Fix bug with multiple regions in PCA and snp_allele_counts #338
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alimanfoo
commented
Feb 22, 2023
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alimanfoo
commented
- Resolves Anopheles PCA cannot handle list of regions #336
- Also resolves Better caching for Ag3.pca() #266 along the way
- Also upgrades pre-commit hooks because of install problems on CI
alimanfoo
commented
Feb 22, 2023
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| # whitespace before ':' - doesn't work well with black | ||
| E203 | ||
| # module level import not at top of file | ||
| E402 | ||
| # line too long - let black worry about that | ||
| E501 | ||
| # do not assign a lambda expression, use a def | ||
| E731 | ||
| # line break before binary operator | ||
| W503 |
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This is needed because of upgrading flake8 in pre-commit config.
alimanfoo
commented
Feb 22, 2023
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| # https://pre-commit.com/ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.3.0 | ||
| rev: v4.4.0 | ||
| hooks: | ||
| - id: trailing-whitespace | ||
| - id: end-of-file-fixer | ||
| - id: check-yaml | ||
| # isort should run before black as black sometimes tweaks the isort output | ||
| - repo: https://github.com/pycqa/isort | ||
| rev: 5.10.1 | ||
| rev: 5.12.0 | ||
| hooks: | ||
| - id: isort | ||
| # https://github.com/python/black#version-control-integration | ||
| - repo: https://github.com/psf/black | ||
| rev: 22.10.0 | ||
| rev: 23.1.0 | ||
| hooks: | ||
| - id: black | ||
| - repo: https://github.com/keewis/blackdoc | ||
| rev: v0.3.8 | ||
| hooks: | ||
| - id: blackdoc | ||
| - repo: https://github.com/pycqa/flake8 | ||
| rev: 5.0.4 | ||
| rev: 6.0.0 | ||
| hooks: | ||
| - id: flake8 |
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Made these upgrades because CI was failing with problems installing the pre-commit hooks.
alimanfoo
commented
Feb 22, 2023
| @@ -4494,7 +4519,7 @@ def _read_cohort_metadata(self, *, sample_set): | |||
| }, | |||
| inplace=True, | |||
| ) | |||
| except FileNotFoundError: | |||
| except Exception: | |||
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This exception seems to have changed, needed to broaden.
leehart
approved these changes
Feb 23, 2023
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LGTM.
Thanks for the helpful inline comments @alimanfoo . How do you do that?
No worries - I just go into the files tab and add single comments, a bit like doing a code review on my own PR. |
alimanfoo
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