Numpy v2 compat #418
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Numpy v2 compat #418
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alimanfoo
commented
Aug 28, 2024
alimanfoo
commented
- Upgrade Python dependency.
- Upgrade numpy build dependency.
Upgrade Python dependency. Upgrade numpy build dependency.
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Getting failures mostly caused by "ValueError: Unable to avoid copy while creating an array as requested." Will attempt to fix using np.asarray() as suggested. |
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Hello @alimanfoo! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-08-29 09:55:54 UTC |
alimanfoo
commented
Aug 29, 2024
| @@ -923,6 +923,7 @@ def test_roh_mhmm_0pct(self): | |||
| fraction_expected = 0.0 | |||
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| gv = np.zeros((4, 2), dtype=np.int16) | |||
| gv[0, 0] = 1 | |||
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This change required because previously the results of the roh_mhmm function were different under np1 and np2. It's not clear why, but noting.
alimanfoo
commented
Aug 29, 2024
Comment on lines
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| # - name: Test with doctest | ||
| # if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.numpy-version == '>=2' | ||
| # run: | | ||
| # pytest -v --cov=allel --doctest-modules allel | ||
| # coverage report -m | ||
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| - name: Build docs | ||
| if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' | ||
| run: | | ||
| cd docs && make html | ||
| # - name: Build docs | ||
| # if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.numpy-version == '>=2' | ||
| # run: | | ||
| # cd docs && make html |
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Disabling these extra tests as too many superficial doctest output changes under numpy v2, not worth maintaining.
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