Docker production image (#80)

* Adds workflow for pushing docker image to docker-hub

Author: Måns Magnusson

.dockerignore

@@ -0,0 +1,79 @@
+# Mac OSX hidden files
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+htmlcov
+.cache/
+.coverage*
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.env
+TRASH*
+*.tar.gz
+.vagrant
+_DEVELOP/
+.vscode/
+
+# Editors
+*.sublime-workspace
+.tm_properties
+.idea
+
+# project files should be version controlled, unless a significant
+# proportion of contributors will probably not be using SublimeText
+# *.sublime-project
+
+# Complexity
+output/*.html
+output/*/index.html
+
+# Docs
+docs/_build
+_book/
+
+# Secrets
+alembic.ini
+
+# Module
+*.mod.yaml
+meta.yaml
+
+# Local files
+local/
+
+housekeeperold/
+testsold/

.github/workflows/build_and_publish.yml

@@ -38,3 +38,17 @@ jobs:
      with:
        user: __token__
        password: ${{ secrets.pypi_password }}
+
+ push_to_registry:
+   name: Push Docker image to Docker Hub
+   runs-on: ubuntu-latest
+   steps:
+     - name: Check out the repo
+       uses: actions/checkout@v2
+     - name: Push to Docker Hub
+       uses: docker/build-push-action@v1
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+         repository: clinicalgenomics/housekeeper
+         tag_with_ref: true

CHANGELOG.md

@@ -12,6 +12,14 @@ Please add a new candidate release at the top after changing the latest one. Fee
 ### Changed
 ### Fixed
 
+## [3.1.0]
+
+### Added
+
+- Adds Dockerfile
+- Add workflow for automatic publish to docker-hub
+- Add __main__ script to run housekeeper without installing 
+
 ## [3.0.1]
 
 ### Changed

Dockerfile

@@ -0,0 +1,39 @@
+FROM python:3.7-slim
+
+LABEL base_image="python:3.7-slim"
+LABEL software="housekeeper"
+LABEL about.summary="Image for housekeeper"
+LABEL about.home="https://github.com/Clinical-Genomics/housekeeper"
+LABEL about.documentation="https://github.com/Clinical-Genomics/housekeeper/README.md"
+LABEL about.license_file="https://github.com/Clinical-Genomics/housekeeper/LICENSE"
+LABEL about.license="MIT License (MIT)"
+LABEL about.tags="files,database"
+LABEL maintainer="Måns Magusson <[email protected]>"
+
+RUN pip install -U pip
+# Avoid running as root for security reasons
+# More about that: https://pythonspeed.com/articles/root-capabilities-docker-security/
+# Solution inspired from
+# https://medium.com/@DahlitzF/run-python-applications-as-non-root-user-in-docker-containers-by-example-cba46a0ff384
+RUN useradd --create-home worker
+USER worker
+WORKDIR /home/worker
+
+# Based on https://pythonspeed.com/articles/pipenv-docker/
+RUN pip install --user micropipenv pymysql cryptography
+# Update the path for micropipenv
+ENV PATH="/home/worker/.local/bin:${PATH}"
+
+# Copy the lockfile to temporary directory. This will be deleted
+COPY --chown=worker:worker Pipfile.lock /tmp/
+# Generate reqs with locked dependencies for deterministic build
+RUN cd /tmp && micropipenv requirements > requirements.txt
+# Install deps
+RUN pip install --user -r /tmp/requirements.txt
+# Copy package
+COPY --chown=worker:worker . /tmp/housekeeper
+# Install package
+RUN pip install /tmp/housekeeper
+
+ENTRYPOINT ["housekeeper"]
+CMD ["--help"]

Pipfile

@@ -23,3 +23,6 @@ python_version = "3.7"
 
 [pipenv]
 allow_prereleases = true
+
+[scripts]
+housekeeper = "python -m housekeeper"

housekeeper/__main__.py

@@ -0,0 +1,15 @@
+"""
+housekeeper.__main__
+
+The main entry point for the command line interface.
+
+Invoke as `housekeeper` (if installed)
+or `python -m housekeeper` (no install required).
+"""
+import sys
+
+from housekeeper.cli.core import base
+
+if __name__ == "__main__":
+    # exit using whatever exit code the CLI returned
+    sys.exit(base())