Merge branch 'main' of github.com:unipept/unipept-index

.github/actions-rs/grcov.yml

@@ -0,0 +1,2 @@
+output-type: lcov
+output-file: ./lcov.info

.github/workflows/coverage.yml

@@ -0,0 +1,40 @@
+on: push
+
+name: Coverage
+
+jobs:
+  coverage:
+    name: Codecov
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install minimal nightly toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: nightly
+          override: true
+
+      - name: Run cargo test
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --all-features --no-fail-fast
+        env:
+          CARGO_INCREMENTAL: 0
+          RUSTFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+          RUSTDOCFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+
+      - name: Gather coverage information
+        id: coverage
+        uses: actions-rs/[email protected]
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ${{ steps.coverage.outputs.report }}
+          verbose: true
+          fail_ci_if_error: true

.github/workflows/lint.yml

@@ -0,0 +1,31 @@
+on: push
+
+name: Lint
+
+jobs:
+  lint:
+    name: Clippy + rustfmt
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install minimal nightly toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: nightly
+          components: rustfmt, clippy
+          override: true
+
+      - name: Run cargo fmt
+        uses: actions-rs/cargo@v1
+        with:
+          command: fmt
+          args: --all -- --check
+
+      - name: Run cargo clippy
+        uses: actions-rs/cargo@v1
+        with:
+          command: clippy
+          args: -- -D warnings

.github/workflows/test.yml

@@ -0,0 +1,28 @@
+on: push
+
+name: Test
+
+jobs:
+  test:
+    name: Check + test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install minimal nightly toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: nightly
+          override: true
+
+      - name: Run cargo check
+        uses: actions-rs/cargo@v1
+        with:
+          command: check
+
+      - name: Run cargo test
+        uses: actions-rs/cargo@v1
+        with:
+          command: test

fa-compression/src/decode.rs

@@ -26,7 +26,7 @@ static PREFIXES: [&str; 3] = ["EC:", "GO:", "IPR:IPR"];
 /// # Examples
 ///
 /// ```
-/// use fa_compression::decode::decode;
+/// use fa_compression::decode;
 ///
 /// let input = &[ 44, 44, 44, 189, 17, 26, 56, 173, 18, 116, 117, 225, 67, 116, 110, 17, 153, 39 ];
 /// let result = decode(input);

fa-compression/src/encode.rs

@@ -23,7 +23,7 @@ use crate::{
 /// # Examples
 ///
 /// ```
-/// use fa_compression::encode::encode;
+/// use fa_compression::encode;
 ///
 /// let input = "IPR:IPR016364;EC:1.1.1.-;GO:0009279";
 /// let encoded = encode(input);

fa-compression/src/lib.rs

@@ -223,4 +223,22 @@ mod tests {
             }
         }
     }
+
+    #[test]
+    #[should_panic]
+    fn test_encode_invalid() {
+        CharacterSet::encode(b'A');
+    }
+
+    #[test]
+    #[should_panic]
+    fn test_decode_invalid() {
+        CharacterSet::decode(15);
+    }
+
+    #[test]
+    #[should_panic]
+    fn test_decode_pair_invalid() {
+        CharacterSet::decode_pair(0b11111111);
+    }
 }