Update vcfpy dependency to a newer version#84
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chrisamiller
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chrisamiller
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It seems odd that there isn't a cleaner way to do the whole repeated if self.REGNERATE_TEST_DATA thing, but I don't have one off the top of my head, so seems fine to me.
| strategy: | ||
| matrix: | ||
| python-version: ["3.8", "3.9", "3.10", "3.11"] | ||
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] |
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Should we be bumping this list to support later versions (up to 3.14) now?
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Sure. We might run into some dependency incompatibility so we'd need to decide how to best resolve them.
| }, | ||
| install_requires=[ | ||
| 'vcfpy==0.12.3', | ||
| 'vcfpy==0.13.8', |
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should we bump this to the newest (0.14.2) at this point?
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I feel like there was some reason to pin this version but I don't remember. I think I was trying to keep it in line with what pVACtools uses (which isn't really required). There might also be some incompatibility with python versions and/or other dependencies.
| vcf_readcount_annotator.main(command) | ||
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| self.assertTrue(cmp(os.path.join(self.test_data_dir, 'complex_indel.readcount.vcf.gz'), os.path.join(temp_path.name, 'input.readcount.vcf.gz'))) | ||
| if self.REGENERATE_TEST_DATA: |
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Do all tests now need to follow this REGENERATE_TEST_DATA pattern? If so, I can help hack on those...
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it's not required but you're welcome to make that change.
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This updated VCFpy version no longer encodes certain special characters so a lot of test files are updated to reflect this. This update also add python 3.12 as a test python version for the GitHub action.