CI fixes (#484)

* Fixes for macOS CI - install conda using miniforge * Troubleshooting * Add tests for clang 15, 16 * Clean-up, add flags for newer clang
bcgsc · Oct 3, 2024 · 98c878e · 98c878e
1 parent d3a0c13
commit 98c878e
Showing 1 changed file with 78 additions and 23 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -33,13 +33,20 @@ jobs:
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
       mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl pandoc meson ninja btllib
     displayName: Install dependencies
   - script: |
@@ -50,68 +57,116 @@ jobs:
     displayName: Compiling ABySS
 
 - job:
-  displayName: mac_clang14
+  displayName: mac_clang16
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.7.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
-      make -j12 distcheck
-    displayName: Compiling ABySS
+      make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
+    displayName: Compiling ABySS with clang 16
 
 - job:
-  displayName: mac_clang13
+  displayName: mac_clang15
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.6.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
-      make -j12 distcheck
-    displayName: Compiling ABySS with clang 13
+      make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
+    displayName: Compiling ABySS with clang 15
 
 - job:
-  displayName: mac_clang12
+  displayName: mac_clang14
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.0 make boost-cpp sparsehash openmpi automake perl pandoc llvm-openmp btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
       make -j12 distcheck
-    displayName: Compiling ABySS with clang 12
+    displayName: Compiling ABySS with clang 14
 
+- job:
+  displayName: mac_clang13
+  pool:
+    vmImage: 'macOS-latest'
+  steps:
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
+  - script: conda create --yes --quiet --name abyss_CI
+    displayName: Create Anaconda environment
+  - script: |
+      source activate abyss_CI
+      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+    displayName: Install dependencies
+  - script: |
+      source activate abyss_CI
+      ./autogen.sh
+      ./configure
+      make -j12 distcheck
+    displayName: Compiling ABySS with clang 13
 
 - job: linux_gcc12
   pool: