[query] Python 3.8, Numpy 1.24.2, Bokeh 3.x.x, fixes to plots.py, fixes to req generation#12929
Merged
Merged
Conversation
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.
added 2 commits
April 26, 2023 22:59
daniel-goldstein
approved these changes
Apr 28, 2023
daniel-goldstein
left a comment
daniel-goldstein
left a comment
Contributor
There was a problem hiding this comment.
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
jmarshall
reviewed
Apr 30, 2023
| hurry.filesize>=0.9,<1 | ||
| Jinja2==3.0.3 | ||
| numpy<2 | ||
| pandas>=1.3.0,<2.1 |
Contributor
There was a problem hiding this comment.
Does this requirement (on line 12/13) also need adjusting to pandas>=2,<3?
daniel-goldstein
previously requested changes
May 1, 2023
daniel-goldstein
left a comment
daniel-goldstein
left a comment
Contributor
There was a problem hiding this comment.
Need to change pandas version in hall requirements
daniel-goldstein
approved these changes
May 1, 2023
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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.