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Becksteinlab / kda

Python package used for the analysis of biochemical kinetic diagrams.
GNU General Public License v3.0
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MAINT: Pin `mpmath` to version 1.3.0 #82

Closed nawtrey closed 5 months ago

nawtrey commented 5 months ago

When running python setup.py test on a fresh install of kda an issue arises where sympy installs a pre-release of mpmath (see my comment):

Here is the output:

Test output ``` $ python setup.py test C:\Users\nikol\Anaconda3\envs\kda_fresh\Lib\site-packages\setuptools\__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) C:\Users\nikol\Anaconda3\envs\kda_fresh\Lib\site-packages\setuptools\dist.py:314: InformationOnly: Normalizing 'v0.2.0+4.g533d243' to '0.2.0+4.g533d243' self.metadata.version = self._normalize_version( running pytest C:\Users\nikol\Anaconda3\envs\kda_fresh\Lib\site-packages\setuptools\command\test.py:193: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! ir_d = dist.fetch_build_eggs(dist.install_requires) C:\Users\nikol\Anaconda3\envs\kda_fresh\Lib\site-packages\setuptools\command\test.py:194: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! tr_d = dist.fetch_build_eggs(dist.tests_require or []) C:\Users\nikol\Anaconda3\envs\kda_fresh\Lib\site-packages\setuptools\command\test.py:195: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! er_d = dist.fetch_build_eggs( running egg_info writing kda.egg-info\PKG-INFO writing dependency_links to kda.egg-info\dependency_links.txt writing requirements to kda.egg-info\requires.txt writing top-level names to kda.egg-info\top_level.txt reading manifest file 'kda.egg-info\SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'kda.egg-info\SOURCES.txt' running build_ext ============================= test session starts ============================= platform win32 -- Python 3.11.8, pytest-8.0.2, pluggy-1.4.0 rootdir: C:\Users\nikol\OneDrive\projects\kinetic_diagram_analysis\packages\kda plugins: cov-4.1.0, xdist-3.5.0, hypothesis-6.98.17 collected 21 items / 1 error =================================== ERRORS ==================================== ___________________ ERROR collecting kda/tests/test_kda.py ____________________ kda\tests\test_kda.py:13: in from kda import calculations, diagrams, graph_utils, expressions, ode, svd kda\calculations.py:25: in from sympy import logcombine c:\users\nikol\anaconda3\envs\kda_fresh\lib\site-packages\sympy-1.12-py3.11.egg\sympy\__init__.py:30: in from sympy.core.cache import lazy_function c:\users\nikol\anaconda3\envs\kda_fresh\lib\site-packages\sympy-1.12-py3.11.egg\sympy\core\__init__.py:9: in from .expr import Expr, AtomicExpr, UnevaluatedExpr c:\users\nikol\anaconda3\envs\kda_fresh\lib\site-packages\sympy-1.12-py3.11.egg\sympy\core\expr.py:4159: in from .mul import Mul c:\users\nikol\anaconda3\envs\kda_fresh\lib\site-packages\sympy-1.12-py3.11.egg\sympy\core\mul.py:2193: in from .numbers import Rational c:\users\nikol\anaconda3\envs\kda_fresh\lib\site-packages\sympy-1.12-py3.11.egg\sympy\core\numbers.py:4567: in _sympy_converter[type(mpmath.rational.mpq(1, 2))] = sympify_mpmath_mpq E AttributeError: module 'mpmath' has no attribute 'rational' ============================== warnings summary =============================== ..\..\..\..\..\anaconda3\envs\kda_fresh\lib\site-packages\mpmath-1.4.0a0-py3.11.egg\mpmath\ctx_mp.py:28 c:\users\nikol\anaconda3\envs\kda_fresh\lib\site-packages\mpmath-1.4.0a0-py3.11.egg\mpmath\ctx_mp.py:28: DeprecationWarning: mpnumeric is deprecated warnings.warn(f"{name} is deprecated", DeprecationWarning) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info =========================== ERROR kda/tests/test_kda.py - AttributeError: module 'mpmath' has no attribut... !!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! ========================= 1 warning, 1 error in 4.29s ========================= ```

As a temporary solution I'm going to pin mpmath to v1.3.0 so the tests can run successfully and we can finally resolve #70.

nawtrey commented 5 months ago

This ended up being an issue with using the deprecated python setup.py install, so I will close this.