Merge branch 'main' into SamuelBrand1/issue7

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

@@ -0,0 +1,40 @@
+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-${{ inputs.version }}-linux-x86_64.tar.gz -O ~/julia/julia.tar.gz
+      shell: bash
+
+    - name: Unzip Julia
+      run: tar -xzf ~/julia/julia.tar.gz -C ~/julia --strip-components=1
+      shell: bash
+
+    - run: echo "$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

.github/workflows/test-EpiAware.yaml

@@ -0,0 +1,17 @@
+name: Test EpiAware
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  test-EpiAware:
+    runs-on: ubuntu-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()'

.pre-commit-config.yaml

@@ -11,49 +11,18 @@ 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
-# - repo: https://github.com/domluna/JuliaFormatter.jl
-#   rev: v1.0.39
-#   hooks:
-#   - id: julia-formatter
+#  and JuliaFormatter.jl installed in the library
+- repo: https://github.com/domluna/JuliaFormatter.jl
+  rev: v1.0.39
+  hooks:
+  - id: julia-formatter
 #####
 # Secrets
 -   repo: https://github.com/Yelp/detect-secrets
     rev: v1.4.0
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
-        exclude: package.lock.json
+        exclude: '.*/Manifest\.toml$'

EpiAware/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.0"
 manifest_format = "2.0"
-project_hash = "994dd97f3407acb923def45029b96a36ab4b1ffe"
+project_hash = "b4d488971893c2da3a7e5ee0a7a6da358a2c3ba6"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245"

EpiAware/Project.toml

@@ -5,7 +5,6 @@ version = "0.1.0-DEV"
 
 [deps]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
@@ -20,9 +19,3 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 
 [compat]
 julia = "1.9,1.10"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]

EpiAware/README.md

@@ -1 +1 @@
-# Readme for EpiAware
+# EpiAware