Merge branch 'master' into patch-3

rust-bio · May 19, 2024 · 4a51951 · 4a51951
2 parents 9cd847d + 56ee2bd
commit 4a51951
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diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
@@ -10,51 +10,32 @@ jobs:
     if: github.repository_owner == 'rust-bio'
     runs-on: ubuntu-latest
     steps:
-
       - uses: actions/checkout@v2
         with:
           submodules: recursive
 
-
-      - uses: GoogleCloudPlatform/release-please-action@v3
-        id: release_sys
-        with:
-          release-type: rust
-          package-name: hts-sys
-          monorepo-tags: true
-          path: hts-sys
-
       - uses: GoogleCloudPlatform/release-please-action@v3
         id: release_main
         with:
           release-type: rust
           package-name: rust-htslib
           bump-minor-pre-major: true
-          monorepo-tags: true
-          path: "."
 
       - name: Install stable toolchain
         uses: actions-rs/toolchain@v1
-        if: ${{ steps.release_main.outputs.release_created || steps.release_sys.outputs.release_created }}
+        if: ${{ steps.release_main.outputs.release_created }}
         with:
           toolchain: stable
           override: true
 
       - name: Install system dependencies
-        if: ${{ steps.release_main.outputs.release_created || steps.release_sys.outputs.release_created }}
+        if: ${{ steps.release_main.outputs.release_created }}
         run: |
-            sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
+          sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
       - uses: Swatinem/[email protected]
-        if: ${{ steps.release_main.outputs.release_created || steps.release_sys.outputs.release_created }}
-
-      - name: Publish hts-sys
-        if: ${{ steps.release_sys.outputs.release_created }}
-        uses: actions-rs/cargo@v1
-        with:
-          command: publish
-          args: --manifest-path hts-sys/Cargo.toml --token ${{ secrets.CRATES_IO_TOKEN }}
-
+        if: ${{ steps.release_main.outputs.release_created }}
+
       - name: Publish rust-htslib
         if: ${{ steps.release_main.outputs.release_created }}
         uses: actions-rs/cargo@v1

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
@@ -2,9 +2,9 @@ name: CI
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   Formatting:
@@ -19,10 +19,10 @@ jobs:
           toolchain: stable
           override: true
           components: rustfmt
-      
+
       - name: Check format
         run: cargo fmt -- --check
-     
+
   Linting:
     runs-on: ubuntu-latest
     steps:
@@ -52,29 +52,31 @@ jobs:
         with:
           submodules: recursive
 
-      - name: Install stable toolchain
+      - name: Install nightly toolchain
         uses: actions-rs/[email protected]
         with:
-          toolchain: stable
+          toolchain: nightly
           override: true
 
       - name: Install system dependencies
         run: |
-            sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
+          sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
       - uses: Swatinem/[email protected]
 
       - name: Run cargo-tarpaulin
         uses: actions-rs/[email protected]
         with:
-          args: '--all-features --out Lcov --exclude-files hts-sys/*_prebuilt_bindings.rs -- --test-threads 1'
+          # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
+          version: "0.22.0"
+          args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
 
       - name: Upload coverage
-        uses: coverallsapp/github-action@v1.1.1
+        uses: coverallsapp/github-action@v1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info
-  
+
   Testing-Features:
     needs: Formatting
     runs-on: ubuntu-latest
@@ -83,9 +85,6 @@ jobs:
         target:
           - no-default-features
           - all-features
-          - musl-release-no-default-features
-          - musl-release-all-features
-          - musl-all-features
         include:
           - target: no-default-features
             args: --no-default-features
@@ -94,19 +93,7 @@ jobs:
             args: --all-features
             toolchain_target: x86_64-unknown-linux-musl
             use_cross: false
-          - target: musl-release-no-default-features
-            args: --release --target x86_64-unknown-linux-musl --no-default-features
-            toolchain_target: x86_64-unknown-linux-musl
-            use_cross: true
-          - target: musl-release-all-features
-            args: --release --target x86_64-unknown-linux-musl --all-features --verbose
-            toolchain_target: x86_64-unknown-linux-musl
-            use_cross: true
-          - target: musl-all-features
-            args: --target x86_64-unknown-linux-musl --all-features --verbose
-            toolchain_target: x86_64-unknown-linux-musl
-            use_cross: true
-
+
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -121,7 +108,7 @@ jobs:
 
       - name: Install system dependencies
         run: |
-            sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
+          sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
       - uses: Swatinem/[email protected]
 
@@ -134,33 +121,32 @@ jobs:
 
   Testing-MacOS:
     needs: Formatting
-    runs-on: macOS-latest
+    runs-on: macos-latest
     strategy:
       matrix:
         target:
-          - intel-catalina
-          - intel-bigsur
-          - m1-bigsur
+          - intel-monterey
+          - intel-ventura
+          - silicon-sonoma
         include:
-          - target: intel-catalina
-            os: macOS-10.15
+          - target: intel-monterey
+            os: macOS-12.0
             toolchain_target: x86_64-apple-darwin
             toolchain: stable
-            aux_args: ""
-            default: false
-          - target: intel-bigsur
-            os: macOS-11.0
+            aux_args: --target x86_64-apple-darwin
+            default: true
+          - target: intel-ventura
+            os: macOS-13.0
             toolchain_target: x86_64-apple-darwin
             toolchain: stable
+            aux_args: --target x86_64-apple-darwin
+            default: true
+          - target: silicon-sonoma
+            os: macOS-14.0
+            toolchain_target: aarch64-apple-darwin
+            toolchain: stable
             aux_args: ""
             default: false
-          # TODO enable again and try to find out why this fails
-          # - target: m1-bigsur
-          #   os: macOS-11.0
-          #   toolchain_target: aarch64-apple-darwin
-          #   toolchain: nightly
-          #   aux_args: --target aarch64-apple-darwin
-          #   default: true
 
     steps:
       - name: Checkout repository
@@ -171,55 +157,49 @@ jobs:
       - name: Install stable toolchain
         uses: actions-rs/[email protected]
         with:
-          toolchain: stable
+          toolchain: ${{ matrix.toolchain }}
+          target: ${{ matrix.toolchain_target }}
           override: true
+          default: ${{ matrix.default }}
 
       - name: Install htslib dependencies
         run: brew install bzip2 zlib xz curl-openssl
 
-      #- uses: actions-rs/[email protected]
-      #  with:
-      #    toolchain: ${{ matrix.toolchain }}
-      #    target: ${{ matrix.toolchain_target }}
-      #    #override: true
-      #    default: ${{ matrix.default }}
-
       - name: Test
         uses: actions-rs/[email protected]
         with:
-          use-cross: false  # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
+          use-cross: false # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
           command: test
           args: --release --all-features --verbose ${{ matrix.aux_args }}
-
 #  Testing-OSX-MUSL-BigSur:
 #   needs: Formatting
 #   runs-on: macOS-11.0
 #   steps:
-      # Test MUSL builds on OSX
-      #
-      # - uses: actions-rs/[email protected]
-      #   with:
-      #     toolchain: stable
-      #     target: x86_64-unknown-linux-musl
-      #     override: true
-
-      # - name: Install OSX musl-cross
-      #   run: brew install FiloSottile/musl-cross/musl-cross
-
-      # # https://github.com/FiloSottile/homebrew-musl-cross/issues/16
-      # - name: Provide musl-gcc symlink for the right musl arch
-      #   run: ln -sf /usr/local/opt/musl-cross/libexec/bin/x86_64-linux-musl-gcc /usr/local/bin/musl-gcc
-
-      # - name: Test musl build without default features
-      #   uses: actions-rs/cargo@v1
-      #   with:
-      #     use-cross: false  # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
-      #     command: test
-      #     args: --release --target x86_64-unknown-linux-musl --no-default-features
-
-      # - name: Test musl build with all features and debug symbols (non --release) on OSX
-      #   uses: actions-rs/[email protected]
-      #   with:
-      #     use-cross: false
-      #     command: test
-      #     args: --target x86_64-unknown-linux-musl --all-features --verbose
+# Test MUSL builds on OSX
+#
+# - uses: actions-rs/[email protected]
+#   with:
+#     toolchain: stable
+#     target: x86_64-unknown-linux-musl
+#     override: true
+
+# - name: Install OSX musl-cross
+#   run: brew install FiloSottile/musl-cross/musl-cross
+
+# # https://github.com/FiloSottile/homebrew-musl-cross/issues/16
+# - name: Provide musl-gcc symlink for the right musl arch
+#   run: ln -sf /usr/local/opt/musl-cross/libexec/bin/x86_64-linux-musl-gcc /usr/local/bin/musl-gcc
+
+# - name: Test musl build without default features
+#   uses: actions-rs/cargo@v1
+#   with:
+#     use-cross: false  # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
+#     command: test
+#     args: --release --target x86_64-unknown-linux-musl --no-default-features
+
+# - name: Test musl build with all features and debug symbols (non --release) on OSX
+#   uses: actions-rs/[email protected]
+#   with:
+#     use-cross: false
+#     command: test
+#     args: --target x86_64-unknown-linux-musl --all-features --verbose
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "htslib"]
-	path = hts-sys/htslib
-	url = https://github.com/samtools/htslib.git