Merge pull request #31 from poseidon-framework/new_release_pipeline

New release pipeline

.github/workflows/release.yaml

@@ -1,5 +1,7 @@
 name: Release
+
 on:
+  # Trigger the workflow on the new 'v*' tag created
   push:
     tags:
       - "v*"
@@ -11,53 +13,100 @@ jobs:
     steps:
       - name: Check out code
         uses: actions/checkout@v4
+
       - name: Create Release
         id: create_release
         uses: ncipollo/release-action@v1
         with:
           name: Release ${{ github.ref_name }}
           draft: true
-  build-on-linux:
+
+  build_normal_artifacts:
     needs: [create_release]
-    runs-on: ubuntu-latest
+    name: ${{ matrix.os }}/${{ github.ref }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macOS-13, macOS-14, windows-latest]
+
     steps:
-    - name: Checkout repo
-      uses: actions/checkout@v4
-    - name: Build Docker image
-      run: docker build -t linux -f Dockerfile.linux .
-    - name: Create container
-      run: docker create --name linuxcontainer linux
-    - name: Copy executable
-      run: docker cp linuxcontainer:/root/.local/bin/xerxes xerxes-Linux
-    - name: Upload Release Asset
-      uses: ncipollo/release-action@v1
-      with:
-        name: Release ${{ github.ref_name }}
-        draft: true
-        allowUpdates: true
-        artifactErrorsFailBuild: true
-        artifacts: xerxes-Linux
-        artifactContentType: application/octet-stream
-  build-on-mac:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set tag name
+        uses: olegtarasov/[email protected]
+        id: tagName
+        with:
+          tagRegex: "v(.*)"
+          tagRegexGroup: 1
+
+      - name: Install stack on macOS, where it is not present # (https://github.com/freckle/stack-action/issues/80)
+        if: ${{ runner.os == 'macOS' }}
+        run: curl -sSL https://get.haskellstack.org/ | sh
+
+      - name: Build executable
+        uses: freckle/stack-action@v5
+        id: stack
+        with:
+          test: false
+          stack-build-arguments: --copy-bins --ghc-options="-O2"
+
+      - name: Set binary path name
+        id: binarypath
+        run: |
+             if [ "$RUNNER_OS" == "Windows" ]; then
+                 newEXE="xerxes-$RUNNER_OS.exe"
+             elif [ "$RUNNER_OS" == "macOS" ]; then
+                 newEXE="xerxes-$RUNNER_OS-$RUNNER_ARCH"
+             else
+                 newEXE="xerxes-$RUNNER_OS"
+             fi
+             currentEXE="${{ steps.stack.outputs.local-bin }}/xerxes"
+             mv $currentEXE $newEXE
+             echo "BINARY_PATH=$newEXE" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Compress binary
+        if: ${{ runner.os != 'macOS' }} # upx is crashing for macOS Ventura or above!
+        uses: svenstaro/upx-action@v2
+        with:
+          files: ${{ steps.binarypath.outputs.BINARY_PATH }}
+
+      - name: Upload Release Asset
+        id: upload-release-asset
+        uses: ncipollo/release-action@v1
+        with:
+          name: Release ${{ github.ref_name }}
+          draft: true
+          allowUpdates: true
+          artifactErrorsFailBuild: true
+          artifacts: ${{ steps.binarypath.outputs.BINARY_PATH }}
+          artifactContentType: application/octet-stream
+
+  build_centos_artifact:
     needs: [create_release]
-    runs-on: macos-latest
+    runs-on: ubuntu-latest
+
     steps:
-    - name: Checkout repo
-      uses: actions/checkout@v4
-    - name: Setup Haskell
-      uses: haskell/actions/setup@v2
-      with:
-        enable-stack: true
-    - name: Build
-      run: stack install
-    - name: Copy executable
-      run: cp ~/.local/bin/xerxes xerxes-macOS
-    - name: Upload Release Asset
-      uses: ncipollo/release-action@v1
-      with:
-        name: Release ${{ github.ref_name }}
-        draft: true
-        allowUpdates: true
-        artifactErrorsFailBuild: true
-        artifacts: xerxes-macOS
-        artifactContentType: application/octet-stream
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Build Docker image
+        run: docker build -t linux -f .github/workflows/Dockerfile.centos .
+
+      - name: Create container
+        run: docker create --name linuxcontainer linux
+
+      - name: Copy executable
+        run: docker cp linuxcontainer:/root/.local/bin/xerxes xerxes-conda-linux
+
+      - name: Upload Release Asset
+        id: upload-release-asset
+        uses: ncipollo/release-action@v1
+        with:
+          name: Release ${{ github.ref_name }}
+          draft: true
+          allowUpdates: true
+          artifactErrorsFailBuild: true
+          artifacts: xerxes-conda-linux
+          artifactContentType: application/octet-stream

CHANGELOGRELEASE.md

@@ -1,3 +1,17 @@
+# V1.0.1.1: new release pipeline
+
+This minor release replaces the pipeline to produce static `xerxes` executables for every release.
+
+Just like `trident`, `xerxes` will now be available in the following pre-compiled versions:
+
+- `xerxes-conda-linux` (for bioconda)
+- `xerxes-Linux` (build on Ubuntu 20.04 for X64 architecture)
+- `xerxes-macOS-ARM64` (build on macOS 14 for ARM64 architecture)
+- `xerxes-macOS-X64` (build on macOS 13 for X64 architecture)
+- `xerxes-Windows`
+
+`xerxes` now also depends on the latest poseidon-hs version 1.5.0.1.
+
 # V1.0.1.0: FST fix and better user input checks
 
 This release fixes a bug in the estimation of FST. We have now exactly implemented the estimator presented in Bhatia et al. 2013

poseidon-analysis-hs.cabal

@@ -1,5 +1,5 @@
 name:                poseidon-analysis-hs
-version:             1.0.1.0
+version:             1.0.1.1
 synopsis:            A package with analysis-tools to work with Poseidon Genotype Data
 description:         The tools in this package analyse Poseidon-formatted genotype databases, a modular system for storing genotype data from thousands of individuals.
 license:             MIT

stack.yaml

@@ -6,7 +6,7 @@ packages:
 
 extra-deps:
   - git: https://github.com/poseidon-framework/poseidon-hs
-    commit: c4460ec52f64a47ff0a292a26828fa507802c9a5
+    commit: 466870a0968aa093a31e02b74e9b802213ab29d8
   - table-layout-0.9.1.0
   - data-default-instances-base-0.1.0.1
   - sequence-formats-1.7.0