Merge pull request #5 from phac-nml/dev

Rustify

.cargo/config.toml

@@ -0,0 +1,24 @@
+# Add the contents of this file to `config.toml` to enable "fast build" configuration. Please read the notes below.
+
+# NOTE: For maximum performance, build using a nightly compiler
+# If you are using rust stable, remove the "-Zshare-generics=y" below.
+
+[target.x86_64-unknown-linux-gnu]
+linker = "clang"
+rustflags = ["-Clink-arg=-fuse-ld=lld"]
+
+# NOTE: you must install [Mach-O LLD Port](https://lld.llvm.org/MachO/index.html) on mac. you can easily do this by installing llvm which ilslsncludes lld with the "brew" package manager:
+# `brew install llvm`
+[target.x86_64-apple-darwin]
+rustflags = ["-C", "link-arg=-fuse-ld=/usr/local/opt/llvm/bin/ld64.lld"]
+
+[target.aarch64-apple-darwin]
+rustflags = ["-C", "link-arg=-fuse-ld=/opt/homebrew/opt/llvm/bin/ld64.lld"]
+
+[target.x86_64-pc-windows-msvc]
+linker = "rust-lld.exe"
+
+# Optional: Uncommenting the following improves compile times, but reduces the amount of debug info to 'line number tables only'
+# In most cases the gains are negligible, but if you are on macos and have slow compile times you should see significant gains.
+#[profile.dev]
+#debug = 1

.github/workflows/build.yaml

@@ -0,0 +1,58 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+  release:
+    types: [published]
+  workflow_call:
+
+jobs:
+
+  # ---------------------------------------------------------------------------
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        arch:
+          #- aarch64-apple-darwin
+          #- aarch64-unknown-linux-gnu
+          #- aarch64-unknown-linux-musl
+          #- x86_64-apple-darwin
+          #- x86_64-pc-windows-gnu
+          - x86_64-unknown-linux-gnu
+          #- x86_64-unknown-linux-musl
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v3
+
+      - name: setup rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: 1.74.0
+
+      - name: build
+        run: |
+          cargo build --release --all-features --target ${{ matrix.arch }}
+
+      - name: compress with upx
+        uses: crazy-max/ghaction-upx@v3
+        with:
+          version: v4.1.0
+          files: |
+            target/${{ matrix.arch }}/release/rebar
+          args: --best --lzma
+
+      - name: upload binary
+        uses: actions/upload-artifact@v3
+        with:
+          name: rebar-${{ matrix.arch }}
+          path: target/${{ matrix.arch }}/release/rebar

.github/workflows/latest.yaml

@@ -0,0 +1,77 @@
+name: Latest
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+  release:
+    types: [published]
+
+  schedule:
+  - cron: '0 0 * * *'
+
+env:
+  tag: "latest"
+
+jobs:
+
+  build:
+    uses: ./.github/workflows/build.yaml
+
+  # ---------------------------------------------------------------------------
+  latest:
+
+    needs: build
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        arch:
+          #- aarch64-apple-darwin
+          #- aarch64-unknown-linux-gnu
+          #- aarch64-unknown-linux-musl
+          #- x86_64-apple-darwin
+          #- x86_64-pc-windows-gnu
+          - x86_64-unknown-linux-gnu
+          #- x86_64-unknown-linux-musl
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v3
+
+      - name: download binary from build
+        uses: actions/download-artifact@v3
+        with:
+          name: rebar-${{ matrix.arch }}
+          path: target/${{ matrix.arch }}/release
+
+      - name: install
+        run: |
+          mkdir -p /home/runner/.local/bin
+          mv target/${{ matrix.arch }}/release/rebar ~/.local/bin
+          chmod +x ~/.local/bin/rebar
+          rebar --help
+
+      - name: dataset download
+        run: |
+          rebar dataset download --name sars-cov-2 --tag $tag --output-dir dataset/sars-cov-2/$tag
+
+      - name: validate
+        run: |
+          rebar run  --dataset-dir dataset/sars-cov-2/$tag --output-dir validate --populations "*" --threads 2
+          if [[ $(grep "fail" validate/linelist.tsv) ]]; then exit 1; fi
+
+      - name: plot
+        run: |
+          rebar plot --dataset-dir dataset/sars-cov-2/$tag --output-dir validate --plot-dir validate/plots
+
+      - name: upload
+        uses: actions/upload-artifact@v3
+        with:
+          name: validate-${{ matrix.arch }}
+          path: validate

.github/workflows/lint.yaml

@@ -9,8 +9,6 @@ on:
       - '*'
   release:
     types: [published]
-#  schedule:
-#    - cron: "0 0 * * *"
 
 jobs:
 
@@ -22,11 +20,16 @@ jobs:
       - name: checkout repo
         uses: actions/checkout@v3
 
-      - name: setup Python
+      - name: setup python
         uses: actions/setup-python@v2
         with:
           python-version: '3.9'
 
+      - name: setup rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: 1.74.0
+
       - name: setup linters
         run: |
           pip install pre-commit==2.17.0

.github/workflows/release.yaml

@@ -7,55 +7,41 @@ on:
 
 jobs:
 
-  release-notes:
-    name: Release Notes 📰
-    runs-on: ubuntu-latest
+  build:
+    uses: ./.github/workflows/build.yaml
 
-    steps:
-      - name: checkout repo
-        uses: actions/checkout@v3
-        with:
-          lfs: true
-          fetch-depth: 0
+  #----------------------------------------------------------------------------
+  release:
 
-      - name: update submodules
-        run: git submodule update --init --recursive
-
-      # Check 2 most recent tags, overwrites
-      - name: Tagged Release Notes
-        run: |
-          ./autologs/autologs \
-            --release \
-            -o release-notes.md \
-            --old-tag `git tag | tail -n2 | head -n1` \
-            --new-tag `git tag | tail -n1`
-      - name: Upload Release Notes
-        uses: actions/upload-artifact@v2
-        with:
-          name: release-notes
-          path: release-notes.md
-          retention-days: 7
-
-  tagged-release:
-    name: Tagged Release
-    needs: [release-notes]
+    needs: build
     runs-on: ubuntu-latest
 
     steps:
 
-      - name: Download Release Notes
-        uses: actions/download-artifact@v2
+      - name: download binaries from build
+        uses: actions/download-artifact@v3
         with:
-          name: release-notes
+          path: target
+
+      - name: rename binaries by architecture
+        run: |
+          mkdir target/release
+          mv target/rebar-x86_64-unknown-linux-gnu/rebar target/release/rebar-x86_64-unknown-linux-gnu
+          ls -l target/release/
 
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: create release
+        uses: ncipollo/release-action@v1
         with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
+          # comma-separated
+          artifacts: "target/release/rebar-x86_64-unknown-linux-gnu"
+          # aarch64-apple-darwin
+          # aarch64-unknown-linux-gnu
+          # aarch64-unknown-linux-musl
+          # x86_64-apple-darwin
+          # x86_64-pc-windows-gnu
+          # x86_64-unknown-linux-musl
+          artifactErrorsFailBuild: true
           draft: true
+          generateReleaseNotes: true
+          makeLatest: true
           prerelease: true
-          body_path: release-notes.md