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Remove deprecated stuff #3906

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merged 4 commits into from
May 3, 2020
Merged

Remove deprecated stuff #3906

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ada2f2e
remove file which is not used
michaelosthege May 2, 2020
3b58d61
remove deprecated code
michaelosthege May 2, 2020
1de8d8e
repair tests and notebooks that used deprecated API
michaelosthege May 2, 2020
9bbfaf2
mention #3906
michaelosthege May 2, 2020
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14 changes: 0 additions & 14 deletions .readthedocs.yml
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This file was deleted.

32 changes: 0 additions & 32 deletions pymc3/sampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -368,36 +368,9 @@ def sample(
"""
model = modelcontext(model)

nuts_kwargs = kwargs.pop("nuts_kwargs", None)
if nuts_kwargs is not None:
warnings.warn(
"The nuts_kwargs argument has been deprecated. Pass step "
"method arguments directly to sample instead",
DeprecationWarning,
)
kwargs.update(nuts_kwargs)
step_kwargs = kwargs.pop("step_kwargs", None)
if step_kwargs is not None:
warnings.warn(
"The step_kwargs argument has been deprecated. Pass step "
"method arguments directly to sample instead",
DeprecationWarning,
)
kwargs.update(step_kwargs)

if cores is None:
cores = min(4, _cpu_count())

if "njobs" in kwargs:
cores = kwargs["njobs"]
warnings.warn(
"The njobs argument has been deprecated. Use cores instead.", DeprecationWarning
)
if "nchains" in kwargs:
chains = kwargs["nchains"]
warnings.warn(
"The nchains argument has been deprecated. Use chains instead.", DeprecationWarning
)
if chains is None:
chains = max(2, cores)
if isinstance(start, dict):
Expand All @@ -412,11 +385,6 @@ def sample(
random_seed = [np.random.randint(2 ** 30) for _ in range(chains)]
if not isinstance(random_seed, Iterable):
raise TypeError("Invalid value for `random_seed`. Must be tuple, list or int")
if "chain" in kwargs:
chain_idx = kwargs["chain"]
warnings.warn(
"The chain argument has been deprecated. Use chain_idx instead.", DeprecationWarning
)

if start is not None:
for start_vals in start:
Expand Down
15 changes: 0 additions & 15 deletions pymc3/stats/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,19 +53,6 @@ def wrapped(*args, **kwargs):
waic = map_args(az.waic)


def gelman_rubin(*args, **kwargs):
warnings.warn("gelman_rubin has been deprecated. In the future, use rhat instead.")
return rhat(*args, **kwargs)

gelman_rubin.__doc__ = rhat.__doc__


def effective_n(*args, **kwargs):
warnings.warn("effective_n has been deprecated. In the future, use ess instead.")
return ess(*args, **kwargs)

effective_n.__doc__ = ess.__doc__

__all__ = [
"bfmi",
"compare",
Expand All @@ -78,6 +65,4 @@ def effective_n(*args, **kwargs):
"rhat",
"summary",
"waic",
"gelman_rubin", # deprecated, remove after 3.8
"effective_n", # deprecated, remove after 3.8
]