v0.1.0

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 arviz plot for posterior predictive by @sbidari in #234
• sample multiple chain sequentially to avoid warning by @sbidari in #257
• Move tutorials in modeldocs to docssourcetutorials by @gvegayon in #233
• Cleanup after move tutorials in modeldocs to docssourcetutorials by @damonbayer in #258
• add ipywidgets as dependency to remove warning by @sbidari in #260
• Forecasting Interface by @damonbayer in #241
• Format Quarto docs in pre-commit by @damonbayer in #265
• Renaming The Infections Seeding Initialization by @AFg6K7h4fhy2 in #261
• Add __call__ As Alias For RandomVariable sample Method by @AFg6K7h4fhy2 in #253
• Fix mislabeled tutorial plots by @dylanhmorris in #269
• Avoid None encountered in jnp array warning by @sbidari in #270
• fix image rendering in basic renewal model tutorial by @sbidari in #272
• Make concentration in NegativeBinomialObservation a RandomVariable by @damonbayer in #267
• Updating instructions on dev docs and moving Make targets by @gvegayon in #264
• Update negativebinomial.py by @dylanhmorris in #277
• change Model.run so parameters always get passed by @dylanhmorris in #279
• Parallel MCMC in tutorials by @damonbayer in #278
• Streamline and bug fix hospital admissions model tutorial by @dylanhmorris in #281
• 188 random walk refactor by @dylanhmorris in #275
• Remove weekday From Hospital Admissions Tutorial by @AFg6K7h4fhy2 in #295
• remove pyrenew_demo from tutorials by @sbidari in #296
• Make MyRt in hospital_admissions_model.qmd more flexible by @damonbayer in #293
• improve x-axis label by @sbidari in #299
• Additional seed To init Changes by @AFg6K7h4fhy2 in #303
• Use Transformed Overdispersion parameter in hospital_admissions_model.qmd by @damonbayer in #302
• Change Naming Of n_timepoints_to_simulate by @AFg6K7h4fhy2 in #305
• remove default name arg by @sbidari in #306
• Maintain Consistent rng_key Valuing by @AFg6K7h4fhy2 in #317
• Remove Usage Of npro In Favor Of Just numpyro by @AFg6K7h4fhy2 in #316
• Bump polars version and merge all pyproject.tomls to single top level pyproject.toml by @damonbayer in #292
• Fixing Remaining Instances Of np.random.seed() For rng_seed by @AFg6K7h4fhy2 in #321
• change tense for "input" by @sbidari in #323
• Solve test_rtperiodicdiff.py Test Failures by @damonbayer in #327
• add note about setting device count by @sbidari in #322
• Change Order Of The name Argument To Match Numpyro by @AFg6K7h4fhy2 in #324
• fix code links formatting in tutorials by @damonbayer in #330
• Rename Deterministic vars Attribute To value by @AFg6K7h4fhy2 in #331
• Implements SampledValue by @gvegayon in #262
• Add matplotlib as a core dependency in pyproject.toml by @dylanhmorris in #336
• Rename random variables in rtperiodicdiff by @damonbayer in #339
• Fix some docstrings and add validation testing for deterministic.py by @dylanhmorris in #342
• Fix name in rtperiodicdiff.py by @damonbayer in #343
• add dependency check workflow by @sbidari in #346
• add test for assert sample and rtype by @sbidari in #341
• add a narrow dependency group for testing in CI by @sbidari in #348
• move ipywidgets to docs dependency group by @sbidari in #352
• add helper function for type error assertion by @sbidari in #351
• Replace ceil with integer division in rtperiodicdiff.py by @damonbayer in #360
• run website CI on all PRs, not just those targeting the default branch by @dylanhmorris in #363
• Fix placeholder rst hook bugs by @dylanhmorris in #365
• refactor website generation by @dylanhmorris in #367
• Refactoring the periodic broadcaster and added warn + error + test by @gvegayon in #349
• replace jax.random.PRNGKey with jax.random.key by @sbidari in #373
• create and use default rt across tests by @sbidari in #372
• Explicitly specify domain for AffineTransform in ScaledLogitTransform by @dylanhmorris in #378
• bump numpy and arviz by @damonbayer in #379
• 374 make predictor_values an argument in GLMPrediction by @sbidari in #375
• rename var in latent/hospitaladmissions.py by @sbidari in #383
• Remove deterministic save from infectionswithfeedback.py by @damonbayer in #371
• change default record to False in DeterministicVariable by @sbidari in #390
• Dynamic and static distributional rvs by @dylanhmorris in #391
• Ensure float in scaled logit constraint by @dylanhmorris in #395
• Moving model to top level by @gvegayon in #388
• remove pipeline folder by @damonbayer in #397
• record TrandformedVariable sample by @sbidari in #387
• Rename instances of Multisignal Renewal to PyRenew by @damonbayer in #399
• Day of the week tutorial by @gvegayon in #344
• Using TransformedRandomVariable by @gvegayon in #406
• Refactor differenced processes, random walks, and AR processes by @dylanhmorris in #380
• Elevate contents of src to root directory by @damonbayer in #409

New Contributors

• @natemcintosh made their first contribution in #42
• @SamuelBrand1 made their first contribution in #44
• @dependabot made their first contribution in #56
• @dylanhmorris made their first contribution in #62
• @cshelley made their first contribution in #77
• @AFg6K7h4fhy2 made their first contribution in #73
• @damonbayer made their first contribution in #82
• @brandomr made their first contribution in #203
• @sbidari made their first contribution in #211

Full Changelog: https://github.com/CDCgov/PyRenew/commits/v0.1.0