Merge pull request #110 from kipoi/singularity

Singularity

.github/workflows/test-images.yml

@@ -51,22 +51,26 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: '3.10'
-    - name: Install
-      uses: conda-incubator/setup-miniconda@v2
+    - name: Setup Go
+      uses: actions/setup-go@v2
       with:
-        activate-environment: py310
-        environment-file: environment.ubuntu.singularity.yml
-        python-version: '3.10'
-        auto-activate-base: false
-    - name: Install dependencies
-      shell: bash -l {0}
+        go-version: 1.17.8
+    - name: Fetch system level dependencies
+      run: sudo apt-get -q update && sudo apt-get install -y build-essential squashfs-tools libseccomp-dev cryptsetup libhdf5-serial-dev pkg-config
+    - name: Build and install Apptainer
+      run: |
+        export VERSION=1.0.1 && \
+        wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-${VERSION}.tar.gz && \
+        tar -xzf apptainer-${VERSION}.tar.gz && \
+        cd apptainer-${VERSION}
+        ./mconfig -v -p /usr/local
+        make -C ./builddir all && sudo make -C ./builddir install
+    - name: Install kipoi_containers
       run: |
         mkdir -p /home/runner/singularity/
-        sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
         python -m pip install --upgrade pip
         pip install .
     - name: Test with pytest
-      shell: bash -l {0}
       run: |
         pytest -s test-containers/test_models_from_command_line.py --model=${{ matrix.model }}
         docker system prune -a -f

environment.ubuntu.singularity.yml

@@ -1,9 +1,8 @@
 name: py310
 channels:
-  - bioconda
   - conda-forge
   - defaults
 dependencies:
   - pip
-  - singularity=3.8.6
+  - singularity
   - python=3.10