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PGScatalog / PGS_Catalog

An open database of polygenic scores and relevant metadata needed to apply and evaluate them correctly.
Apache License 2.0
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Fix/downgrade numpy #376

Closed fyvon closed 3 months ago

fyvon commented 3 months ago

Just-released numpy 2.0.0 is causing the following error with pandas and needs to be downgraded to the previous version at the moment:

ImportError: Failed to import test module: test_import Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name import(name) File "/home/runner/work/PGS_Catalog/PGS_Catalog/curation/tests/test_import.py", line 2, in from curation.imports.curation import CurationImport File "/home/runner/work/PGS_Catalog/PGS_Catalog/curation/imports/curation.py", line 1, in import pandas as pd File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pandas/init.py", line 22, in from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pandas/compat/init.py", line 18, in from pandas.compat.numpy import ( File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pandas/compat/numpy/init.py", line 4, in from pandas.util.version import Version File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pandas/util/init.py", line 2, in from pandas.util._decorators import ( # noqa:F401 File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pandas/util/_decorators.py", line 14, in from pandas._libs.properties import cache_readonly File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pandas/_libs/init.py", line 13, in from pandas._libs.interval import Interval File "pandas/_libs/interval.pyx", line 1, in init pandas._libs.interval ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

fyvon commented 3 months ago

Pandas 2.2.2 now supports Numpy 2.0.0. To be upgraded later after proper testing.