Downloads ImmunoFluorescent image data from Human Protein Atlas
- Free software: MIT license
- Documentation: https://cellmaps-imagedownloader.readthedocs.io.
- Python 3.8+
pip install cellmaps_imagedownloader
Or directly from source:
git clone https://github.com/idekerlab/cellmaps_imagedownloader cd cellmaps_imagedownloader make dist pip install dist/cellmaps_imagedownloader*whl
Run make command with no arguments to see other build/deploy options including creation of Docker image
make
Output:
clean remove all build, test, coverage and Python artifacts clean-build remove build artifacts clean-pyc remove Python file artifacts clean-test remove test and coverage artifacts lint check style with flake8 test run tests quickly with the default Python test-all run tests on every Python version with tox coverage check code coverage quickly with the default Python docs generate Sphinx HTML documentation, including API docs servedocs compile the docs watching for changes testrelease package and upload a TEST release release package and upload a release dist builds source and wheel package install install the package to the active Python's site-packages dockerbuild build docker image and store in local repository dockerpush push image to dockerhub
Before running tests, please install pip install -r requirements_dev.
- samples file: CSV file with list of IF images to download (see sample samples file in examples folder)
- unique file: CSV file of unique samples (see sample unique file in examples folder)
- provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)
For information invoke cellmaps_imagedownloadercmd.py -h
Example usage
cellmaps_imagedownloadercmd.py ./cellmaps_imagedownloader_outdir --samples examples/samples.csv --unique examples/unique.csv --provenance examples/provenance.json
Example usage
Coming soon...
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.