Added pipeline files for repo

Added three different pipeline files: Cargo clippy and fmt workflow Cargo check and test workflow And full on tests with coverage and upload to codecov.
acg-team · Nov 16, 2023 · c06b32d · c06b32d
1 parent 03b8c9f
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diff --git a/.github/workflows/clippy.yml b/.github/workflows/clippy.yml
@@ -0,0 +1,65 @@
+name: rustfmt and clippy with annotations
+
+on:
+  push:
+    branches:    
+      - "**"
+  workflow_dispatch:
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  fmt_lib:
+    name: rustfmt on parsimony lib
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - run: rustup component add rustfmt
+      - uses: actions-rs/cargo@v1
+        with:
+          command: fmt
+          args: --manifest-path ./parsimony/Cargo.toml --all -- --check
+
+  clippy_check_lib:
+    name: clippy on parsimony lib
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: rustup component add clippy
+      - uses: actions-rs/clippy-check@v1.0.7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          args: --manifest-path ./parsimony/Cargo.toml --all-features -- -D warnings
+
+  fmt_bin:
+    name: rustfmt on indelMaP bin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - run: rustup component add rustfmt
+      - uses: actions-rs/cargo@v1
+        with:
+          command: fmt
+          args: --manifest-path ./indelMaP/Cargo.toml --all -- --check
+
+  clippy_check_bin:
+    name: clippy on indelMaP bin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: rustup component add clippy
+      - uses: actions-rs/clippy-check@v1.0.7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          args: --manifest-path ./indelMaP/Cargo.toml --all-features -- -D warnings
diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
@@ -0,0 +1,40 @@
+name: library tests with coverage
+
+on:
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  test:
+    name: tests with coverage
+    runs-on: ubuntu-latest
+    env:
+      CARGO_INCREMENTAL: 0
+      RUSTFLAGS: -Cinstrument-coverage -Zprofile -Ccodegen-units=1 -Copt-level=0 -Clink-dead-code -Coverflow-checks=off -Zpanic_abort_tests -Cpanic=abort
+      RUSTDOCFLAGS: -Cinstrument-coverage -Zprofile -Ccodegen-units=1 -Copt-level=0 -Clink-dead-code -Coverflow-checks=off -Zpanic_abort_tests -Cpanic=abort
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions-rs/toolchain@v1.0.6
+      with:
+        toolchain: nightly
+        override: true
+    - name: Generate test results and coverage report
+      run: |
+          cargo install cargo2junit grcov;
+          rustup component add llvm-tools-preview;
+          cargo test --manifest-path ./parsimony/Cargo.toml -- -Z unstable-options --format json | cargo2junit > results.xml;
+          grcov . -s . --binary-path ./parsimony/target/debug/deps -t lcov --branch --ignore "**/*tests.rs" -o lcov.info;
+    - name: publish test results to github
+      uses: EnricoMi/publish-unit-test-result-action@v2
+      if: always()
+      with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          files: results.xml
+    - name: upload coverage report to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+          files: lcov.info
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -0,0 +1,85 @@
+name: tests on stable
+
+on:
+  push:
+    branches:    
+      - "**"
+  workflow_dispatch:
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  check_lib:
+    name: cargo check lib
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - uses: actions-rs/cargo@v1
+        with:
+          command: check
+          args: --manifest-path ./parsimony/Cargo.toml
+
+  test_lib:
+    name: cargo test lib
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions-rs/toolchain@v1.0.6
+      with:
+        toolchain: nightly
+        override: true
+    - name: install cargo2junit
+      run: |
+          cargo install cargo2junit
+    - name: tests with cargo2junit
+      run: |
+        cargo test --manifest-path ./parsimony/Cargo.toml -- -Z unstable-options --format json --report-time | cargo2junit > results.xml 
+    - name: Publish test results
+      uses: EnricoMi/publish-unit-test-result-action@v2
+      if: always()
+      with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          files: results.xml
+
+  check_bin:
+    name: cargo check bin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - uses: actions-rs/cargo@v1
+        with:
+          command: check
+          args: --manifest-path ./indelMaP/Cargo.toml
+
+  test_bin:
+    name: cargo test bin
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions-rs/toolchain@v1.0.6
+      with:
+        toolchain: nightly
+        override: true
+    - name: install cargo2junit
+      run: |
+          cargo install cargo2junit
+    - name: tests with cargo2junit
+      run: |
+        cargo test --manifest-path ./indelMaP/Cargo.toml -- -Z unstable-options --format json --report-time | cargo2junit > results.xml 
+    - name: Publish test results
+      uses: EnricoMi/publish-unit-test-result-action@v2
+      if: always()
+      with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          files: results.xml