in #107
Correct spacing in distutil.py by @damonbayer in #119
117 Improves website and README.md by @gvegayon in #118
Fix docstrings typo in admissionsmodel.py by @damonbayer in #125
Bump requests from 2.31.0 to 2.32.0 in /docs by @dependabot in #129
Bump requests from 2.31.0 to 2.32.2 in /model by @dependabot in #130
docstring wording tweak: change "inputted" to "passed" by @dylanhmorris in #136
Renaming sample_infections to compute_future_infections by @gvegayon in #137
New metaclass.DistributionalRV by @gvegayon in #138
Fix docstring typo in logistic_susceptibility_adjustment by @dylanhmorris in #141
Refactor transform module to wrap numpyro.distributions.transforms by @gvegayon in #140
Rt with infection feedback by @gvegayon in #123
Read columns with correct data types in datasets module by @damonbayer in #153
Record deterministic RandomVariables by default by @damonbayer in #148
Renaming datautils to arrayutils by @gvegayon in #154
Weekly Rt with autoregressive difference by @gvegayon in #131
Re-remove transform.py by @damonbayer in #160
Bump tornado from 6.4 to 6.4.1 in /model by @dependabot in #164
Rework Initial Infections and Support Exponential Growth Initializations by @damonbayer in #124
Remove poetry.lock from version control by @damonbayer in #173
Standardize documentation file names and modularize docs in makefile by @damonbayer in #172
Remove InfectionSeedingProcess_demo.py by @damonbayer in #175
Upx3 typos fix by @gvegayon in #121
Renaming variables throughout for clarity by @damonbayer in #179
restrict filelock version by @damonbayer in #182
Revert "restrict filelock version" by @damonbayer in #183
Removing defaults from RtRandomWalkProcess by @gvegayon in #184
Refactor convolve scanner factory functions by @dylanhmorris in #161
Fix offset in Hospital Admissions Model Figures and clean up code by @damonbayer in #186
Adding the periodic and ~~weekly~~ day of the week effects and refactoring by @gvegayon in #158
Rename data variables in models for clarity by @damonbayer in #195
Pseudo-Random Number Generation For None Input For JAX PRNGKey In Metaclass by @AFg6K7h4fhy2 in #192
Adding Repository Structure And Resources Sections To The README by @AFg6K7h4fhy2 in #197
Sync package versions and update numpyro by @damonbayer in #199
Fix dangling sentence in demo doc by @brandomr in #203
Clean up Rt infections renewal model by @damonbayer in #204
Remove unneeded abstractions in model code (2) by @damonbayer in #207
Renaming infections_mean_varname to infections_varname by @gvegayon in #205
201 add visualizations using arviz to tutorials by @sbidari in #211
Add diagnostics using arviz to tutorials by @sbidari in #219
Update tutorials formatting by @damonbayer in #220
Update CODEOWNERS file by @damonbayer in #222
Create methods for simulating from prior and computing predictive distributions by @damonbayer in #218
Add Developer Documentation (First Round) by @damonbayer in #224
Adding t_start and t_unit by @gvegayon in #217
Fix docstring for compute_infections_from_rt_with_feedback() by @dylanhmorris in #246
Update actions/upload-artifact version in website.yaml by @dylanhmorris in #247
Rename SeedInfectionsExponential For Clarity by @AFg6K7h4fhy2 in #251
Changing Model.sample To Model.model by @AFg6K7h4fhy2 in #248
Pyrenew tutorial review by @sbidari in #191
Add RST to makefile by @damonbayer in #250
add...