Add Docker image and example scripts (#47)

* Add docker image
* Add shell script to analyse images in a containerised instance of ColonyScanalyser
* Add shell script to build docker image
* Version bump and update documentation with Docker information

.dockerignore

@@ -0,0 +1,94 @@
+# Project specific
+data/
+images/
+figures/
+site/
+docs/images/
+tests/
+
+# Git
+.git
+.gitignore
+
+# CI
+.codeclimate.yml
+.travis.yml
+.taskcluster.yml
+
+# Docker
+docker-compose.yml
+.docker
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+**/__pycache__/
+**/*.py[cod]
+**/*.pyc
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Virtual environment
+.env/
+.venv/
+venv/
+
+# IDEs
+.idea
+.vscode
+
+# Python mode for VIM
+.ropeproject
+**/.ropeproject
+
+# Vim swap files
+*.swp
+**/*.swp

.gitignore

@@ -2,6 +2,7 @@
 data
 figures
 plots
+images
 
 # IDEs
 .vscode

Dockerfile

@@ -0,0 +1,22 @@
+# Build image with multi-stage builds
+# Ensures image is built faster and smaller
+FROM python:3.8-slim AS compile-image
+RUN apt-get update
+RUN apt-get install -y --no-install-recommends build-essential gcc
+
+# Install with pip‘s --user option, so all files will be installed in
+# the .local directory of the current user’s home directory
+COPY . /ColonyScanalyser
+WORKDIR /ColonyScanalyser
+RUN pip install --user .
+
+# Copy compiled artefacts to fresh image, without compiler baggage
+FROM python:3.8-slim AS build-image
+COPY --from=compile-image /root/.local /root/.local
+
+# Make sure scripts in .local are usable:
+ENV PATH=/root/.local/bin:$PATH
+
+# Return help if no arguments are passed to ColonyScanalyser
+ENTRYPOINT ["colonyscanalyser"]
+CMD ["-h"]

README.md

@@ -42,7 +42,7 @@ The remaining Python package dependencies are automatically handled by Pip when
 
 <img align="right" src="docs/images/plate_map_small.png">
 
-Optionally use a virtual environment, such as [Pipenv](https://github.com/pypa/pipenv).
+Optionally use a virtual environment, such as [Pipenv](https://github.com/pypa/pipenv), or a [containerised instance of the package](https://hub.docker.com/r/erikwhite/colonyscanalyser).
 
 For testing:
 * [Pytest](https://pytest.org/)

docs/CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.1] - 2020-05-11
+### Added
+- Dockerfile and utility scripts
+- Docker image is now available: https://hub.docker.com/r/erikwhite/colonyscanalyser
 ## [0.4.0] - 2020-03-26
 ### Added
 - `plate_labels` command line argument

docs/installation.md

@@ -48,4 +48,14 @@ Then run the ColonyScanalyser package:
 pipenv run scanalyser /path/to/images
 ```
 
-[More detailed instructions](https://packaging.python.org/tutorials/managing-dependencies/) can be found on the Python packaging site.
+[More detailed instructions](https://packaging.python.org/tutorials/managing-dependencies/) can be found on the Python packaging site.
+
+## Docker
+The image is available on [Docker Hub](https://hub.docker.com/r/erikwhite/colonyscanalyser).
+
+Alternatively, you can build the image yourself using the Dockerfile included with the package. The container can be built by running `docker-build.sh` in the `scripts` directory.
+
+`scripts/docker-run.sh` is an example of how to use a containerised instance of ColonyScanalyser to analyse images in a directory on the host machine. Run the script as you normally would ColonyScanalyser, passing it the target image directory followed by any other command line arguments:
+```
+scripts/docker-run.sh /absolute/path/to/images/ --verbose 3 --plate_size 100
+```

scripts/docker-build.sh

@@ -0,0 +1,2 @@
+# Create a containerised image of ColonyScanalyser
+docker build --pull --rm -f "./Dockerfile" -t colonyscanalyser:latest "."

scripts/docker-run.sh

@@ -0,0 +1,21 @@
+# Use a containerised instance of ColonyScanalyser to analyse
+# a directory of images in the host system
+#
+# Pass the directory path to this script, followed by any
+# other command line arguments for ColonyScanalyser
+# The directory path must be absolute, not relative
+#
+# Example:
+# docker-run.sh /path/to/images/ --verbose 5 --plate_size 100
+
+# Store images directory and mount in docker image
+# Shift remaining arguments and pass to ColonyScanalyser
+img_dir="$1"
+shift
+# Run ColonyScanalyser on the images in the mounted directory
+docker run \
+  --rm \
+  --name colonyscanalyser \
+  --mount type=bind,source=$img_dir,target=/data \
+  colonyscanalyser /data \
+  $@

setup.py

@@ -15,7 +15,7 @@ def read(*names, **kwargs):
 setup(
     python_requires = ">=3.7",
     name = "colonyscanalyser",
-    version = "0.4.0",
+    version = "0.4.1",
     description = "An image analysis tool for measuring microorganism colony growth",
     long_description = "%s\n%s" % (
         re.compile("^.. start-badges.*^.. end-badges", re.M | re.S).sub("", read("README.md")),