diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 79fc54e5c..c413ef215 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-19T10:27:23","documenter_version":"1.4.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-21T12:00:49","documenter_version":"1.4.1"}} \ No newline at end of file diff --git a/dev/checklist/index.html b/dev/checklist/index.html index a16aa7eef..38b674568 100644 --- a/dev/checklist/index.html +++ b/dev/checklist/index.html @@ -20,4 +20,4 @@ Either of those should automatically publish a new version to the Julia registry. - Once registered, the `TagBot.yml` workflow should create a tag, and rebuild the documentation for this tag. - - These steps can take quite a bit of time (1 hour or more), so don't be surprised if the new documentation takes a while to appear. + - These steps can take quite a bit of time (1 hour or more), so don't be surprised if the new documentation takes a while to appear. diff --git a/dev/contributing/index.html b/dev/contributing/index.html index 4d8f86559..1280712c9 100644 --- a/dev/contributing/index.html +++ b/dev/contributing/index.html @@ -1,2 +1,2 @@ -Contributing · EpiAware.jl
GitHub

Contributing

This page details the some of the guidelines that should be followed when contributing to this package. It is adapted from Documenter.jl.

Branches

release-* branches are used for tagged minor versions of this package. This follows the same approach used in the main Julia repository, albeit on a much more modest scale.

Please open pull requests against the master branch rather than any of the release-* branches whenever possible.

Backports

Bug fixes are backported to the release-* branches using git cherry-pick -x by a EpiAware member and will become available in point releases of that particular minor version of the package.

Feel free to nominate commits that should be backported by opening an issue. Requests for new point releases to be tagged in METADATA.jl can also be made in the same way.

release-* branches

  • Each new minor version x.y.0 gets a branch called release-x.y (a protected branch).
  • New versions are usually tagged only from the release-x.y branches.
  • For patch releases, changes get backported to the release-x.y branch via a single PR with the standard name "Backports for x.y.z" and label "Type: Backport". The PR message links to all the PRs that are providing commits to the backport. The PR gets merged as a merge commit (i.e. not squashed).
  • The old release-* branches may be removed once they have outlived their usefulness.
  • Patch version milestones are used to keep track of which PRs get backported etc.

Style Guide

Follow the style of the surrounding text when making changes. When adding new features please try to stick to the following points whenever applicable. This project follows the SciML style guide.

Tests

Unit tests

As is conventional for Julia packages, unit tests are located at test/*.jl with the entrypoint test/runtests.jl.

End to end testing

Tests that build example package docs from source and inspect the results (end to end tests) are located in /test/examples. The main entry points are test/examples/make.jl for building and test/examples/test.jl for doing some basic checks on the generated outputs.

+Contributing · EpiAware.jl
GitHub

Contributing

This page details the some of the guidelines that should be followed when contributing to this package. It is adapted from Documenter.jl.

Branches

release-* branches are used for tagged minor versions of this package. This follows the same approach used in the main Julia repository, albeit on a much more modest scale.

Please open pull requests against the master branch rather than any of the release-* branches whenever possible.

Backports

Bug fixes are backported to the release-* branches using git cherry-pick -x by a EpiAware member and will become available in point releases of that particular minor version of the package.

Feel free to nominate commits that should be backported by opening an issue. Requests for new point releases to be tagged in METADATA.jl can also be made in the same way.

release-* branches

  • Each new minor version x.y.0 gets a branch called release-x.y (a protected branch).
  • New versions are usually tagged only from the release-x.y branches.
  • For patch releases, changes get backported to the release-x.y branch via a single PR with the standard name "Backports for x.y.z" and label "Type: Backport". The PR message links to all the PRs that are providing commits to the backport. The PR gets merged as a merge commit (i.e. not squashed).
  • The old release-* branches may be removed once they have outlived their usefulness.
  • Patch version milestones are used to keep track of which PRs get backported etc.

Style Guide

Follow the style of the surrounding text when making changes. When adding new features please try to stick to the following points whenever applicable. This project follows the SciML style guide.

Tests

Unit tests

As is conventional for Julia packages, unit tests are located at test/*.jl with the entrypoint test/runtests.jl.

End to end testing

Tests that build example package docs from source and inspect the results (end to end tests) are located in /test/examples. The main entry points are test/examples/make.jl for building and test/examples/test.jl for doing some basic checks on the generated outputs.

diff --git a/dev/examples/getting_started/index.html b/dev/examples/getting_started/index.html index 6472268b5..f449eac6e 100644 --- a/dev/examples/getting_started/index.html +++ b/dev/examples/getting_started/index.html @@ -234,4 +234,4 @@

- + diff --git a/dev/index.html b/dev/index.html index 2cc6f8ef7..1ed0517c7 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -EpiAware.jl: Real-time epidemic monitoring · EpiAware.jl
GitHub

EpiAware.jl

Infectious disease situational awareness modelling toolkit for Julia.

A package for building and fitting situational awareness models for infectious diseases. The package is designed to be flexible and extensible, and to provide a consistent interface for fitting and simulating models.

Package Features

  • Flexible: The package is designed to be flexible and extensible, and to provide a consistent interface for fitting and simulating models.
  • Modular: The package is designed to be modular, with a clear separation between the model and the data.
  • Extensible: The package is designed to be extensible, with a clear separation between the model and the data.
  • Consistent: The package is designed to provide a consistent interface for fitting and simulating models.
  • Efficient: The package is designed to be efficient, with a clear separation between the model and the data.

See the Index for the complete list of documented functions and types.

Manual Outline

    Library Outline

    Index

    +EpiAware.jl: Real-time epidemic monitoring · EpiAware.jl
    GitHub

    EpiAware.jl

    Infectious disease situational awareness modelling toolkit for Julia.

    A package for building and fitting situational awareness models for infectious diseases. The package is designed to be flexible and extensible, and to provide a consistent interface for fitting and simulating models.

    Package Features

    • Flexible: The package is designed to be flexible and extensible, and to provide a consistent interface for fitting and simulating models.
    • Modular: The package is designed to be modular, with a clear separation between the model and the data.
    • Extensible: The package is designed to be extensible, with a clear separation between the model and the data.
    • Consistent: The package is designed to provide a consistent interface for fitting and simulating models.
    • Efficient: The package is designed to be efficient, with a clear separation between the model and the data.

    See the Index for the complete list of documented functions and types.

    Manual Outline

      Library Outline

      Index

      diff --git a/dev/lib/internals/index.html b/dev/lib/internals/index.html index cdd6f5199..8d70c50ae 100644 --- a/dev/lib/internals/index.html +++ b/dev/lib/internals/index.html @@ -1,2 +1,2 @@ -Internals · EpiAware.jl
      GitHub
      +Internals · EpiAware.jl
      GitHub
      diff --git a/dev/lib/public/index.html b/dev/lib/public/index.html index 57b9bb50c..a391c0f24 100644 --- a/dev/lib/public/index.html +++ b/dev/lib/public/index.html @@ -1,2 +1,2 @@ -Public API · EpiAware.jl
      GitHub

      Public Documentation

      Documentation for EpiAware.jl's public interface.

      See the Internals section of the manual for internal package docs covering all submodules.

      Contents

      Index

      Public API

      EpiAware.EpiAware — Module
      module EpiAware

      EpiAware provides functionality for fitting epidemiological models to data. It is built on top of the Turing probabilistic programming language, and provides a set of utilities for constructing and fitting models to data.

      Core model structure

      An epidemiological model in EpiAware consists of composable structs with core abstract types. The core types are:

      1. AbstractModel: This overarching type is used to abstract Turing models and is inherited by the other abstract types we use.
      2. AbstractTuringEpiModel: Subtypes of this abstract type represent different models for the spread of an infectious disease. Each model type has a corresponding make_epi_aware function that constructs a Turing model for fitting the model to data. Implemented concrete subtypes:
        • Renewal: A renewal process model for the spread of an infectious disease.
        • ExpGrowthRate: An exponential growth rate model for the spread of an infectious disease.
        • DirectInfections: A model for the spread of an infectious disease based on modelling direct infections.
      3. AbstractLatentModel: Subtypes of this abstract type represent different latent processes that can be used in an epidemiological model. Implemented concrete subtype:
        • RandomWalk: A random walk latent process.
      4. AbstractObservationModel: Subtypes of this abstract type represent different observation models that can be used in an epidemiological model. Implemented concrete subtypes:
        • DelayObservation: An observation process that models the delay between the time of infection and the time of observation as a convolution, followed by a negative binomial distributed sample.
      source
      +Public API · EpiAware.jl
      GitHub

      Public Documentation

      Documentation for EpiAware.jl's public interface.

      See the Internals section of the manual for internal package docs covering all submodules.

      Contents

      Index

      Public API

      EpiAware.EpiAware — Module
      module EpiAware

      EpiAware provides functionality for fitting epidemiological models to data. It is built on top of the Turing probabilistic programming language, and provides a set of utilities for constructing and fitting models to data.

      Core model structure

      An epidemiological model in EpiAware consists of composable structs with core abstract types. The core types are:

      1. AbstractModel: This overarching type is used to abstract Turing models and is inherited by the other abstract types we use.
      2. AbstractTuringEpiModel: Subtypes of this abstract type represent different models for the spread of an infectious disease. Each model type has a corresponding make_epi_aware function that constructs a Turing model for fitting the model to data. Implemented concrete subtypes:
        • Renewal: A renewal process model for the spread of an infectious disease.
        • ExpGrowthRate: An exponential growth rate model for the spread of an infectious disease.
        • DirectInfections: A model for the spread of an infectious disease based on modelling direct infections.
      3. AbstractLatentModel: Subtypes of this abstract type represent different latent processes that can be used in an epidemiological model. Implemented concrete subtype:
        • RandomWalk: A random walk latent process.
      4. AbstractObservationModel: Subtypes of this abstract type represent different observation models that can be used in an epidemiological model. Implemented concrete subtypes:
        • DelayObservation: An observation process that models the delay between the time of infection and the time of observation as a convolution, followed by a negative binomial distributed sample.
      source
      diff --git a/dev/man/guide/index.html b/dev/man/guide/index.html index 76773e7e4..8090c5efe 100644 --- a/dev/man/guide/index.html +++ b/dev/man/guide/index.html @@ -1,2 +1,2 @@ -Guide · EpiAware.jl
      GitHub
      +Guide · EpiAware.jl
      GitHub
      diff --git a/dev/release-notes/index.html b/dev/release-notes/index.html index c65211637..6e012234c 100644 --- a/dev/release-notes/index.html +++ b/dev/release-notes/index.html @@ -1,2 +1,2 @@ -Release notes · EpiAware.jl
      GitHub
      +Release notes · EpiAware.jl
      GitHub