weekly tests #30
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name: weekly tests | |
on: | |
schedule: | |
# every Sunday at 0:00 | |
# ┌───────────── minute (0 - 59) | |
# │ ┌───────────── hour (0 - 23) | |
# │ │ ┌───────────── day of the month (1 - 31) | |
# │ │ │ ┌───────────── month (1 - 12) | |
# │ │ │ │ ┌───────────── day of the week (0 - 6) | |
# │ │ │ │ │ | |
# │ │ │ │ │ | |
# │ │ │ │ │ | |
# * * * * * | |
- cron: "0 0 * * 0" | |
env: | |
cache-version: "cache-v1" | |
jobs: | |
tests: | |
timeout-minutes: 720 | |
defaults: | |
run: | |
shell: bash -l {0} | |
strategy: | |
max-parallel: 10 | |
matrix: | |
config: | |
- { python-version: 3.7, os: ubuntu-latest } | |
- { python-version: 3.8, os: ubuntu-latest } | |
- { python-version: 3.9, os: ubuntu-latest } | |
- { python-version: "3.10", os: ubuntu-latest } | |
- { python-version: 3.7, os: macos-latest } | |
- { python-version: 3.8, os: macos-latest } | |
- { python-version: 3.9, os: macos-latest } | |
- { python-version: "3.10", os: macos-latest } | |
# disabled until it's fixed. | |
runs-on: ${{ matrix.config.os }} | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
NOT_CRAN: true | |
TZ: UTC | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: actions/setup-node@v3 | |
- name: Install ubuntu system dependencies | |
if: matrix.config.os == 'ubuntu-latest' | |
run: | | |
sudo apt-get install libcurl4-openssl-dev | |
sudo apt-get update -y && sudo apt-get install -y zlib1g-dev libglpk-dev libgmp3-dev libxml2-dev libicu-dev libhdf5-serial-dev libcurl4-gnutls-dev | |
- name: Install macOS system dependencies | |
if: matrix.config.os == 'macos-latest' | |
run: | | |
brew install cairo pkg-config autoconf automake libtool | |
- name: Cache conda | |
uses: actions/cache@v3 | |
env: | |
# Increase this value to reset cache if etc/example-environment.yml has not changed | |
CACHE_NUMBER: 1 | |
with: | |
path: ~/conda_pkgs_dir | |
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ | |
hashFiles('environment.yml') }} | |
- name: Setup Miniconda | |
uses: conda-incubator/setup-miniconda@v2.1.1 | |
with: | |
auto-activate-base: true | |
auto-update-conda: true | |
activate-environment: dandelion | |
channels: conda-forge, bioconda, anaconda, defaults | |
channel-priority: true | |
python-version: ${{ matrix.config.python-version }} | |
environment-file: environment.yml | |
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
- name: Display Python version | |
run: | | |
python --version | |
which python | |
- name: Setup blast and igblast | |
# just in case this happens again in the future | |
# conda install -c bioconda igblast blast ncbi-vdb=2.11.0 | |
# https://github.com/bioconda/bioconda-recipes/issues/33479 | |
run: | | |
conda install -c bioconda "igblast>=1.17.0" blast | |
- name: Test if blast works | |
run: | | |
blastn -h | |
- name: Test if igblast works | |
run: | | |
igblastn -h | |
- id: R | |
name: Check R version | |
run: | | |
R --version > VERSION | |
echo "version=$(head -1 VERSION | awk '{print $3}')" >> $GITHUB_OUTPUT | |
echo "mainbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT | |
echo "subbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')" >> $GITHUB_OUTPUT | |
echo "biocversion=$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT | |
shell: bash -l {0} | |
- name: Set up R | |
uses: r-lib/actions/setup-r@v2 | |
with: | |
r-version: ${{ steps.R.outputs.version}} | |
- name: Cache ubuntu R packages | |
if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'" | |
uses: actions/cache@v3 | |
with: | |
path: /home/runner/work/_temp/Library | |
key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}- | |
- name: Cache macOS R packages | |
if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os != 'ubuntu-latest'" | |
uses: actions/cache@v3 | |
with: | |
path: ${{ env.R_LIBS_USER }} | |
key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}- | |
- name: Setup r-lib/remotes | |
run: | | |
options(install.packages.compile.from.source = "never") | |
install.packages(c('remotes', 'optparse', 'RCurl', 'XML','matrixStats', 'stringi')) | |
shell: Rscript {0} | |
- name: Install Dandelion | |
run: | | |
python -m pip install git+https://github.com/emdann/milopy.git palantir==1.0.1 | |
python -m pip install . | |
- name: Install ubuntu R dependencies | |
if: matrix.config.os == 'ubuntu-latest' | |
run: | | |
options(install.packages.compile.from.source = "never") | |
remotes::install_cran("BiocManager") | |
BiocManager::install(c('Biostrings', 'GenomicAlignments', 'IRanges')) | |
install.packages(c('shazam', 'alakazam', 'tigger', 'optparse')) | |
shell: Rscript {0} | |
- name: Install macOS R dependencies | |
if: matrix.config.os != 'ubuntu-latest' | |
run: | | |
options(install.packages.compile.from.source = "never") | |
remotes::install_cran("BiocManager") | |
BiocManager::install(c('Biostrings', 'GenomicAlignments', 'IRanges')) | |
install.packages(c('shazam', 'alakazam', 'tigger', 'optparse')) | |
shell: Rscript {0} | |
- name: Test if R dependencies are installed properly | |
run: | | |
Rscript tests/r_dependencies.R | |
shell: bash -l {0} | |
- name: Test with pytest | |
run: | | |
python -m pytest --cov=dandelion --cov-report=xml --ignore=container -rP -W ignore::DeprecationWarning -W ignore::PendingDeprecationWarning -W ignore::FutureWarning | |
- name: Show coverage | |
run: | | |
coverage report |