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Bump PyTensor dependency and support Python 3.12 #7203

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merged 4 commits into from
Mar 22, 2024
Merged

Bump PyTensor dependency and support Python 3.12 #7203

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6a1862a
Bump PyTensor dependency
ricardoV94 Mar 20, 2024
5e89b69
Test on Python 3.12
ricardoV94 Mar 20, 2024
64e99fe
Ignore DeprecationWarning triggered by arviz
ricardoV94 Mar 20, 2024
fc98122
Remove filter for solved warning
ricardoV94 Mar 22, 2024
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8 changes: 4 additions & 4 deletions .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ jobs:
matrix:
os: [ubuntu-20.04]
floatx: [float64]
python-version: ["3.11"]
python-version: ["3.12"]
test-subset:
- |
tests/test_util.py
Expand Down Expand Up @@ -263,7 +263,7 @@ jobs:
matrix:
os: [macos-latest]
floatx: [float64]
python-version: ["3.10"]
python-version: ["3.12"]
test-subset:
- |
tests/sampling/test_parallel.py
Expand Down Expand Up @@ -342,7 +342,7 @@ jobs:
matrix:
os: [ubuntu-20.04]
floatx: [float64]
python-version: ["3.11"]
python-version: ["3.12"]
test-subset:
- tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
fail-fast: false
Expand Down Expand Up @@ -410,7 +410,7 @@ jobs:
matrix:
os: [windows-latest]
floatx: [float32]
python-version: ["3.11"]
python-version: ["3.12"]
test-subset:
- tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py tests/distributions/test_transform.py
fail-fast: false
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2 changes: 1 addition & 1 deletion conda-envs/environment-dev.yml
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Expand Up @@ -14,7 +14,7 @@ dependencies:
- numpy>=1.15.0
- pandas>=0.24.0
- pip
- pytensor>=2.18.1,<2.19
- pytensor>=2.19,<2.20
- python-graphviz
- networkx
- scipy>=1.4.1
Expand Down
2 changes: 1 addition & 1 deletion conda-envs/environment-docs.yml
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Expand Up @@ -12,7 +12,7 @@ dependencies:
- numpy>=1.15.0
- pandas>=0.24.0
- pip
- pytensor>=2.18.1,<2.19
- pytensor>=2.19,<2.20
- python-graphviz
- scipy>=1.4.1
- typing-extensions>=3.7.4
Expand Down
6 changes: 3 additions & 3 deletions conda-envs/environment-jax.yml
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Expand Up @@ -13,15 +13,15 @@ dependencies:
- h5py>=2.7
# Jaxlib version must not be greater than jax version!
- blackjax>=1.0.0
- jaxlib==0.4.14
- jax==0.4.16
- jaxlib==0.4.23
- jax==0.4.23
- libblas=*=*mkl
- mkl-service
- numpy>=1.15.0
- numpyro>=0.8.0
- pandas>=0.24.0
- pip
- pytensor>=2.18.1,<2.19
- pytensor>=2.19,<2.20
- python-graphviz
- networkx
- scipy>=1.4.1
Expand Down
2 changes: 1 addition & 1 deletion conda-envs/environment-test.yml
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Expand Up @@ -17,7 +17,7 @@ dependencies:
- numpy>=1.15.0
- pandas>=0.24.0
- pip
- pytensor>=2.18.1,<2.19
- pytensor>=2.19,<2.20
- python-graphviz
- networkx
- scipy>=1.4.1
Expand Down
2 changes: 1 addition & 1 deletion conda-envs/windows-environment-dev.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ dependencies:
- numpy>=1.15.0
- pandas>=0.24.0
- pip
- pytensor>=2.18.1,<2.19
- pytensor>=2.19,<2.20
- python-graphviz
- networkx
- scipy>=1.4.1
Expand Down
2 changes: 1 addition & 1 deletion conda-envs/windows-environment-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ dependencies:
- numpy>=1.15.0
- pandas>=0.24.0
- pip
- pytensor>=2.18.1,<2.19
- pytensor>=2.19,<2.20
- python-graphviz
- networkx
- scipy>=1.4.1
Expand Down
2 changes: 1 addition & 1 deletion pymc/sampling/forward.py
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Expand Up @@ -200,7 +200,7 @@ def shared_value_matches(var):
# Walk the graph from inputs to outputs and tag the volatile variables
nodes: list[Variable] = general_toposort(
fg.outputs, deps=lambda x: x.owner.inputs if x.owner else []
)
) # type: ignore
volatile_nodes: set[Any] = set()
for node in nodes:
if (
Expand Down
2 changes: 1 addition & 1 deletion requirements-dev.txt
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Expand Up @@ -18,7 +18,7 @@ numpydoc
pandas>=0.24.0
polyagamma
pre-commit>=2.8.0
pytensor>=2.18.1,<2.19
pytensor>=2.19,<2.20
pytest-cov>=2.5
pytest>=3.0
scipy>=1.4.1
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -4,6 +4,6 @@ cloudpickle
fastprogress>=0.2.0
numpy>=1.15.0
pandas>=0.24.0
pytensor>=2.18.1,<2.19
pytensor>=2.19,<2.20
scipy>=1.4.1
typing-extensions>=3.7.4
1 change: 1 addition & 0 deletions setup.py
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Expand Up @@ -33,6 +33,7 @@
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"License :: OSI Approved :: Apache Software License",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering",
Expand Down
12 changes: 10 additions & 2 deletions tests/backends/test_arviz.py
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Expand Up @@ -32,7 +32,11 @@
from pymc.exceptions import ImputationWarning

# Turn all warnings into errors for this module
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@maresb maresb Mar 22, 2024 •
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My suggestion was to also inline this. (Turn all warnings into errors for this module)

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But now I'm getting to the nittiest of nits. :)

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@ricardoV94 ricardoV94 Mar 22, 2024 •
edited
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But that's why the filterwarnings is there in the first place? Without the temporary filters it looks like

# Turn all warnings ...
pytest.mark.filterwarnings("error")

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Do I misunderstand how filterwarnings works? The arguments get stacked, right?

pytestmark = pytest.mark.filterwarnings(
    # Turn all warnings into errors for this module
    "error",
    # except those related to https://github.com/arviz-devs/arviz/issues/2327
    "ignore:datetime.datetime.utcnow():DeprecationWarning",
)

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@ricardoV94 ricardoV94 Mar 22, 2024 •
edited
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My point is that, without the temporary ignores, it makes more sense to have the comment above the call. That also explains why the call is there in the first place.

# Turn all warnings ...
pytest.mark.filterwarnings("error")

Makes more sense than

pytest.mark.filterwarnings(
  # Turn all warnings ...
  "error",
)

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I'm gonna take the nitpick hint and merge as is

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https://en.wikipedia.org/wiki/Law_of_triviality

pytestmark = pytest.mark.filterwarnings("error")
pytestmark = pytest.mark.filterwarnings(
"error",
# Related to https://github.com/arviz-devs/arviz/issues/2327
"ignore:datetime.datetime.utcnow():DeprecationWarning",
)


@pytest.fixture(scope="module")
Expand Down Expand Up @@ -672,13 +676,17 @@ def test_include_transformed(self):
)
assert "p_interval__" in inference_data.posterior

@pytest.mark.filterwarnings(
"error",
# Related to https://github.com/arviz-devs/arviz/issues/2327
"ignore:datetime.datetime.utcnow():DeprecationWarning",
)
@pytest.mark.parametrize("chains", (1, 2))
def test_single_chain(self, chains):
# Test that no UserWarning is raised when sampling with NUTS defaults

# When this test was added, a `UserWarning: More chains (500) than draws (1)` used to be issued
# when sampling with a single chain
warnings.simplefilter("error")
with pm.Model():
pm.Normal("x")
pm.sample(chains=chains, return_inferencedata=True)
Expand Down
7 changes: 5 additions & 2 deletions tests/distributions/test_timeseries.py
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Expand Up @@ -47,8 +47,11 @@
from pymc.testing import assert_support_point_is_expected, select_by_precision

# Turn all warnings into errors for this module
# Ignoring NumPy deprecation warning tracked in https://github.com/pymc-devs/pytensor/issues/146
pytestmark = pytest.mark.filterwarnings("error", "ignore: NumPy will stop allowing conversion")
pytestmark = pytest.mark.filterwarnings(
"error",
# Related to https://github.com/arviz-devs/arviz/issues/2327
"ignore:datetime.datetime.utcnow():DeprecationWarning",
)


class TestRandomWalk:
Expand Down
2 changes: 1 addition & 1 deletion tests/sampling/test_mcmc_external.py
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Expand Up @@ -47,7 +47,7 @@ def test_external_nuts_sampler(recwarn, nuts_sampler):
warns = {
(warn.category, warn.message.args[0])
for warn in recwarn
if warn.category is not FutureWarning
if warn.category not in (FutureWarning, DeprecationWarning)
}
expected = set()
if nuts_sampler == "nutpie":
Expand Down
22 changes: 17 additions & 5 deletions tests/variational/test_inference.py
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Expand Up @@ -172,7 +172,13 @@ def test_fit_oo(inference, fit_kwargs, simple_model_data):
warn_ctxt = nullcontext()

with warn_ctxt:
trace = inference.fit(**fit_kwargs).sample(10000)
with warnings.catch_warnings():
# Related to https://github.com/arviz-devs/arviz/issues/2327
warnings.filterwarnings(
"ignore", message="datetime.datetime.utcnow()", category=DeprecationWarning
)

trace = inference.fit(**fit_kwargs).sample(10000)
mu_post = simple_model_data["mu_post"]
d = simple_model_data["d"]
np.testing.assert_allclose(np.mean(trace.posterior["mu"]), mu_post, rtol=0.05)
Expand Down Expand Up @@ -207,10 +213,16 @@ def test_fit_start(inference_spec, simple_model):
expected_warning = observed_value.name.startswith("minibatch")
with warnings.catch_warnings(record=True) as record:
warnings.simplefilter("always")
try:
trace = inference.fit(n=0).sample(10000)
except NotImplementedInference as e:
pytest.skip(str(e))
with warnings.catch_warnings():
# Related to https://github.com/arviz-devs/arviz/issues/2327
warnings.filterwarnings(
"ignore", message="datetime.datetime.utcnow()", category=DeprecationWarning
)

try:
trace = inference.fit(n=0).sample(10000)
except NotImplementedInference as e:
pytest.skip(str(e))

if expected_warning:
assert len(record) > 0
Expand Down
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