This package contains python based command line imaging utilities for the Hedwig project.
The Sphinx documentation can be found here: https://niaid.github.io/tomojs-pytools
This pytools is a proper Python package, and can be installed from published wheels, tarballs or from the git repository.
The wheels are packaged as part of the Github Actions and can be manually downloaded for the action interface. They are also published to the bcbb-pypi hosted by NIAID actifactory. This extra repository can be configured with the --extra-index option on the pip install command line. However, the argument needs to include the username and password. The specifics can be found the the NIAID artifactory.
Use pip to install the tomojs_pytools package:
python3 -m pip install -extra-index https://USERNAME:PASSWORD@artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi/simple tomojs_pytools
The requirements are specified conventionally in requirements.txt and setup.py, so they will be enforced at installation time. Additionally, the installation process installs the scripts as executables.
Alternatively, the package can be installed from the git repository:
python3 -m pip install git+https://github.com/niaid/tomojs-pytools.git@v1.3.2
Note for Mac M1 development: The imagecodec package does not provide a Mac OSX ARM binary at this time. The current workaround is to use an x86_64 python version on the M1 Mac in order to use the exiting binaries on PyPi.