Added test coverage generation to workflow

.clang-format

@@ -1,7 +1,9 @@
 ---
 Language: Cpp
 BasedOnStyle: LLVM
+IndentWidth: 4
 PointerAlignment: Left
 AlwaysBreakTemplateDeclarations: Yes
-#EmptyLineBeforeAccessModifier: Always
-AccessModifierOffset: -1
+AccessModifierOffset: -2
+IndentCaseLabels: true
+IncludeBlocks: Regroup

.github/workflows/checks.yml

@@ -0,0 +1,72 @@
+# Runs all required checks of any code being committed to the main branch
+name: code checks
+
+on:
+  pull_request:
+    branches: [master]
+  push:
+    branches: [master]
+  workflow_dispatch:
+
+jobs:
+  build-and-test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Boost (Linux)
+        if: runner.os == 'Linux'
+        run: sudo apt-get update && sudo apt-get install -yq libboost-all-dev
+
+      - name: Install Boost (macOS)
+        if: runner.os == 'macOS'
+        run: brew install boost
+
+      - name: Install code coverage tools
+        if: runner.os == 'Linux'
+        run: sudo pip install codecov && sudo apt-get install -y lcov
+
+      - name: Create build environment
+        run: mkdir build
+
+      - name: Create makefiles (Linux)
+        if: runner.os == 'Linux'
+        run: cmake -Bbuild -H.
+
+      - name: Create makefiles (masOS)
+        if: runner.os == 'macOs'
+        run: cmake -Bbuild -H. -DBOOST_ROOT=/usr/local/Cellar/boost
+
+      - name: Build
+        run: cmake --build build/ --target all --config
+
+      - name: Generate coverage report
+        if: runner.os == 'Linux'
+        run: lcov --directory src --capture --output-file coverage.info
+
+      - name: Run unit tests
+        run: cd build && ctest --verbose
+
+      - name: list
+        run: ls && cd src && ls && cd ../build && ls
+
+      - name: Upload coverage report
+        if: runner.os == 'Linux'
+        run: bash <(curl -s https://codecov.io/bash) -f coverage.info || echo "Codecov did not collect coverage reports"
+
+  linter:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: DoozyX/clang-format-lint-action@v0.11
+        with:
+          source: "src include"
+          extensions: "h,cpp"
+          clangFormatVersion: 11
+          exclude: test/*

.github/workflows/models.yml

@@ -0,0 +1,54 @@
+on:
+  pull_request:
+    branches: [model-integration]
+  workflow_dispatch:
+
+jobs:
+  train-models:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - name: Change to package dir
+        run: cd models
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          install.packages('sessioninfo')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}