Merge pull request #88 from vrbouza/master

Added link & reference to the sandbox.bio tutorial.

.github/workflows/codecov.yml

@@ -22,29 +22,25 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions-rs/toolchain@v1
       with:
-        toolchain: nightly
+        toolchain: stable
         override: true
     - name: Build
       run: cargo build --verbose
-    - name: Run tests
-      run: cargo test --verbose --no-fail-fast
+    - name: Install cargo-llvm-cov and run tests
+      run: cargo install cargo-llvm-cov && cargo llvm-cov --lcov --output-path=./lcov.info
       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: rust-grcov
-      # You may pin to the exact commit or the version.
-      # uses: actions-rs/grcov@bb47b1ed7883a1502fa6875d562727ace2511248
-      uses: actions-rs/[email protected]
-      with:
-        config: .github/config/grcov.yml
+        RUSTFLAGS: '-Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cinstrument-coverage'
+        RUSTDOCFLAGS: '-Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cinstrument-coverage'
     - name: Codecov
       # You may pin to the exact commit or the version.
       # uses: codecov/codecov-action@81cd2dc8148241f03f5839d295e000b8f761e378
-      uses: codecov/[email protected]
+      # uses: codecov/[email protected]
+      uses: codecov/[email protected]
       with:
         # Repository upload token - get it from codecov.io. Required only for private repositories
         token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./lcov.info
         # Specify whether the Codecov output should be verbose
         verbose: true
         fail_ci_if_error: true

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ska"
-version = "0.3.11"
+version = "0.3.12"
 authors = [
     "John Lees <[email protected]>",
     "Simon Harris <[email protected]>",

README.md

@@ -37,6 +37,7 @@ https://genome.cshlp.org/content/34/10/1661.abstract
 Can be found at https://docs.rs/ska. We also have some tutorials available:
 
 - [From genomes to trees](https://www.bacpop.org/guides/building_trees_with_ska/).
+- [From genomes to trees - Interactive tutorial in sandbox.bio](https://sandbox.bio/tutorials/ska2-intro).
 - [Filtering options](https://www.bacpop.org/guides/snp_alignment_with_ska/).
 
 ## Installation