Initial addition of GitHub actions

.github/workflows/build-test-coverage.yml

@@ -0,0 +1,59 @@
+name: Test
+
+on:
+  push:
+    branches: [main, master]
+    tags: ["*"]
+  pull_request:
+
+jobs:
+  Test:
+    name: Julia (v${{ matrix.version }}) on ${{ matrix.os }}-${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        ### NOTE: Scope
+        ###   - for testing and early development, focusing on just latest 
+        ###     version testing against linux
+
+        version:
+          - 1 # automatically expands to the latest stable 1.x release of Julia
+          # - 1.0
+          # - nightly
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+          # - x86
+        # include:
+        #   # test macOS and Windows with latest Julia only
+        #   - os: macOS-latest
+        #     arch: x64
+        #     version: 1
+        #   - os: windows-latest
+        #     arch: x64
+        #     version: 1
+        #   - os: windows-latest
+        #     arch: x86
+        #     version: 1
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+
+      - uses: julia-actions/cache@v1
+
+      - uses: julia-actions/julia-buildpkg@v1
+
+      - uses: julia-actions/julia-runtest@v1
+
+      - uses: julia-actions/julia-processcoverage@v1
+
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/docs.yml

@@ -0,0 +1,20 @@
+name: Documenter
+
+on:
+  push:
+    branches: [main, master]
+    tags: [v*]
+  pull_request:
+
+jobs:
+  Documenter:
+    permissions:
+      contents: write
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Project.toml

@@ -11,7 +11,5 @@ ExpectationMaximization = "e1fe09cc-5134-44c2-a941-50f4cd97986a"
 FreqTables = "da1fdf0e-e0ff-5433-a45f-9bb5ff651cb1"
 Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"

docs/.gitignore

@@ -0,0 +1,8 @@
+*.jl.cov
+*.jl.*.cov
+*.jl.mem
+docs/build/
+docs/site/
+Manifest.toml
+.DS_Store
+.vscode

docs/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -0,0 +1,15 @@
+using Documenter
+using SafetySignalDetection
+
+makedocs(
+    sitename = "SafetySignalDetection",
+    format = Documenter.HTML(),
+    modules = [SafetySignalDetection]
+)
+
+# Documenter can also automatically deploy documentation to gh-pages.
+# See "Hosting Documentation" and deploydocs() in the Documenter manual
+# for more information.
+deploydocs(
+    repo = "https://github.com/openpharma/SafetySignalDetection.jl.git"
+)

docs/src/index.md

@@ -0,0 +1,7 @@
+# SafetySignalDetection.jl
+
+Documentation for SafetySignalDetection.jl
+
+```@autodocs
+Modules = [SafetySignalDetection]
+```

src/meta_analytic.jl

@@ -1,7 +1,16 @@
 """
-    Meta Analytic Prior Model
+
+Meta Analytic Prior Model
 
 This Turing model is used to generate posterior samples of the parameters `a` and `b`.
+
+    meta_analytic(
+    y::Vector{Bool}, 
+    time::Vector{Float64}, 
+    trialindex::Vector{Int64}, 
+    prior_a::Distribution, 
+    prior_b::Distribution)
+
 """
 @model function meta_analytic(
     y::Vector{Bool}, 

test/Project.toml

@@ -0,0 +1,7 @@
+[deps]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"