added CI/CD

Author: kosuri-indu

.github/workflows/CI-Nightly.yml

@@ -0,0 +1,76 @@
+name: Nightly Latest Deps
+
+on:
+  schedule:
+    - cron: '0 6 * * 1'
+  workflow_dispatch:
+
+jobs:
+
+  test-latest:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        workflow:
+          - patient_level_prediction
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+
+      - uses: julia-actions/cache@v2
+
+      - name: Instantiate and update
+        run: |
+          julia --project=src/workflows/${{ matrix.workflow }} -e '
+            using Pkg
+            Pkg.instantiate()
+            Pkg.update()
+          '
+
+      - name: Load packages
+        run: |
+          julia --project=src/workflows/${{ matrix.workflow }} -e '
+            using Pkg
+            for (_,pkg) in Pkg.dependencies()
+                pkg.is_direct_dep || continue
+                @eval using $(Symbol(pkg.name))
+                println(pkg.name)
+            end
+          '
+
+  notify-failure:
+    needs: test-latest
+    if: failure()
+    runs-on: ubuntu-latest
+
+    permissions:
+      issues: write
+
+    steps:
+      - uses: actions/github-script@v7
+        with:
+          script: |
+            const title = `Nightly CI failure ${new Date().toISOString().slice(0,10)}`
+            const body = `Nightly ecosystem integration test failed.\n\nRun: ${context.serverUrl}/${context.repo.owner}/${context.repo.repo}/actions/runs/${context.runId}`
+
+            const issues = await github.rest.issues.listForRepo({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              state: 'open'
+            })
+
+            if (!issues.data.some(i => i.title.includes('Nightly CI failure'))) {
+              await github.rest.issues.create({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                title,
+                body,
+                labels: ['ci-failure']
+              })
+            }

.github/workflows/CI.yml

@@ -0,0 +1,52 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  test:
+    name: Workflow Tests (${{ matrix.workflow }}, Julia ${{ matrix.julia-version }})
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: ['1.10', '1', 'pre']
+        workflow:
+          - patient_level_prediction
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: julia-actions/cache@v2
+
+      - name: Instantiate environment
+        run: |
+          julia --project=src/workflows/${{ matrix.workflow }} -e '
+            using Pkg
+            Pkg.instantiate()
+          '
+
+      - name: Load dependencies
+        run: |
+          julia --project=src/workflows/${{ matrix.workflow }} -e '
+            using Pkg
+            for (_,pkg) in Pkg.dependencies()
+                pkg.is_direct_dep || continue
+                @eval using $(Symbol(pkg.name))
+                println(pkg.name)
+            end
+          '

.github/workflows/CompatHelper.yml

@@ -0,0 +1,28 @@
+name: CompatHelper
+
+on:
+  schedule:
+    - cron: '0 */6 * * *'
+  workflow_dispatch:
+
+jobs:
+
+  CompatHelper:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+
+      - name: Run CompatHelper
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: |
+          julia -e '
+            using Pkg
+            Pkg.add("CompatHelper")
+            using CompatHelper
+            CompatHelper.main()
+          '

src/workflows/patient_level_prediction/.gitignore

@@ -1,2 +1,3 @@
-# Julia artifacts
-Manifest.toml
+# Local runtime artifacts
+config.toml
+output/

src/workflows/patient_level_prediction/Project.toml

@@ -1,4 +1,4 @@
-name = "Patient Level Prediction"
+name = "PatientLevelPrediction"
 authors = ["kosuri-indu"]
 
 [deps]
@@ -11,7 +11,6 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DuckDB = "d2f5444f-75bc-4fdf-ac35-56f514c445e1"
 FunSQL = "cf6cc811-59f4-4a10-b258-a8547a8f6407"
 InvertedIndices = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
-JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 LibPQ = "194296ae-ab2e-5f79-8cd4-7183a0a5a0d1"
 MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 MLJDecisionTreeInterface = "c6f25543-311c-4c74-83dc-3ea6d1015661"
@@ -48,3 +47,9 @@ ROCAnalysis = "0.3.6"
 Tables = "1"
 XGBoost = "2.5.1"
 julia = "1.10"
+
+[extras]
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+
+[targets]
+dev = ["JuliaFormatter"]