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[query] Python 3.8, Numpy 1.24.2, Bokeh 3.x.x, fixes to plots.py, fixes to req generation #12929
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CHANGELOG: Bokeh 3.x.x is now required which allows for compatibility with pandas 2.x.x. There were a lot of issues in this file that I tried to clean up. The mypy errors are now just things that are poorly typed by Bokeh. I also changed how manhattan plot hides irrelevant tooltip information. I made it an explicit argument to the `_get_scatter_plot_elements`. I verified the plots in the GWAS Tutorial look the same by eye. I also verified the tooltips look the same with a few spot checks. I also built the docs to ensure those were fine.
Bumps [numpy](https://github.com/numpy/numpy) from 1.21.6 to 1.24.2. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.21.6...v1.24.2) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
CHANGELOG: Hail no longer officially supports Python 3.7.
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This all looks fine but I added WIP so that we can replicate Ben's issue with the same version of python/our dependencies. Once that's done merge at your leisure
hail/python/requirements.txt
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decorator<5 | ||
Deprecated>=1.2.10,<1.3 | ||
dill>=0.3.1.1,<0.4 | ||
frozenlist>=1.3.1,<2 | ||
hurry.filesize>=0.9,<1 | ||
Jinja2==3.0.3 | ||
numpy<2 | ||
pandas>=1.3.0,<2.1 |
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Does this requirement (on line 12/13) also need adjusting to pandas>=2,<3
?
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Yes @danking
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Good catch thanks @jmarshall
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Need to change pandas version in hall requirements
CHANGELOG: Hail no longer officially supports Python 3.7.
Combines #12927 and #12908.
Many changes. All seem to be necessary together.
I fixed any new mypy errors or deprecation warnings. I also cleaned up plots.py (which isn't CI'd by mypy) because I was in there and it was a mess. I unified all our pip-tools versions. Require pandas 2 now. That requires Bokeh 3.x.x. Fix the pinned-requirements.txt dependencies so they reflect the actual necessary runtime harmony. Upgraded Sphinx. The method names lose their fixed-width styling but I think it looks fine. Version policy added. Updating everything means Jinja2 can jump to the latest version too. Numpy deprecated some of its types, using
_
gets rid of the warning.