Merge db6ae9d into 6b9cf66

.github/workflows/test-images.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: CI
 
 on:
@@ -75,9 +72,12 @@ jobs:
         pytest -s test-containers/test_models_from_command_line.py --model=${{ matrix.model }}
         docker system prune -a -f
 
-  testdocker:
+  testdockerandsingularity:
 
     runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODOACCESSTOKEN }}
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.9
@@ -89,30 +89,9 @@ jobs:
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
         python -m pip install --upgrade pip
         pip install -e .
-    - name: Test updateoradd
+    - name: Test kipoi_containers and send coverage report to coveralls.io
       run: |-
+        pip install coveralls
         docker pull kipoi/kipoi-docker:mmsplice
-        pytest -s test-docker/test_docker_handler.py
-
-
-  testsingularity:
-
-    runs-on: ubuntu-latest
-    env:
-      ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODOACCESSTOKEN }}
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install pip dependencies
-      run: |
-        sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
-        python -m pip install --upgrade pip
-        pip install -e .
-    - name: Test singularity
-      run: |
-        pytest -s test-singularity
-        pytest -s test-containers/test_update_all_singularity_images.py
-
+        coverage run -m pytest -s test-docker/test_docker_handler.py test-singularity test-containers/test_update_all_singularity_images.py
+        coveralls --service=github

README.md

@@ -1,12 +1,9 @@
 # kipoi-containers
 
-<a href=https://www.python.org/downloads>
-	<img alt='Python' src=https://img.shields.io/badge/Python-%20%3E=3.9-cyan
- style="max-height:20px;width:auto;">
-</a>
-<a href=https://opensource.org/licenses/MIT>
-	<img alt='License: MIT' src=https://img.shields.io/badge/License-MIT-yellow.svg style="max-height:20px;width:auto;">
-</a>
+[![Python 3.9](https://img.shields.io/badge/python-3.9-cyan.svg)](https://www.python.org/downloads/release/python-390/)
+![](https://github.com/kipoi/kipoi-containers/actions/workflows/test-images.yml/badge.svg)
+[![Coverage Status](https://coveralls.io/repos/github/kipoi/kipoi-containers/badge.svg)](https://coveralls.io/github/kipoi/kipoi-containers)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 ![alt text](misc/kipoicontainers.png?raw=true "kipoi-containers")
 This repository contains necessary infrastructure elements for adding and updating docker and singularity images for models and model groups in [Kipoi model zoo](https://kipoi.org/). These images are pre-activated with a compatible conda environment where all the model (group) specific dependencies have been installed.
@@ -75,7 +72,7 @@ kipoi predict Basset \
 
 - Install kipoi_containers using ```pip install -e .```
 
-## Required environment variables
+## Environment variables
 
 1. `DOCKER_USERNAME`, `DOCKER_PASSWORD`  
     - Only required for pushing the image to kipoi/kipoi-docker
@@ -89,6 +86,9 @@ kipoi predict Basset \
     - Required for syncing with [Kipoi model zoo](https://kipoi.org/)
     - Get it [here](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token). Make sure to add both read and write access
 
+4. `SINGULARITY_PULL_FOLDER` (Optional)
+    - If specified, singularity images will be downloaded, built into and pushed from this folder. Otherwise, the current working directory is chosen as default.
+
 ## Map between models (groups) and docker and singularity images
 
 - Docker: [here](https://github.com/kipoi/models/blob/master/shared/containers/model-to-docker.json)