pip dev(deps-dev): update sphinx requirement from <7 to <8 #888
Workflow file for this run
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name: Test Singularity Build | |
on: | |
# push: | |
# branches: | |
# - master | |
# Do the builds on all pull requests (to test them) | |
pull_request: | |
branches: | |
- "*" | |
jobs: | |
changes: | |
name: Checking changed files | |
runs-on: ubuntu-latest | |
outputs: | |
keepgoing: ${{ steps.changed-files.outputs.any_changed }} | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/changed-files@v35 | |
with: | |
files: | | |
**/*.{yml,yaml,py} | |
container/database | |
container/tests | |
container/*.{yml,yaml,py} | |
tests | |
- name: List all changed files | |
run: | | |
for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
echo "$file was changed" | |
done | |
echo ${{ steps.changed-files.outputs.any_changed }} | |
container: | |
needs: | |
- changes | |
if: needs.changes.outputs.keepgoing == 'true' | |
runs-on: ubuntu-latest | |
steps: | |
- name: Set up Go 1.13 | |
uses: actions/setup-go@v1 | |
with: | |
go-version: 1.13 | |
id: go | |
- name: Install Dependencies | |
run: | | |
sudo apt-get update && sudo apt-get install -y \ | |
build-essential \ | |
libssl-dev \ | |
uuid-dev \ | |
libgpgme11-dev \ | |
squashfs-tools \ | |
libseccomp-dev \ | |
pkg-config | |
- name: Install Singularity | |
env: | |
SINGULARITY_VERSION: 3.8.1 | |
GOPATH: /tmp/go | |
run: | | |
mkdir -p $GOPATH | |
sudo mkdir -p /usr/local/var/singularity/mnt && \ | |
mkdir -p $GOPATH/src/github.com/sylabs && \ | |
cd $GOPATH/src/github.com/sylabs && \ | |
wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \ | |
tar xzv && \ | |
cd singularity-ce-${SINGULARITY_VERSION} && \ | |
./mconfig -p /usr/local && \ | |
make -C builddir && \ | |
sudo make -C builddir install | |
- name: Check out code for the container build | |
uses: actions/checkout@v2 | |
- name: Extract repository location | |
shell: bash | |
run: | | |
echo "location=$(echo " - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT | |
id: extract_location | |
- name: Build Container | |
run: | | |
ls container | |
cd container | |
wget https://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.19.0/ncbi-igblast-1.19.0-x64-linux.tar.gz | |
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-x64-linux.tar.gz | |
tar -xzvf ncbi-igblast-1.19.0-x64-linux.tar.gz | |
tar -xzvf ncbi-blast-2.13.0+-x64-linux.tar.gz | |
echo '${{ steps.extract_location.outputs.location }}' >> environment_test.yml | |
sudo -E singularity build --notest sc-dandelion.sif sc-dandelion_test.def | |
- name: Test Container | |
run: | | |
cd container | |
sudo singularity test --writable-tmpfs sc-dandelion.sif | |
singularity run -B $PWD sc-dandelion.sif dandelion-preprocess --help |