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Fix test script for new window averaging option handling #99

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Fix test script for new window averaging option handling

Fix test script for new window averaging option handling #99

Workflow file for this run

.github/workflows/ci.yaml at c24a14a
# ==================================================================================================
# Header
# ==================================================================================================
name: CI
on: [push, pull_request]
# ==================================================================================================
# Jobs
# ==================================================================================================
jobs:
# ==========================================================================
# CI Matrix
# ==========================================================================
ci:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
# -------------------------------------------------------
# matrix
# -------------------------------------------------------
# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#choosing-github-hosted-runners
# https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners
matrix:
# Need dummy entries for the matrix to pick up the variables.
# We later set all other combinations that we want explicitly.
os:
- ubuntu-latest
- macos-latest
compiler:
- gcc
- llvm
# -------------------------------------------------------
# include
# -------------------------------------------------------
# Instead of a matrix where we only have some combinations that work, and others that do not,
# we just directly opt for a list of all combinations that we actually want to test.
# Easier to reason about, easier to maintain, easier to extend.
# Newer compiler versions are not available on all Ubuntu, so some are excluded.
# Older GCC versions are also not supported by MacOS 12 any more.
# Currently, llvm-9 causes weird segfauls on Ubuntu, which do not seem to be our fault,
# but rather a bug in their thread forking, according to valgrind.
# Need to investiage further at some point. We used setup-cpp locally to install
# the very same version of llvm-9, and got tons of segfauls for all kind of functions.
# We also currently exclude clang from macos, as it fails with different types of
# linker errors. As this is merely a problem in the setup, we defer solving this for now.
include:
# -------------------------------
# Ubuntu 20.04
# -------------------------------
- os: ubuntu-20.04
compiler: gcc-7
- os: ubuntu-20.04
compiler: gcc-8
- os: ubuntu-20.04
compiler: gcc-9
- os: ubuntu-20.04
compiler: gcc-10
# Setup fails
# - os: ubuntu-20.04
# compiler: gcc-11
# - os: ubuntu-20.04
# compiler: gcc-12
- os: ubuntu-20.04
compiler: gcc-13
# Too new
# - os: ubuntu-20.04
# compiler: gcc-14
- os: ubuntu-20.04
compiler: llvm-6
- os: ubuntu-20.04
compiler: llvm-7
- os: ubuntu-20.04
compiler: llvm-8
# Weird segfault
# - os: ubuntu-20.04
# compiler: llvm-9
- os: ubuntu-20.04
compiler: llvm-10
- os: ubuntu-20.04
compiler: llvm-11
- os: ubuntu-20.04
compiler: llvm-12
- os: ubuntu-20.04
compiler: llvm-13
- os: ubuntu-20.04
compiler: llvm-14
- os: ubuntu-20.04
compiler: llvm-15
# Setup fails
# - os: ubuntu-20.04
# compiler: llvm-16
- os: ubuntu-20.04
compiler: llvm-17
- os: ubuntu-20.04
compiler: llvm-18
# -------------------------------
# Ubuntu 22.04
# -------------------------------
# Too old
# - os: ubuntu-22.04
# compiler: gcc-7
# - os: ubuntu-22.04
# compiler: gcc-8
- os: ubuntu-22.04
compiler: gcc-9
- os: ubuntu-22.04
compiler: gcc-10
- os: ubuntu-22.04
compiler: gcc-11
- os: ubuntu-22.04
compiler: gcc-12
- os: ubuntu-22.04
compiler: gcc-13
# Setup fails
# - os: ubuntu-22.04
# compiler: gcc-14
- os: ubuntu-22.04
compiler: llvm-6
- os: ubuntu-22.04
compiler: llvm-7
- os: ubuntu-22.04
compiler: llvm-8
# Weird segfault
# - os: ubuntu-22.04
# compiler: llvm-9
- os: ubuntu-22.04
compiler: llvm-10
- os: ubuntu-22.04
compiler: llvm-11
- os: ubuntu-22.04
compiler: llvm-12
- os: ubuntu-22.04
compiler: llvm-13
- os: ubuntu-22.04
compiler: llvm-14
- os: ubuntu-22.04
compiler: llvm-15
- os: ubuntu-22.04
compiler: llvm-16
- os: ubuntu-22.04
compiler: llvm-17
- os: ubuntu-22.04
compiler: llvm-18
# -------------------------------
# Ubuntu 24.04
# -------------------------------
# Too old
# - os: ubuntu-24.04
# compiler: gcc-7
# - os: ubuntu-24.04
# compiler: gcc-8
- os: ubuntu-24.04
compiler: gcc-9
- os: ubuntu-24.04
compiler: gcc-10
- os: ubuntu-24.04
compiler: gcc-11
- os: ubuntu-24.04
compiler: gcc-12
- os: ubuntu-24.04
compiler: gcc-13
- os: ubuntu-24.04
compiler: gcc-14
# Setup fails
# - os: ubuntu-24.04
# compiler: llvm-6
# - os: ubuntu-24.04
# compiler: llvm-7
# - os: ubuntu-24.04
# compiler: llvm-8
# - os: ubuntu-24.04
# compiler: llvm-9
# - os: ubuntu-24.04
# compiler: llvm-10
# - os: ubuntu-24.04
# compiler: llvm-11
# - os: ubuntu-24.04
# compiler: llvm-12
# - os: ubuntu-24.04
# compiler: llvm-13
# - os: ubuntu-24.04
# compiler: llvm-14
# - os: ubuntu-24.04
# compiler: llvm-15
# - os: ubuntu-24.04
# compiler: llvm-16
# - os: ubuntu-24.04
# compiler: llvm-17
- os: ubuntu-24.04
compiler: llvm-18
# -------------------------------
# MacOS 12
# -------------------------------
# Setup fails (too old?)
# - os: macos-12
# compiler: gcc-7
# - os: macos-12
# compiler: gcc-8
- os: macos-12
compiler: gcc-9
- os: macos-12
compiler: gcc-10
- os: macos-12
compiler: gcc-11
- os: macos-12
compiler: gcc-12
# Weird compiler errors
# - os: macos-12
# compiler: gcc-13
- os: macos-12
compiler: gcc-14
# Setup fails
# - os: macos-12
# compiler: llvm-6
# - os: macos-12
# compiler: llvm-7
# - os: macos-12
# compiler: llvm-8
# - os: macos-12
# compiler: llvm-9
# - os: macos-12
# compiler: llvm-10
# - os: macos-12
# compiler: llvm-11
# Weird compiler errors
# - os: macos-12
# compiler: llvm-12
- os: macos-12
compiler: llvm-13
- os: macos-12
compiler: llvm-14
- os: macos-12
compiler: llvm-15
# Setup fails
# - os: macos-12
# compiler: llvm-16
# - os: macos-12
# compiler: llvm-17
# - os: macos-12
# compiler: llvm-18
# -------------------------------
# MacOS 13
# -------------------------------
# Setup fails
# - os: macos-13
# compiler: gcc-7
# - os: macos-13
# compiler: gcc-8
- os: macos-13
compiler: gcc-9
- os: macos-13
compiler: gcc-10
- os: macos-13
compiler: gcc-11
- os: macos-13
compiler: gcc-12
# Weird compiler errors
# - os: macos-13
# compiler: gcc-13
- os: macos-13
compiler: gcc-14
# Setup fails
# - os: macos-13
# compiler: llvm-6
# - os: macos-13
# compiler: llvm-7
# - os: macos-13
# compiler: llvm-8
# - os: macos-13
# compiler: llvm-9
# Weird compiler errors
# - os: macos-13
# compiler: llvm-10
# - os: macos-13
# compiler: llvm-11
# - os: macos-13
# compiler: llvm-12
- os: macos-13
compiler: llvm-13
- os: macos-13
compiler: llvm-14
- os: macos-13
compiler: llvm-15
# Setup fails
# - os: macos-13
# compiler: llvm-16
# - os: macos-13
# compiler: llvm-17
# - os: macos-13
# compiler: llvm-18
# -------------------------------
# MacOS 14
# -------------------------------
# Setup fails for all
# - os: macos-14
# compiler: gcc-7
# - os: macos-14
# compiler: gcc-8
# - os: macos-14
# compiler: gcc-9
# - os: macos-14
# compiler: gcc-10
# - os: macos-14
# compiler: gcc-11
# - os: macos-14
# compiler: gcc-12
# - os: macos-14
# compiler: gcc-13
# - os: macos-14
# compiler: gcc-14
# - os: macos-14
# compiler: llvm-6
# - os: macos-14
# compiler: llvm-7
# - os: macos-14
# compiler: llvm-8
# - os: macos-14
# compiler: llvm-9
# - os: macos-14
# compiler: llvm-10
# - os: macos-14
# compiler: llvm-11
# - os: macos-14
# compiler: llvm-12
# - os: macos-14
# compiler: llvm-13
# - os: macos-14
# compiler: llvm-14
# - os: macos-14
# compiler: llvm-15
# - os: macos-14
# compiler: llvm-16
# - os: macos-14
# compiler: llvm-17
# - os: macos-14
# compiler: llvm-18
# -------------------------------
# AppleClang
# -------------------------------
- os: macos-12
compiler: apple
- os: macos-13
compiler: apple
- os: macos-14
compiler: apple
- os: macos-latest
compiler: apple
# ==========================================================================
# Steps
# ==========================================================================
steps:
- name: Checkout
uses: actions/[email protected]
# -------------------------------------------------------
# Setup
# -------------------------------------------------------
- name: Setup C++
# Reference: https://github.com/marketplace/actions/setup-cpp-c-c
uses: aminya/[email protected]
if: ${{ matrix.compiler != 'apple' && matrix.os != 'macos-latest' }}
with:
compiler: ${{ matrix.compiler }}
cmake: true
make: true
- name: Setup C++ - AppleClang
if: matrix.compiler == 'apple'
run: |
brew install cmake
# -------------------------------------------------------
# Dependencies
# -------------------------------------------------------
- name: Install Dependencies - Ubuntu
if: runner.os == 'linux'
# 1: htslib dependencies, see https://github.com/samtools/htslib/blob/develop/INSTALL
# 2: clang on ubuntu 22 is not properly set up, we need libtinfo5,
# see https://github.com/aminya/setup-cpp/issues/149
run: |
sudo apt-get install autoconf automake zlib1g-dev libbz2-dev liblzma-dev
if [[ ${{ matrix.os }} != ubuntu-24.04 ]] ; then
sudo apt-get install libtinfo5
fi
- name: Install Dependencies - MacOS
if: runner.os == 'macos'
# - Install simple dependencies of htslib
# - For our test script, we might need gdate, see https://apple.stackexchange.com/a/47181
# This is not used at the moment, but we keep it here for the future.
# - switch xcode mode, see https://stackoverflow.com/a/67654877
run: |
brew install autoconf automake libdeflate
brew install coreutils
if [[ "${{ matrix.compiler }}" == gcc* ]]; then
echo "Patching xcode gcc issues"
sudo xcode-select --switch /Library/Developer/CommandLineTools
fi
# -------------------------------------------------------
# Configure
# -------------------------------------------------------
- name: Configure
run: |
# Need to set the xcode patch here as well, as job steps don't keep status.
if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then
echo "Patching xcode gcc issues"
sudo xcode-select --switch /Library/Developer/CommandLineTools
fi
# For static builds, set the according CMake option
export GRENEDALF_BUILD_STATIC=""
# if [[ "${{ matrix.os }}" == "ubuntu-latest" ]] && [[ "${{ matrix.compiler }}" == "gcc" ]]; then
if [[ "${{ matrix.os }}" == "ubuntu-latest" ]] ; then
export GRENEDALF_BUILD_STATIC="-DGRENEDALF_BUILD_STATIC=ON"
fi
cmake -S . -B ./build ${GRENEDALF_BUILD_STATIC}
# -------------------------------------------------------
# Build
# -------------------------------------------------------
- name: Build
run: |
# Weird workarounds. On some CI builds, this is needed somehow for LLVM under Ubuntu.
if [[ "${RUNNER_OS}" != "macOS" ]] && [[ ! -f /usr/bin/gmake ]]; then
sudo ln -s /usr/bin/make /usr/bin/gmake
fi
# Need to set the xcode patch here as well, as job steps don't keep status.
if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then
echo "Patching xcode gcc issues"
sudo xcode-select --switch /Library/Developer/CommandLineTools
fi
cmake --build ./build -- -j 2
- name: Upload Logs
if: always()
uses: actions/upload-artifact@v4
with:
name: logs-${{ matrix.os }}-${{ matrix.compiler }}
path: |
build/**/*.log
# -------------------------------------------------------
# Upload Binaries
# -------------------------------------------------------
# We upload the static binaries for the most important systems.
# These are the ones that we want to publish with release versions.
- name: Upload Binaries
# If the Ubuntu binary here is changed, it needs to be changed above as well,
# to enable static building for that version!
# if: ( matrix.os == 'ubuntu-latest' && matrix.compiler == 'gcc' ) || matrix.compiler == 'apple'
if: matrix.os == 'ubuntu-latest' || matrix.compiler == 'apple'
uses: actions/upload-artifact@v4
with:
name: binary-${{ matrix.os }}-${{ matrix.compiler }}
path: |
bin/grenedalf
# -------------------------------------------------------
# Test
# -------------------------------------------------------
# We also run the test case, comparing grenedalf against our independent implementation.
# This covers several OS and compiler combionations, so hopefully good enough.
- name: Python Setup
if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Install Test Dependencies
if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
run: |
# Install the dependencies for the tests
pip install -r test/pip.txt
# Verify the installation
pip list
python --version
- name: Run Test
if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
run: |
cd ./test
./run.sh
cd ..
# We need to manually compress the test result files here, as there are many files,
# and we run into https://github.com/actions/upload-artifact/issues/485
tar -czf ./test.tar.gz ./test
- name: Upload Tests
if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
uses: actions/upload-artifact@v4
with:
name: test-${{ matrix.os }}-${{ matrix.compiler }}
path: |
# test
./test.tar.gz