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Remove SGMCMC and fix flaky mypy results #5631

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Merged
merged 3 commits into from
Mar 21, 2022
Merged

Remove SGMCMC and fix flaky mypy results #5631

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73b510b
Remove `BaseStochasticGradient` step method
michaelosthege Mar 20, 2022
b98bc44
Upgrade dependencies in pre-commit environment
michaelosthege Mar 20, 2022
319ec85
Ignore flaky sampling_jax.py mypy results
michaelosthege Mar 20, 2022
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Expand Up @@ -26,8 +26,8 @@ repos:
- types-filelock
- types-setuptools
- arviz
- aesara==2.4.0
- aeppl==0.0.26
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Oh great, even more places for the dependencies xD

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You can't imagine how delighted I was to learn that the greatness of YAML required me to add the dependencies in yet another place! </sarcasm>

- aesara==2.5.1
- aeppl==0.0.27
always_run: true
require_serial: true
pass_filenames: false
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2 changes: 1 addition & 1 deletion RELEASE-NOTES.md
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Expand Up @@ -15,7 +15,6 @@ We plan to get these working again, but at this point their inner workings have
- Timeseries distributions (see [#4642](https://github.com/pymc-devs/pymc/issues/4642))
- Nested Mixture distributions (see [#5533](https://github.com/pymc-devs/pymc/issues/5533))
- Elliptical slice sampling (see [#5137](https://github.com/pymc-devs/pymc/issues/5137))
- `BaseStochasticGradient` (see [#5138](https://github.com/pymc-devs/pymc/issues/5138))
- `pm.sample_posterior_predictive_w` (see [#4807](https://github.com/pymc-devs/pymc/issues/4807))
- Partially observed Multivariate distributions (see [#5260](https://github.com/pymc-devs/pymc/issues/5260))

Expand All @@ -28,6 +27,7 @@ Also check out the [milestones](https://github.com/pymc-devs/pymc/milestones) fo
All of the above apply to:

- BART was removed [#5566](https://github.com/pymc-devs/pymc/pull/5566). It is now available from [pymc-experimental](https://github.com/pymc-devs/pymc-experimental)
- `BaseStochasticGradient` was removed (see [#5630](https://github.com/pymc-devs/pymc/pull/5630))
- ⚠ The library is now named, installed and imported as "pymc". For example: `pip install pymc`.
- ⚠ Theano-PyMC has been replaced with Aesara, so all external references to `theano`, `tt`, and `pymc3.theanof` need to be replaced with `aesara`, `at`, and `pymc.aesaraf` (see [4471](https://github.com/pymc-devs/pymc/pull/4471)).
- `pm.Distribution(...).logp(x)` is now `pm.logp(pm.Distribution(...), x)`.
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2 changes: 1 addition & 1 deletion pymc/distributions/shape_utils.py
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Expand Up @@ -618,4 +618,4 @@ def find_size(

def rv_size_is_none(size: Variable) -> bool:
"""Check wether an rv size is None (ie., at.Constant([]))"""
return size.type.shape == (0,)
return size.type.shape == (0,) # type: ignore [attr-defined]
3 changes: 3 additions & 0 deletions pymc/sampling.py
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Expand Up @@ -45,6 +45,7 @@

from aesara.compile.mode import Mode
from aesara.graph.basic import Constant, Variable
from aesara.tensor import TensorVariable
from aesara.tensor.sharedvar import SharedVariable
from arviz import InferenceData
from fastprogress.fastprogress import progress_bar
Expand Down Expand Up @@ -1690,6 +1691,8 @@ def sample_posterior_predictive(
return trace
return {}

inputs: Sequence[TensorVariable]
input_names: Sequence[str]
if not hasattr(_trace, "varnames"):
inputs_and_names = [
(rv, rv.name)
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226 changes: 0 additions & 226 deletions pymc/step_methods/sgmcmc.py
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6 changes: 5 additions & 1 deletion scripts/run_mypy.py
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Expand Up @@ -159,7 +159,11 @@ def check_no_unexpected_results(mypy_lines: Iterator[str]):
print("\n".join(sorted(map(str, unexpected_failing))))
sys.exit(1)

if unexpected_passing:
if unexpected_passing == {"pymc/sampling_jax.py"}:
print("Letting you know that 'pymc/sampling_jax.py' unexpectedly passed.")
print("But this file is known to sometimes pass and sometimes not.")
print("Unless tried to resolve problems in sampling_jax.py just ignore this message.")
elif unexpected_passing:
print(f"{len(unexpected_passing)} files unexpectedly passed the type checks:")
print("\n".join(sorted(map(str, unexpected_passing))))
print("This is good news! Go to scripts/run-mypy.py and add them to the list.")
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