PyRenew v0.1.6

What's Changed

time helper functions for reporting data #600

New Contributors

• @star1327p made their first contribution in #512
• @cdc-mitzimorris made their first contribution in #566

Full Changelog: v0.1.4...v0.1.6

PyRenew v0.1.5

What's Changed (highlights)

• Add offset computation to compute_delay_ascertained_incidence by @dylanhmorris in #493
• Migrate from Poetry to UV by @damonbayer in #502
• Migrate documentation from Sphinx to MkDocs by @damonbayer in #579
• Remove type annotations from numpydoc docstring Parameters sections by @Copilot in #587
• Revise tutorials by @cdc-mitzimorris in #595
• Update CODEOWNERS by @dylanhmorris in #607

New Contributors

• @star1327p made their first contribution in #512
• @cdc-mitzimorris made their first contribution in #566

Full Changelog: v0.1.4...v0.1.5

Pyrenew v0.1.4

What's Changed

• Add weekly_to_daily functionality
• Breaking change: move time handling functions to their own module by @dylanhmorris in #483

Full Changelog: v.0.1.3...v0.1.4

Pyrenew 0.1.3

What's Changed

• Add stable age distribution initialization by @dylanhmorris in #482

Full Changelog: v0.1.2...v.0.1.3

v0.1.2

What's Changed

• add daily_to_weekly function by @sbidari in #478

Full Changelog: v0.1.1...v0.1.2

v0.1.1

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

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...