Merge pull request #62 from CDCgov/issue58

Issue 58: Add new GitHub Actions

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style="sciml"

.github/workflows/CompatHelper-EpiAware.yaml

@@ -0,0 +1,30 @@
+name: Compatibility Helper
+
+on:
+  schedule:
+    - cron: '00 * * * *'
+  issues:
+    types: [opened, reopened]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  compatibility:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: EpiAware
+          sparse-checkout-cone-mode: false
+      - name: Move EpiAware to root
+        run: mv EpiAware/* .
+      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/cache@v1
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/codecoverage-EpiAware.yaml

@@ -0,0 +1,34 @@
+name: Code coverage
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: EpiAware
+          sparse-checkout-cone-mode: false
+      - name: Move EpiAware to root
+        run: mv EpiAware/* .
+      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          annotate: true
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.github/workflows/pre-commit.yaml

@@ -11,8 +11,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v3
-    - uses: ./.github/actions/install-julia
-      with:
-        version: '1.10.0'
+    - uses: julia-actions/setup-julia@v1
+    - uses: julia-actions/cache@v1
     - run: julia -e 'using Pkg; Pkg.add("JuliaFormatter")'
     - uses: ./.github/actions/pre-commit

.github/workflows/test-EpiAware.yaml

@@ -1,17 +1,33 @@
 name: Test EpiAware
 
 on:
-  pull_request:
   push:
-    branches: [main]
+    branches:
+      - main
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  test-EpiAware:
-    runs-on: ubuntu-latest
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        julia-version: ['1']
+        os: [ubuntu-latest, windows-latest, macOS-latest]
     steps:
-    - uses: actions/checkout@v3
-    - uses: ./.github/actions/install-julia
-      with:
-        version: '1.10.0'
-    - name: Run unit tests for EpiAware
-      run: julia --project=EpiAware -e 'using Pkg; Pkg.test(coverage = true)'
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: EpiAware
+          sparse-checkout-cone-mode: false
+      - name: Move EpiAware to root
+        run: mv EpiAware/* .
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1

EpiAware/.JuliaFormatter.toml

@@ -0,0 +1 @@
+style="sciml"

EpiAware/README.md

@@ -1,5 +1,8 @@
 # EpiAware
 
+[![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
+[![Test EpiAware](https://github.com/CDCgov/Rt-without-renewal/actions/workflows/test-EpiAware.yaml/badge.svg)](https://github.com/CDCgov/Rt-without-renewal/actions/workflows/test-EpiAware.yaml)
+[![codecov](https://codecov.io/gh/CDCgov/Rt-without-renewal/graph/badge.svg?token=IX4GIA8F0H)](https://codecov.io/gh/CDCgov/Rt-without-renewal)
 
 ## Model Diagram
 

EpiAware/src/EpiAware.jl

@@ -20,16 +20,16 @@ This module provides functionality for calculating Rt (effective reproduction nu
 module EpiAware
 
 using Distributions,
-    Turing,
-    LogExpFunctions,
-    LinearAlgebra,
-    SparseArrays,
-    Random,
-    ReverseDiff,
-    Optim,
-    Parameters,
-    QuadGK,
-    DataFramesMeta
+      Turing,
+      LogExpFunctions,
+      LinearAlgebra,
+      SparseArrays,
+      Random,
+      ReverseDiff,
+      Optim,
+      Parameters,
+      QuadGK,
+      DataFramesMeta
 
 # Exported utilities
 export create_discrete_pmf, default_rw_priors, default_delay_obs_priors, spread_draws

EpiAware/src/epimodel.jl

@@ -1,9 +1,9 @@
 abstract type AbstractEpiModel end
 
-struct EpiData{T<:Real,F<:Function}
+struct EpiData{T <: Real, F <: Function}
     gen_int::Vector{T}
     delay_int::Vector{T}
-    delay_kernel::SparseMatrixCSC{T,Integer}
+    delay_kernel::SparseMatrixCSC{T, Integer}
     cluster_coeff::T
     len_gen_int::Integer
     len_delay_int::Integer
@@ -12,44 +12,43 @@ struct EpiData{T<:Real,F<:Function}
 
     #Inner constructors for EpiData object
     function EpiData(
-        gen_int,
-        delay_int,
-        cluster_coeff,
-        time_horizon::Integer,
-        transformation::Function,
+            gen_int,
+            delay_int,
+            cluster_coeff,
+            time_horizon::Integer,
+            transformation::Function
     )
         @assert all(gen_int .>= 0) "Generation interval must be non-negative"
         @assert all(delay_int .>= 0) "Delay interval must be non-negative"
-        @assert sum(gen_int) ≈ 1 "Generation interval must sum to 1"
-        @assert sum(delay_int) ≈ 1 "Delay interval must sum to 1"
+        @assert sum(gen_int)≈1 "Generation interval must sum to 1"
+        @assert sum(delay_int)≈1 "Delay interval must sum to 1"
 
         K = generate_observation_kernel(delay_int, time_horizon)
 
-        new{eltype(gen_int),typeof(transformation)}(
+        new{eltype(gen_int), typeof(transformation)}(
             gen_int,
             delay_int,
             K,
             cluster_coeff,
             length(gen_int),
             length(delay_int),
             time_horizon,
-            transformation,
+            transformation
         )
     end
 
     function EpiData(
-        gen_distribution::ContinuousDistribution,
-        delay_distribution::ContinuousDistribution,
-        cluster_coeff,
-        time_horizon::Integer;
-        D_gen,
-        D_delay,
-        Δd = 1.0,
-        transformation::Function = exp,
+            gen_distribution::ContinuousDistribution,
+            delay_distribution::ContinuousDistribution,
+            cluster_coeff,
+            time_horizon::Integer;
+            D_gen,
+            D_delay,
+            Δd = 1.0,
+            transformation::Function = exp
     )
-        gen_int =
-            create_discrete_pmf(gen_distribution, Δd = Δd, D = D_gen) |>
-            p -> p[2:end] ./ sum(p[2:end])
+        gen_int = create_discrete_pmf(gen_distribution, Δd = Δd, D = D_gen) |>
+                  p -> p[2:end] ./ sum(p[2:end])
         delay_int = create_discrete_pmf(delay_distribution, Δd = Δd, D = D_delay)
 
         return EpiData(gen_int, delay_int, cluster_coeff, time_horizon, transformation)
@@ -81,11 +80,11 @@ function (epimodel::Renewal)(_Rt, init)
     Rt = epimodel.data.transformation.(_Rt)
 
     r_approx = R_to_r(Rt[1], epimodel)
-    init = I₀ * [exp(-r_approx * t) for t = 0:(epimodel.data.len_gen_int-1)]
+    init = I₀ * [exp(-r_approx * t) for t in 0:(epimodel.data.len_gen_int - 1)]
 
     function generate_infs(recent_incidence, Rt)
         new_incidence = Rt * dot(recent_incidence, epimodel.data.gen_int)
-        [new_incidence; recent_incidence[1:(epimodel.data.len_gen_int-1)]], new_incidence
+        [new_incidence; recent_incidence[1:(epimodel.data.len_gen_int - 1)]], new_incidence
     end
 
     I_t, _ = scan(generate_infs, init, Rt)

EpiAware/src/latent-processes.jl

@@ -1,7 +1,7 @@
 function default_rw_priors()
     return (
         var_RW_dist = truncated(Normal(0.0, 0.05), 0.0, Inf),
-        init_rw_value_dist = Normal(),
+        init_rw_value_dist = Normal()
     )
 end
 
@@ -13,8 +13,8 @@ end
     rw = Vector{eltype(ϵ_t)}(undef, n)
 
     rw[1] = σ_RW * ϵ_t[1]
-    for t = 2:n
-        rw[t] = rw[t-1] + σ_RW * ϵ_t[t]
+    for t in 2:n
+        rw[t] = rw[t - 1] + σ_RW * ϵ_t[t]
     end
     return rw, init, (; σ_RW,)
 end

EpiAware/src/models.jl

@@ -1,15 +1,15 @@
 @model function make_epi_inference_model(
-    y_t,
-    epimodel::AbstractEpiModel,
-    latent_process,
-    observation_process;
-    process_priors,
-    pos_shift = 1e-6,
+        y_t,
+        epimodel::AbstractEpiModel,
+        latent_process,
+        observation_process;
+        process_priors,
+        pos_shift = 1e-6
 )
     #Latent process
     time_steps = epimodel.data.time_horizon
-    @submodel latent_process, init, latent_process_aux =
-        latent_process(time_steps; latent_process_priors = process_priors)
+    @submodel latent_process, init, latent_process_aux = latent_process(
+        time_steps; latent_process_priors = process_priors)
 
     #Transform into infections
     I_t = epimodel(latent_process, init)
@@ -20,14 +20,14 @@
         I_t,
         epimodel::AbstractEpiModel;
         observation_process_priors = process_priors,
-        pos_shift = pos_shift,
+        pos_shift = pos_shift
     )
 
     #Generate quantities
     return (;
         generated_y_t,
         I_t,
         latent_process,
-        process_aux = merge(latent_process_aux, generated_y_t_aux),
+        process_aux = merge(latent_process_aux, generated_y_t_aux)
     )
 end

EpiAware/src/observation-processes.jl

@@ -3,19 +3,18 @@ function default_delay_obs_priors()
 end
 
 @model function delay_observations(
-    y_t,
-    I_t,
-    epimodel::AbstractEpiModel;
-    observation_process_priors = default_delay_obs_priors(),
-    pos_shift = 1e-6,
+        y_t,
+        I_t,
+        epimodel::AbstractEpiModel;
+        observation_process_priors = default_delay_obs_priors(),
+        pos_shift = 1e-6
 )
     #Parameters
     neg_bin_cluster_factor ~ observation_process_priors.neg_bin_cluster_factor_prior
 
     #Predictive distribution
-    case_pred_dists =
-        (epimodel.data.delay_kernel * I_t) .+ pos_shift .|>
-        μ -> mean_cc_neg_bin(μ, neg_bin_cluster_factor)
+    case_pred_dists = (epimodel.data.delay_kernel * I_t) .+ pos_shift .|>
+                      μ -> mean_cc_neg_bin(μ, neg_bin_cluster_factor)
 
     #Likelihood
     y_t ~ arraydist(case_pred_dists)