maint(test): suppress warnings from the test suite #23745

oscarbenjamin · 2022-07-08T18:17:45Z

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#23061

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oscarbenjamin · 2022-07-10T13:06:09Z

sympy/printing/aesaracode.py

@@ -139,7 +139,7 @@ def _get_or_create(self, s, name=None, dtype=None, broadcastable=None):
        if key in self.cache:
            return self.cache[key]

-        value = aet.tensor(name=name, dtype=dtype, broadcastable=broadcastable)
+        value = aet.tensor(name=name, dtype=dtype, shape=broadcastable)


@brandonwillard is this change safe for both Theano and Aesara?

Also another warning that I haven't managed to suppress yet:

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/aesara/link/c/lazylinker_c.py", line 129, in <module> code = open(cfile).read() ResourceWarning: unclosed file <_io.TextIOWrapper name='/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/aesara/link/c/c_code/lazylinker_c.c' mode='r' encoding='UTF-8'>

The complaint is about not using with but it's coming from the Aesara code.

@brandonwillard is this change safe for both Theano and Aesara?

No, it won't work for Theano.

Also another warning that I haven't managed to suppress yet:

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/aesara/link/c/lazylinker_c.py", line 129, in <module> code = open(cfile).read() ResourceWarning: unclosed file <_io.TextIOWrapper name='/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/aesara/link/c/c_code/lazylinker_c.c' mode='r' encoding='UTF-8'>

The complaint is about not using with but it's coming from the Aesara code.

We can create an Aesara issue for that, but let's see if we can reproduce it in isolation first.

No, it won't work for Theano.

Thanks. I made a spinout PR from this one that included that change but I guess I'll need to revert that and give this more thought: https://github.com/sympy/sympy/pull/23754/files#r917456138

let's see if we can reproduce it in isolation first.

The warning is seen with -Werror as in

$ python -Werror myscript.py

or alternatively

$ PYTHONWARNINGS=error python myscript.py

Either way the line code = open(cfile).read() should be changed to use with if that line is in the codebase.

I've opened a PR to clean up those issues: aesara-devs/aesara#1049.

https://github.com/aesara-devs/aesara/releases/tag/rel-2.7.7

Thanks.

Another one that I often see is this:

>>> import aesara WARNING (aesara.tensor.blas): Using NumPy C-API based implementation for BLAS functions.

That one is a logger warning rather than a Warning warning so it isn't filtered in the usual way. There is some code here to hide it:

sympy/sympy/printing/tests/test_aesaracode.py

Lines 18 to 21 in d983589

aesaralogger = logging.getLogger('aesara.configdefaults')

aesaralogger.setLevel(logging.CRITICAL)

aesara = import_module('aesara')

aesaralogger.setLevel(logging.WARNING)

The problem is that the warning is emitted on import so we would need to guard every place that imports aesara in case some other place imports it first:

sympy/sympy/testing/runtests.py

Line 704 in d983589

if import_module('aesara') is None:

I'm not sure what the best approach is for that warning but emitting a visible message to stderr during import doesn't seem great. Note that the line of code above is just testing to see if aesara is installed but that triggers the warning.

oscarbenjamin · 2022-07-10T13:09:58Z

sympy/plotting/tests/test_plot.py

+        # XXX: This should be fixed in experimental_lambdify or by using
+        # ordinary lambdify so that it doesn't warn. The error results from
+        # passing an array of values as the integration limit.
+        #
+        # UserWarning: The evaluation of the expression is problematic. We are
+        # trying a failback method that may still work. Please report this as a
+        # bug.
+        with ignore_warnings(UserWarning):
+            p.save(os.path.join(tmpdir, filename))


I'm not sure if there is already an issue for this but I seem to remember a PR that attempted to fix this.

The issue is #19996

oscarbenjamin · 2022-07-10T13:13:21Z

sympy/plotting/tests/test_textplot.py

-    assert list(textplot_str(sqrt(x), -1, 1)) == lines
+    # RuntimeWarning: invalid value encountered in sqrt
+    with ignore_warnings(RuntimeWarning):
+        assert list(textplot_str(sqrt(x), -1, 1)) == lines


Maybe the plotting module should use np.errstate if it expects to deliberately pass invalid values:
https://numpy.org/doc/stable/reference/generated/numpy.errstate.html

oscarbenjamin · 2022-07-10T13:16:28Z

sympy/external/tests/test_numpy.py

@@ -138,9 +139,11 @@ def test_Matrix1():

 def test_Matrix2():
    m = Matrix([[x, x**2], [5, 2/x]])
-    assert (matrix(m.subs(x, 2)) == matrix([[2, 4], [5, 1]])).all()
+    with ignore_warnings(PendingDeprecationWarning):
+        assert (matrix(m.subs(x, 2)) == matrix([[2, 4], [5, 1]])).all()


As far as I can tell all the tests involving np.matrix are just checking that it can be used with sympy. It doesn't look like sympy actually uses np.matrix for anything.

oscarbenjamin · 2022-07-10T13:17:26Z

sympy/external/tests/test_codegen.py

-                stderr=subprocess.STDOUT)
-        if retcode != 0:
-            return False
+    with open(os.devnull, 'w') as null:


I found cases where with should be used to ensure that files are closed properly. That should probably be reviewed in bulk across the codebase.

oscarbenjamin · 2022-07-10T13:21:50Z

sympy/external/tests/test_autowrap.py

+    # The ufuncify function generates a setup.py that uses distutils which
+    # is now deprecated:
+    #
+    # DeprecationWarning: The distutils package is deprecated and slated
+    # for removal in Python 3.12. Use setuptools or check PEP 632 for
+    # potential alternatives


Places where distutils is used:

$ git grep distutils bin/test_travis.sh:import distutils.sysconfig bin/test_travis.sh:with open(os.path.join(distutils.sysconfig.get_python_lib(), 'coverage.pth'), 'w') as pth: doc/src/modules/utilities/autowrap.rst:system installed f2py command. The Cython backend runs a distutils setup script release/fabfile.py: distutils_check() release/fabfile.py:def distutils_check(): setup.py:This uses Distutils (https://python.org/sigs/distutils-sig/) the standard setup.py:from distutils.command.sdist import sdist setup.py: from distutils.core import setup, Command setup.py: user_options = [] # distutils complains if this is not here. setup.py: def initialize_options(self): # distutils wants this setup.py: user_options = [] # distutils complains if this is not here. setup.py: def initialize_options(self): # distutils wants this setup.py: user_options = [] # distutils complains if this is not here. setup.py: def initialize_options(self): # distutils wants this sympy/external/importtools.py: # Simplified from distutils.version.LooseVersion which was deprecated in sympy/utilities/_compilation/compilation.py: # from distutils/command/build_ext.py: sympy/utilities/_compilation/util.py: # distutils: language = c++ sympy/utilities/autowrap.py: from distutils.core import setup sympy/utilities/autowrap.py: from distutils.extension import Extension sympy/utilities/autowrap.py: The following optional parameters get passed to ``distutils.Extension`` sympy/utilities/autowrap.py: from numpy.distutils.misc_util import Configuration sympy/utilities/autowrap.py: from numpy.distutils.core import setup sympy/utilities/tests/test_autowrap.py: from distutils.core import setup sympy/utilities/tests/test_autowrap.py: from distutils.extension import Extension sympy/utilities/tests/test_autowrap.py: from distutils.core import setup sympy/utilities/tests/test_autowrap.py: from distutils.extension import Extension sympy/utilities/tests/test_autowrap.py: from distutils.core import setup sympy/utilities/tests/test_autowrap.py: from distutils.extension import Extension

Travis and fabfile don't matter.

The main setup.py should be removed and replaced with pyproject.toml.

The external module only shows up because of a comment.

The problematic cases are all in autowrap.

The autowrap module needs to be changed to not use distutils or numpy.distutils which are both deprecated. It isn't immediately clear to me what the appropriate replacements for these are for a nontrivial setup.py that actually needs to compile some C code.

oscarbenjamin · 2022-07-10T13:24:55Z

examples/all.py

 def load_example_module(example):
    """Loads modules based upon the given package name"""
-    mod = __import__(example)
-    return mod
+    from importlib import import_module
+
+    exmod = os.path.split(EXAMPLE_DIR)[1]
+    modname = exmod + '.' + example
+    return import_module(modname)


I'm not sure if this code is precisely equivalent but the previous code was somewhat over engineered for what actually needs to be done here.

oscarbenjamin · 2022-07-10T13:25:48Z

sympy/core/tests/test_args.py

+            # aesaracode imports aesara which imports distutils which warns:
+            #
+            # DeprecationWarning: The distutils package is deprecated and
+            # slated for removal in Python 3.12. Use setuptools or check PEP
+            # 632 for potential alternatives
+            if submodule == 'sympy.printing.aesaracode':
+                warnings = DeprecationWarning
+            else:
+                warnings = ()


Lots of places where we need to suppress warnings from Aesara. This can be reverted if Aesara stops using distutils.

I don't think we have an issue for this change, but I can quickly make a PR regardless.

There is aesara-devs/aesara#758

Oh, I was thinking of just plain distutils. I've already created a PR for that, though: aesara-devs/aesara#1050.

It's both kinds of distutils :)

The numpy.distutils deprecation is just a bit louder:

$ python -Werror -c 'import aesara' Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/__init__.py", line 126, in <module> from aesara import scalar, tensor File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/scalar/__init__.py", line 1, in <module> from .basic import * File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/scalar/basic.py", line 25, in <module> from aesara import printing File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/printing.py", line 20, in <module> from aesara.compile import Function, SharedVariable File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/compile/__init__.py", line 19, in <module> from aesara.compile.mode import ( File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/compile/mode.py", line 28, in <module> from aesara.link.c.basic import CLinker, OpWiseCLinker File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/link/c/basic.py", line 26, in <module> from aesara.link.c.cmodule import ( File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/aesara/link/c/cmodule.py", line 25, in <module> import numpy.distutils File "/home/oscar/current/sympy/sympy.git/38venv/lib/python3.8/site-packages/numpy/distutils/__init__.py", line 31, in <module> warnings.warn("\n\n" DeprecationWarning: `numpy.distutils` is deprecated since NumPy 1.23.0, as a result of the deprecation of `distutils` itself. It will be removed for Python >= 3.12. For older Python versions it will remain present. It is recommended to use `setuptools < 60.0` for those Python versions. For more details, see: https://numpy.org/devdocs/reference/distutils_status_migration.html

All right, I added both to that PR.

oscarbenjamin · 2022-07-10T13:28:18Z

sympy/printing/tests/test_jax.py

+
+# Warning when importing jax (comes indirectly because jax imports
+# flatbuffers):
+#
+# DeprecationWarning: the imp module is deprecated in favour of importlib; see
+# the module's documentation for alternative uses
+with ignore_warnings(DeprecationWarning):
+    jax = import_module('jax')


google/flatbuffers#6957 (comment)

oscarbenjamin · 2022-07-10T13:29:27Z

sympy/printing/tests/test_tensorflow.py

+with ignore_warnings(DeprecationWarning):
+    # Warnings when importing tensorflow:
+    #
+    # DeprecationWarning: The distutils package is deprecated and slated for
+    # removal in Python 3.12. Use setuptools or check PEP 632 for potential
+    # alternatives
+    from sympy.printing.tensorflow import tensorflow_code
+    tf = tensorflow = import_module("tensorflow")


Similar to Aesara. When tensorflow stops using distutils these kinds of changes can be reverted.

oscarbenjamin · 2022-07-10T13:31:05Z

sympy/stats/sampling/tests/test_sample_continuous_rv.py

+    # XXX: Sampling with scipy under -Werror fails with
+    #
+    # RuntimeWarning: invalid value encountered in _cdf_single (vectorized)
+    #
+    # It isn't immediately clear if this is a bug in SciPy or SymPy.
+
+    with ignore_warnings(RuntimeWarning):
+        assert sample(Z) in Z.pspace.domain.set
+        sym, val = list(Z.pspace.sample().items())[0]


This warrants further investigation. When I checked in the debugger it looked as if sympy was passing valid inputs to scipy so I don't know if the warning arises from a bug in the scipy code. Need to distil a reproducer that doesn't involve the layers of sympy code that make this quite convoluted to debug.

oscarbenjamin · 2022-07-10T13:34:50Z

sympy/stats/tests/test_rv.py

+    # XXX: This should be fixed in lambdify to not use numpy functions from the
+    # scipy module.
+    #
+    # DeprecationWarning: scipy.greater is deprecated and will be removed
+    # in SciPy 2.0.0, use numpy.greater instead
+    # DeprecationWarning: scipy.sin is deprecated and will be removed in SciPy
+    # 2.0.0, use numpy.sin instead
+    with ignore_warnings(DeprecationWarning):
+        assert P(X + Y > 0, Y < 0, numsamples=10).is_number


This is a significant problem in lambdify. The scipy module has lots of functions that are really just imported from numpy like scipy.sin etc. These are all now deprecated. That means that lambdify should always prefer a function like numpy.sin over scipy.sin even if the module is set to "scipy".

I'm not sure how easy it is to fix this in lambdify because it isn't clear to me exactly how these names are picked from one module or the other e.g.:

In [8]: f = lambdify(x, sin(x), 'scipy') In [9]: print(inspect.getsource(f)) def _lambdifygenerated(x): return sin(x)

oscarbenjamin · 2022-07-10T13:35:57Z

sympy/testing/runtests.py

@@ -2030,7 +2057,7 @@ def findout_terminal_width():
                process = subprocess.Popen(['stty', '-a'],
                    stdout=subprocess.PIPE,
                    stderr=subprocess.PIPE)
-                stdout = process.stdout.read()
+                stdout, stderr = process.communicate()


Similar to using with open this is needed to ensure that the subprocess completes rather than becoming a dangling zombie process.

oscarbenjamin added this to the SymPy 1.11 milestone Jul 8, 2022

oscarbenjamin changed the title ~~maint(test): suppress warnigns from the test suite~~ maint(test): suppress warnings from the test suite Jul 8, 2022

oscarbenjamin force-pushed the pr_test_warnings branch 2 times, most recently from ead1b96 to 6c9db2a Compare July 10, 2022 13:01

oscarbenjamin commented Jul 10, 2022

View reviewed changes

oscarbenjamin mentioned this pull request Jul 10, 2022

Cleanup of warnings from the test suite #23754

Merged

brandonwillard mentioned this pull request Jul 12, 2022

Use context managers with open aesara-devs/aesara#1049

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oscarbenjamin force-pushed the pr_test_warnings branch from e1924c7 to 577ae22 Compare July 12, 2022 10:39

oscarbenjamin modified the milestones: SymPy 1.11, SymPy 1.12 Aug 8, 2022

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oscarbenjamin force-pushed the pr_test_warnings branch from 577ae22 to eb05e47 Compare January 26, 2023 20:15

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oscarbenjamin added 3 commits March 10, 2023 23:39

maint(test): suppress warnigns from the test suite

02e2c88

maint(ci): disallow warnings from tests in CI

38befa8

maint(test): suppress warnings from importing tensorflow

687425f

oscarbenjamin added 7 commits March 10, 2023 23:39

maint(test): do not pass PYTHONWARNINGS to subprocess

1926713

maint(test): suppress warnings from importing tensorflow

b1e2308

maint(test): silence warnings from importing jax

81cafd7

maint(test): ignore warnings when importing Aesara

e461353

test(external): suppress warnings in autowrap tests

61a41b1

maint(test): suppress warnings from importing numpy under pypy

be06c23

maint(test): suppress warnings from pymc

e643011

oscarbenjamin force-pushed the pr_test_warnings branch from eb05e47 to e643011 Compare March 10, 2023 23:39

oscarbenjamin modified the milestones: SymPy 1.12, SymPy 1.13 Mar 11, 2023

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maint(test): suppress warnings from the test suite #23745

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	aesaralogger = logging.getLogger('aesara.configdefaults')
	aesaralogger.setLevel(logging.CRITICAL)
	aesara = import_module('aesara')
	aesaralogger.setLevel(logging.WARNING)

maint(test): suppress warnings from the test suite #23745

maint(test): suppress warnings from the test suite #23745

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oscarbenjamin commented Jul 8, 2022

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