Update Python-Bioformats dependency version #70
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- Use logging instead of the warning package when unable to import a Bioformats-related package - Reorganize package imports for greater consistency with the rest of the package
Provide a script based on the Javabridge build script to build custom wheels for Python-Bioformats. This customization allows the package to use packages build from the original Javabridge repository rather than the forked version renamed to Python-Javabridge currently required by Python-Bioformats. These repositories are reportedly compatible (see CellProfiler/python-javabridge#8 (comment)), but the forked Python-Javabridge has additional changes for finding Java installations and a more stringent NumPy requirement that would otherwise preclude Python 3.6.
Bump the Python-Bioformats package to 4.0.5. Use a custom wheel built to use Javabridge rather than Python-Javabridge to avoid the requirement for NumPy incompatible with Python 3.6 in the current Python-Javabridge wheel.
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The Python-Bioformats dependency has been pinned in MagellanMapper to v1.1.0 because of a heap space error encountered with later versions of the package when importing some large image files (see CellProfiler/python-bioformats#95). Since the Bio-Formats library included in this version of the package is relatively old (Bio-Formats v5.1.8 from 2016), this PR updates the package to bring in the current Bio-Formats version (v6.6.0). The library was tested on a large (40GB), multi-series CZI file that previously could not be loaded because of a JPEG-XR not supported error but now loads with this new library.
Python-Bioformats now depends on a fork of the original Javabridge package, named Python-Javabridge, pinned to its latest version. This latest version in turn requires NumPy 1.20, which has dropped Python 3.6 support. To maintain Python 3.6 compatibility, we have posted a custom wheel from a fork that uses that original Javabridge. This wheel thus can use the custom Javabridge wheels that we have previously posted to allow installation without a compiler or JDK and continues to work with Python >= 3.6. A simple Bash script used to build the wheel and based on the custom Javabridge wheel script is also included in this PR.