OG-Core
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Published
20 hours ago •
PSLmodels
PSLmodels
Test failures in Python 3.12.0 on Mac M1
I recently rebuilt the ogcore-dev environment and tried to run the OG-Core testing suite. It resulted in an error when collecting tests:
(ogcore-dev) jason.debacker@JDEBACKER-7 OG-Core % pytest
============================= test session starts ==============================
platform darwin -- Python 3.12.0, pytest-7.4.2, pluggy-1.3.0
rootdir: /Users/jason.debacker/repos/OG-Core
configfile: pytest.ini
testpaths: ./tests
plugins: xdist-3.3.1
collecting 239 items Fatal Python error: Illegal instruction
Current thread 0x0000000200983240 (most recent call first):
File "/Users/jason.debacker/anaconda3/envs/ogzaf-dev/lib/python3.11/site-packages/paramtools/sorted_key_list.py", line 53 in <lambda>
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/sortedcontainers/sortedlist.py", line 1878 in update
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/sortedcontainers/sortedlist.py", line 1750 in __init__
File "/Users/jason.debacker/repos/OG-Core/ogcore/utils.py", line 393 in safe_read_pickle
File "/Users/jason.debacker/repos/OG-Core/tests/test_output_plots.py", line 26 in <module>
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/assertion/rewrite.py", line 178 in exec_module
File "<frozen importlib._bootstrap>", line 929 in _load_unlocked
File "<frozen importlib._bootstrap>", line 1325 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 1354 in _find_and_load
File "<frozen importlib._bootstrap>", line 1381 in _gcd_import
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/importlib/__init__.py", line 90 in import_module
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/pathlib.py", line 567 in import_path
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/python.py", line 617 in _importtestmodule
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/python.py", line 528 in _getobj
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/python.py", line 310 in obj
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/python.py", line 545 in _inject_setup_module_fixture
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/python.py", line 531 in collect
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/runner.py", line 372 in <lambda>
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/runner.py", line 341 in from_call
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/runner.py", line 372 in pytest_make_collect_report
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/runner.py", line 547 in collect_one_node
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/main.py", line 842 in genitems
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/main.py", line 675 in perform_collect
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/main.py", line 335 in pytest_collection
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/main.py", line 324 in _main
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/main.py", line 271 in wrap_session
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/main.py", line 318 in pytest_cmdline_main
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/config/__init__.py", line 169 in main
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/lib/python3.12/site-packages/_pytest/config/__init__.py", line 192 in console_main
File "/Users/jason.debacker/anaconda3/envs/ogcore-dev/bin/pytest", line 10 in <module>
Extension modules: yaml._yaml, cytoolz.utils, cytoolz.itertoolz, cytoolz.functoolz, cytoolz.dicttoolz, cytoolz.recipes, psutil._psutil_osx, psutil._psutil_posix, markupsafe._speedups, tornado.speedups, msgpack._cmsgpack, lz4._version, lz4.block._block, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, _brotli, pyarrow.lib, pyarrow._hdfsio, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, pyarrow._compute, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.indexing, pandas._libs.index, pandas._libs.internals, pandas._libs.join, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, matplotlib._image, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.special.cython_special, scipy.stats._stats, scipy.stats.beta_ufunc, scipy.stats._boost.beta_ufunc, scipy.stats.binom_ufunc, scipy.stats._boost.binom_ufunc, scipy.stats.nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, scipy.stats.hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats.ncf_ufunc, scipy.stats._boost.ncf_ufunc, scipy.stats.ncx2_ufunc, scipy.stats._boost.ncx2_ufunc, scipy.stats.nct_ufunc, scipy.stats._boost.nct_ufunc, scipy.stats.skewnorm_ufunc, scipy.stats._boost.skewnorm_ufunc, scipy.stats.invgauss_ufunc, scipy.stats._boost.invgauss_ufunc, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._statlib, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, lz4.frame._frame (total: 176)
zsh: illegal hardware instruction pytest
I've not seen this before an a quick search didn't reveal an obvious solution.
Follow up. I've been able to run pytest tests/test_module_name.py for most modules. The only one I've noted giving an error like the above is test_parameter_plots.py. So perhaps issues with with M1, 3.12, and a package called there?
Following up on this issue... it appears the issue is with reading files that were saved via CloudPickle in versions of Python < 3.12.
I have no problems running the model generally, but when running tests, those test modules that import objects saved via CloudPickle (e.g., Specifications objects or tax functions of the mono form) such as test_parameter_plots.py and test_ouptut_tables.py, I get a failure:
(ogcore-dev) jason.debacker@JDEBACKER-8 OG-Core % pytest tests/test_parameter_plots.py
============================= test session starts ==============================
platform darwin -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0
rootdir: /Users/jason.debacker/repos/OG-Core
configfile: pytest.ini
plugins: cov-5.0.0, anyio-4.4.0, xdist-3.6.1
collecting ... zsh: trace trap pytest tests/test_parameter_plots.py
The lack of any traceback makes it not clear, but I if I comment out the lines reading in these CloudPickled files, I do get some tests collected and run (of course there is an error noting that I don't the the parameters object available since I didn't import it, but we can at least see that tests try to run):
(ogcore-dev) jason.debacker@JDEBACKER-8 OG-Core % pytest tests/test_parameter_plots.py
============================= test session starts ==============================
platform darwin -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0
rootdir: /Users/jason.debacker/repos/OG-Core
configfile: pytest.ini
plugins: cov-5.0.0, anyio-4.4.0, xdist-3.6.1
collected 1 item
tests/test_parameter_plots.py F [100%]
=================================== FAILURES ===================================
_____________________________ test_plot_imm_rates ______________________________
def test_plot_imm_rates():
fig = parameter_plots.plot_imm_rates(
> base_params.imm_rates,
base_params.start_year,
[base_params.start_year],
include_title=True,
)
E NameError: name 'base_params' is not defined
tests/test_parameter_plots.py:46: NameError
=========================== short test summary info ============================
FAILED tests/test_parameter_plots.py::test_plot_imm_rates - NameError: name 'base_params' is not defined
============================== 1 failed in 1.83s ===============================
We already have separate parameter files for Python 3.11 and Python 3.9/10:
if sys.version_info[1] < 11:
base_params = utils.safe_read_pickle(
os.path.join(CUR_PATH, "test_io_data", "model_params_baseline.pkl")
)
else:
base_params = utils.safe_read_pickle(
os.path.join(
CUR_PATH, "test_io_data", "model_params_baseline_v311.pkl"
)
)
Other times, we don't run certain parameterizations under a different Python version:
if sys.version_info[1] < 11:
test_list = [
(base_taxfunctions, 43, "DEP", "etr", True, None, None),
(base_taxfunctions, 43, "DEP", "etr", False, None, "Test title"),
(GS_nonage_spec_taxfunctions, None, "GS", "etr", True, None, None),
(base_taxfunctions, 43, "DEP", "etr", True, [micro_data], None),
(base_taxfunctions, 43, "DEP", "mtry", True, [micro_data], None),
(base_taxfunctions, 43, "DEP", "mtrx", True, [micro_data], None),
(mono_nonage_spec_taxfunctions, None, "mono", "etr", True, None, None),
]
id_list = [
"over_labinc=True",
"over_labinc=False",
"Non age-specific",
"with data",
"MTR capital income",
"MTR labor income",
"Mono functions",
]
else:
test_list = [
(base_taxfunctions, 43, "DEP", "etr", True, None, None),
(base_taxfunctions, 43, "DEP", "etr", False, None, "Test title"),
(GS_nonage_spec_taxfunctions, None, "GS", "etr", True, None, None),
(base_taxfunctions, 43, "DEP", "etr", True, [micro_data], None),
(base_taxfunctions, 43, "DEP", "mtry", True, [micro_data], None),
(base_taxfunctions, 43, "DEP", "mtrx", True, [micro_data], None),
]
id_list = [
"over_labinc=True",
"over_labinc=False",
"Non age-specific",
"with data",
"MTR capital income",
"MTR labor income",
]
@pytest.mark.parametrize(
"tax_funcs,age,tax_func_type,rate_type,over_labinc,data,title",
test_list,
ids=id_list,
)
def test_plot_2D_taxfunc(
tax_funcs, age, tax_func_type, rate_type, over_labinc, data, title
):
"""
Test of plot_2D_taxfunc
"""
if sys.version_info[1] < 11:
fig = parameter_plots.plot_2D_taxfunc(
2030,
2021,
[tax_funcs],
age=age,
tax_func_type=[tax_func_type],
rate_type=rate_type,
over_labinc=over_labinc,
data_list=data,
title=title,
)
assert fig
else:
assert True
@rickecon What do you want to do for Python 3.12? Create a third pkl file for parameters? Skip tests that require these Cloudpickled objects on 3.12? Note we may have to update this with each Python version we want to test against because CloudPickle is not really suited for long term storage due to changes in Python.