Merge branch 'main' into add-manuscript

.github/actions/install-julia/action.yaml

@@ -0,0 +1,35 @@
+name: Install Julia
+description: Installs a user-specified version of Julia
+inputs:
+  version:
+    description: 'The version of Julia to install (e.g., 1.10.0)'
+    required: true
+    default: '1.10.0'
+runs:
+  using: composite
+  steps:
+    - name: Cache Julia binary
+      id: cache-julia
+      uses: actions/cache@v3
+      with:
+        path: ~/julia
+        key: julia-binary-${{ inputs.version }}
+        restore-keys: |
+          julia-binary-${{ inputs.version }}
+    - name: Install Julia
+      if: steps.cache-julia.outputs.cache-hit != 'true'
+      run: |
+        mkdir -p ~/julia
+        version=$(echo ${{ inputs.version }} | cut -d. -f1,2)
+        wget https://julialang-s3.julialang.org/bin/linux/x64/$version/julia-${{ inputs.version }}-linux-x86_64.tar.gz -O ~/julia/julia.tar.gz
+      shell: bash
+    - run: tar -xzf ~/julia/julia.tar.gz -C ~/julia --strip-components=1
+      shell: bash
+    - run: echo "$HOME/julia/bin" >> $GITHUB_PATH
+      shell: bash
+    - uses: actions/cache@v3
+      with:
+        path: |
+          ~/.julia
+          ~/.cache/julia
+        key: julia-${{ inputs.version }}-${{ hashFiles('**/*.toml') }}

.github/workflows/pre-commit.yaml

@@ -11,4 +11,8 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v3
+    - uses: ./.github/actions/install-julia
+      with:
+        version: '1.10.0'
+    - run: julia -e 'using Pkg; Pkg.add("JuliaFormatter")'
     - uses: ./.github/actions/pre-commit

.pre-commit-config.yaml

@@ -11,37 +11,6 @@ repos:
     -   id: mixed-line-ending
     -   id: trailing-whitespace
 #####
-# Python
--   repo: https://github.com/psf/black
-    rev: 23.10.0
-    hooks:
-    -   id: black
-        args: ['--line-length', '79']
--   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-    -   id: isort
-        args: ['--profile', 'black',
-               '--line-length', '79']
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.0
-  hooks:
-    - id: ruff
-#####
-# R
--   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9023
-    hooks:
-    -   id: style-files
-    -   id: lintr
-#####
-# Java
-- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.11.0
-  hooks:
-  - id: pretty-format-java
-    args: [--aosp,--autofix]
-#####
 # Julia
 # Due to lack of first-class Julia support, this needs Julia local install
 #  and JuliaFormatter.jl installed in the library
@@ -56,4 +25,4 @@ repos:
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
-        exclude: package.lock.json
+        exclude: EpiAware/Manifest.toml

EpiAware/src/epimodel.jl

@@ -9,7 +9,7 @@ The `EpiModel` struct represents a basic renewal model.
 # Fields
 - `gen_int::Vector{T}`: Discrete generation distribution.
 - `delay_int::Vector{T}`: Discrete delay distribution.
-- `delay_kernel::SparseMatrixCSC{T,Integer}`: Sparse matrix representing the action of convoluting 
+- `delay_kernel::SparseMatrixCSC{T,Integer}`: Sparse matrix representing the action of convoluting
     a series of infections with observation delay.
 - `cluster_coeff::T`: Cluster coefficient for negative binomial distribution of observations.
 - `len_gen_int::Integer`: Length of `gen_int` vector.

EpiAware/src/utilities.jl

@@ -2,9 +2,9 @@
     scan(f, init, xs)
 
 Apply a function `f` to each element of `xs` along with an accumulator hidden state with intial
-value `init`. The function `f` takes the current accumulator value and the current element of `xs` as 
-arguments, and returns a new accumulator value and a result value. The function `scan` returns a tuple 
-`(ys, carry)`, where `ys` is an array containing the result values and `carry` is the final accumulator 
+value `init`. The function `f` takes the current accumulator value and the current element of `xs` as
+arguments, and returns a new accumulator value and a result value. The function `scan` returns a tuple
+`(ys, carry)`, where `ys` is an array containing the result values and `carry` is the final accumulator
 value. This is similar to the JAX function `jax.lax.scan`.
 
 # Arguments
@@ -58,7 +58,7 @@ end
 """
     growth_rate_to_reproductive_ratio(r, w)
 
-Compute the reproductive ratio given exponential growth rate `r` 
+Compute the reproductive ratio given exponential growth rate `r`
     and discretized generation interval `w`.
 
 # Arguments

EpiAware/test/prior_predictive_checking/README.md

@@ -1 +1 @@
-# Folder for prior predictive checking
+# Folder for prior predictive checking

EpiAware/test/prior_predictive_checking/ppc-latent-processes.jl

@@ -19,7 +19,7 @@ prior_chn = sample(model, Prior(), n_samples)
 sampled_walks = prior_chn |> chn -> mapreduce(hcat, generated_quantities(model, chn)) do gen
     gen[1]
 end
-## From law of total variance and known mean of HalfNormal distribution    
+## From law of total variance and known mean of HalfNormal distribution
 theoretical_std =
     [
         t * latent_process_priors.var_RW_dist.untruncated.σ * sqrt(2) / sqrt(π) for t = 1:n