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Failing mypy checks

See original GitHub issue

I’m not entirely sure if I’m doing something wrong now or there has been some change to another package that perhaps broke mypy checks. In https://github.com/pystatgen/sgkit/pull/653 I had no trouble with it, but now even with a clean environment I get the errors below.

pre-commit failure

$ pre-commit run --all-files
Check for merge conflicts................................................Passed
Debug Statements (Python)................................................Passed
Mixed line ending........................................................Passed
Check for case conflicts.................................................Passed
Check Yaml...............................................................Passed
isort....................................................................Passed
black....................................................................Passed
flake8...................................................................Passed
mypy.....................................................................Failed
- hook id: mypy
- exit code: 1

sgkit/stats/utils.py:71: error: unused 'type: ignore' comment
sgkit/tests/test_stats_utils.py:25: error: unused 'type: ignore' comment
sgkit/io/vcf/vcf_partition.py:161: error: unused 'type: ignore' comment
sgkit/io/vcf/vcf_partition.py:164: error: unused 'type: ignore' comment
sgkit/utils.py:101: error: unused 'type: ignore' comment
sgkit/utils.py:302: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:7: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/stats/regenie.py:85: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:87: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:88: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:89: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:92: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:133: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:161: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:163: error: unused 'type: ignore' comment
sgkit/stats/regenie.py:487: error: unused 'type: ignore' comment
sgkit/window.py:231: error: unused 'type: ignore' comment
sgkit/window.py:244: error: unused 'type: ignore' comment
sgkit/window.py:245: error: unused 'type: ignore' comment
sgkit/window.py:246: error: unused 'type: ignore' comment
sgkit/window.py:320: error: unused 'type: ignore' comment
sgkit/window.py:322: error: unused 'type: ignore' comment
sgkit/window.py:348: error: unused 'type: ignore' comment
sgkit/window.py:406: error: unused 'type: ignore' comment
sgkit/window.py:429: error: unused 'type: ignore' comment
sgkit/io/utils.py:38: error: unused 'type: ignore' comment
sgkit/io/utils.py:157: error: unused 'type: ignore' comment
sgkit/io/utils.py:205: error: unused 'type: ignore' comment
sgkit/stats/popgen.py:794: error: unused 'type: ignore' comment
sgkit/stats/hwe.py:6: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/stats/ld.py:158: error: unused 'type: ignore' comment
sgkit/testing.py:73: error: unused 'type: ignore' comment
sgkit/testing.py:74: error: unused 'type: ignore' comment
sgkit/tests/test_pca.py:8: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/tests/test_pca.py:33: error: unused 'type: ignore' comment
sgkit/tests/test_aggregation.py:108: error: unused 'type: ignore' comment
sgkit/tests/test_aggregation.py:218: error: unused 'type: ignore' comment
sgkit/tests/test_aggregation.py:253: error: unused 'type: ignore' comment
sgkit/tests/test_mis.py:8: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/io/bgen/bgen_reader.py:26: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/io/bgen/bgen_reader.py:149: error: unused 'type: ignore' comment
sgkit/io/bgen/bgen_reader.py:330: error: unused 'type: ignore' comment
sgkit/tests/test_pc_relate.py:9: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/tests/test_regenie.py:18: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/tests/test_regenie.py:345: error: unused 'type: ignore' comment
sgkit/tests/test_regenie.py:394: error: unused 'type: ignore' comment
sgkit/io/plink/plink_reader.py:10: error: Module 'numpy.typing' has no attribute 'NDArray'  [attr-defined]
sgkit/io/plink/plink_reader.py:88: error: unused 'type: ignore' comment
sgkit/tests/io/vcf/test_vcf_reader.py:548: error: unused 'type: ignore' comment
sgkit/tests/io/vcf/test_vcf_reader.py:553: error: unused 'type: ignore' comment
sgkit/tests/io/bgen/test_bgen_reader.py:134: error: unused 'type: ignore' comment
validation/gwas/method/pc_relate/validate_pc_relate.py:36: error: unused 'type: ignore' comment
Found 52 errors in 21 files (checked 98 source files)

I created a clean environment with:

conda create -n sgkit python=3.8
conda activate sgkit
git clone https://github.com/pystatgen/sgkit
cd sgkit
pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt

Any ideas if this is me doing something wrong or it’s possibly due to upstream changes elsewhere?

Issue Analytics

State:
Created 2 years ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

pentschevcommented, Sep 10, 2021

Yes, sorry I didn’t copy/paste here, instead I rebuilt the steps and missed the conda activate sgkit while writing this issue, but I had sgkit activated for the next steps. Also fixed that in the description now.

0reactions

pentschevcommented, Sep 10, 2021

I’m not experienced with mypy in general, but it does indeed looks a bit off. What I noticed now is that whenever I changed numpy==x.xx.x, pre-commit would install that new NumPy version. When I actually added numpy>=1.21.2, there was no package being installed but the number of errors reduced dramatically:

$ pre-commit run --all-files
Check for merge conflicts................................................Passed
Debug Statements (Python)................................................Passed
Mixed line ending........................................................Passed
Check for case conflicts.................................................Passed
Check Yaml...............................................................Passed
isort....................................................................Passed
black....................................................................Passed
flake8...................................................................Passed
mypy.....................................................................Failed
- hook id: mypy
- exit code: 1

sgkit/stats/popgen.py:794: error: unused 'type: ignore' comment
sgkit/tests/test_aggregation.py:108: error: unused 'type: ignore' comment
sgkit/tests/test_aggregation.py:218: error: unused 'type: ignore' comment
sgkit/tests/test_aggregation.py:253: error: unused 'type: ignore' comment
Found 4 errors in 2 files (checked 98 source files)

I’ve added that change and the fix for the 4 errors above in https://github.com/pystatgen/sgkit/pull/664 .