[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.
daniel-goldstein
approved these changes
Apr 28, 2023
jmarshall
reviewed
Apr 30, 2023
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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Good catch thanks @jmarshall
daniel-goldstein
previously requested changes
May 1, 2023
daniel-goldstein
approved these changes
May 1, 2023
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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.