Remove several functions and objects from PyMC root namespace by ricardoV94 · Pull Request #6973 · pymc-devs/pymc

ricardoV94 · 2023-10-26T11:17:50Z

All arviz plots must be retrieved from pymc.plots.foo
All arviz stats must be retrieved from pymc.stats.foo
Removed many rare or non-user facing objects
Remove rare or non-user facing VI objects (I am not familiar enough to know which ones should stay and which ones should not)

Also

Move all custom Exceptions to pymc.exceptions.py

The following script prints 174 after and 272 before this PR:

import pymc
from types import ModuleType
len([a for a in dir(pymc) if not isinstance(getattr(pymc, a), ModuleType) and not a.startswith("__")])

The following entries were removed:

CallableTensor
DictToArrayBijection
ELPDData
GeneratorAdapter
ImputationWarning
IncorrectArgumentsError
SamplingError
ShapeError
ShapeWarning
TraceDirectoryError
_calculate_ics
apply_test_function
autocorr
autocorrplot
autocov
bfmi
bool_types
compare
compareplot
complex_types
compute_log_likelihood
cont_inputs
continuous_types
convert_observed_data
densityplot
discrete_types
drop_warning_stat
energyplot
ess
expand_packed_triangular
float_types
forestplot
generator
guess_scaling
hdi
int_types
invlogit
invprobit
isgenerator
join_nonshared_inputs
kde
kdeplot
logaddexp
logit
logsumexp
loo
loo_pit
make_shared_replacements
make_ufunc
mcse
pairplot
plot_autocorr
plot_bf
plot_bpv
plot_compare
plot_density
plot_dist
plot_dist_comparison
plot_dot
plot_ecdf
plot_elpd
plot_energy
plot_ess
plot_forest
plot_hdi
plot_kde
plot_khat
plot_lm
plot_loo_pit
plot_mcse
plot_pair
plot_parallel
plot_posterior
plot_ppc
plot_rank
plot_separation
plot_trace
plot_ts
plot_violin
predictions_to_inference_data
probit
psislw
r2_samples
r2_score
reloo
rhat
smartfloatX
str_for_dist
str_for_model
str_for_potential_or_deterministic
summary
to_inference_data
trace_cov
traceplot
typefilter
waic
weight_predictions
wrap_xarray_ufunc

📚 Documentation preview 📚: https://pymc--6973.org.readthedocs.build/en/6973/

maresb · 2023-10-26T11:29:20Z

Depending on how semver-y people feel, this might be best targeted for PyMC v6.

ricardoV94 · 2023-10-26T11:36:44Z

Depending on how semver-y people feel, this might be best targeted for PyMC v6.

I think that will be a strong argument not to go on with these changes

codecov · 2023-10-26T11:49:22Z

Codecov Report

❌ Patch coverage is 82.05128% with 14 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (v6@5fa428c). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
pymc/_deprecations.py	59.09%	9 Missing ⚠️
pymc/variational/opvi.py	66.66%	3 Missing ⚠️
pymc/step_methods/metropolis.py	87.50%	1 Missing ⚠️
pymc/variational/operators.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@          Coverage Diff          @@
##             v6    #6973   +/-   ##
=====================================
  Coverage      ?   91.89%           
=====================================
  Files         ?      125           
  Lines         ?    20258           
  Branches      ?        0           
=====================================
  Hits          ?    18616           
  Misses        ?     1642           
  Partials      ?        0

Files with missing lines	Coverage Δ
pymc/__init__.py	`100.00% <100.00%> (ø)`
pymc/distributions/multivariate.py	`94.24% <100.00%> (ø)`
pymc/exceptions.py	`100.00% <ø> (ø)`
pymc/func_utils.py	`88.63% <100.00%> (ø)`
pymc/math.py	`74.17% <100.00%> (ø)`
pymc/sampling/__init__.py	`100.00% <100.00%> (ø)`
pymc/sampling/jax.py	`93.47% <ø> (ø)`
pymc/sampling/mcmc.py	`92.03% <100.00%> (ø)`
pymc/step_methods/__init__.py	`100.00% <100.00%> (ø)`
pymc/tuning/__init__.py	`100.00% <100.00%> (ø)`
... and 8 more

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

ColCarroll · 2023-10-26T14:23:21Z

I'll put in a vote against this -- there are enough pymc scripts and libraries out there that don't follow library updates very closely, but would like to continue to benefit from better sampling routines by having liberal version specifications.

Probably the right way would be to use some deprecations library that issued a warning for ~a year, and provided a copy/paste upgrade path. I'm not sure the benefits (tidier namespace? are there others?) outweigh the work and downsides.

maresb · 2023-10-26T16:24:43Z

-def alias_deprecation(func, alias: str):
-    original = func.__name__
-
-    @functools.wraps(func)
-    def wrapped(*args, **kwargs):
-        raise FutureWarning(
-            f"The function `{alias}` from PyMC was an alias for `{original}` from ArviZ. "
-            "It was removed in PyMC 4.0. "
-            f"Switch to `pymc.{original}` or `arviz.{original}`."
-        )
-
-    return wrapped
-
-
-# Aliases of ArviZ functions
-autocorrplot = alias_deprecation(az.plot_autocorr, alias="autocorrplot")
-forestplot = alias_deprecation(az.plot_forest, alias="forestplot")
-kdeplot = alias_deprecation(az.plot_kde, alias="kdeplot")
-energyplot = alias_deprecation(az.plot_energy, alias="energyplot")
-densityplot = alias_deprecation(az.plot_density, alias="densityplot")
-pairplot = alias_deprecation(az.plot_pair, alias="pairplot")
-traceplot = alias_deprecation(az.plot_trace, alias="traceplot")
-compareplot = alias_deprecation(az.plot_compare, alias="compareplot")


It looks to me like this has already been issuing deprecation warnings. Was this working and warning against using everything slated to be removed since v4?

That was just for utilities whose names have changed. Those could be safely removed by now yes

Ah, then I agree with @ColCarroll that we should definitely deprecate all the other stuff well in advance of removing it.

Also why remove the deprecation warning? In case you want to clear up the namespace then you could refactor it into something like https://peps.python.org/pep-0562/

I removed this deprecation warning because I removed the objects that were being deprecated as well

These one specifically were deprecated since v4, seems safe no?

Aren't there still lots of people who use PyMC3 because of the name recognition and all the SEO? Seems pretty low-effort to provide explicit instructions for them.

Sounds silly. This will not be the thing that people switching from v3 to v5 will find challenging

Ya, I agree it's silly in the case of these ArviZ warnings, but you could do something similar to provide a transition period for the rest of the stuff. Proof-of-concept: ricardoV94#4

I agree, I am going to try and do that!

twiecki · 2023-10-26T21:18:57Z

I'm in favor. Cruft accumulates in any code base and it requires consistent effort to stem the tide, which this attempts. I don't think many people are using these functions and those can easily adjust their imports. In a version or two we'll all have forgotten about it, just like with aesara and pytensor.

review-notebook-app · 2026-04-23T04:18:30Z

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

jessegrabowski · 2026-04-23T04:20:01Z

re-hydrated this PR. Commits are small and focused so if we want to argue about them we can, and it's easy to drop one. Number of items in the main namespace drops from 305 -> 143.

read-the-docs-community · 2026-04-23T04:28:20Z

Documentation build overview

📚 pymc | 🛠️ Build #32497907 | 📁 Comparing a9d4cc1 against latest (4b0b6ee)

🔍 Preview build

437 files changed · + 50 added · ± 259 modified · - 128 deleted

+ Added

± Modified

- Deleted

ricardoV94 · 2026-04-23T09:39:05Z

let's add a test to avoid accidental root creep like we did in pymc-devs/pytensor#1863

jessegrabowski · 2026-04-26T16:33:50Z

let's add a test to avoid accidental root creep like we did in pymc-devs/pytensor#1863

Added, lmk what you think.

ricardoV94

Do we want to add a deprecation getter to help with the transition?

jessegrabowski · 2026-04-26T21:24:13Z

Do we want to add a deprecation getter to help with the transition?

I guess if we're being responsible we should. Can we give a firm cut-over date in the warning so it doesn't linger around for 2 years?

ricardoV94 · 2026-04-27T10:33:54Z

Can we give a firm cut-over date in the warning so it doesn't linger around for 2 years?

Sure

…t via `from sampling import *`

jessegrabowski · 2026-04-28T00:40:29Z

I added the getter in _deprecation.py. The warning says we'll delete the forwarding in the first release of 2027, which gives everyone plenty of time.

ricardoV94 · 2026-04-28T02:13:20Z

Looks great @jessegrabowski just some standing minor comments from me and @aloctavodia that you haven't incorporated (and something I spotted now)

aloctavodia

I added a couple more comments not directly related to the aim of this PR. So happy if they are solved in this PR or a separate one.

ricardoV94 · 2026-04-28T09:09:47Z

@aloctavodia tried to address your comments above

aloctavodia · 2026-04-28T09:18:09Z

Thanks, LGTM!

jessegrabowski · 2026-05-01T02:11:42Z

is anything left to be done here?

ricardoV94 added maintenance major Include in major changes release notes section request discussion labels Oct 26, 2023

ricardoV94 force-pushed the cleanup_namespace branch from 9fd14d6 to ce10976 Compare October 26, 2023 11:26

ricardoV94 force-pushed the cleanup_namespace branch from ce10976 to e7e8a54 Compare October 26, 2023 11:35

maresb reviewed Oct 26, 2023

View reviewed changes

ricardoV94 added this to the v6 milestone Mar 23, 2026

jessegrabowski force-pushed the cleanup_namespace branch from e7e8a54 to 0584aa8 Compare April 23, 2026 04:18

jessegrabowski changed the base branch from main to v6 April 23, 2026 04:18

github-actions Bot added docs hackathon Suitable for hackathon labels Apr 23, 2026

jessegrabowski force-pushed the cleanup_namespace branch from 0584aa8 to de73d46 Compare April 23, 2026 04:20

jessegrabowski marked this pull request as ready for review April 23, 2026 04:21

aloctavodia reviewed Apr 23, 2026

View reviewed changes

Comment thread docs/source/api.rst Outdated

Comment thread docs/source/api.rst Outdated

ricardoV94 commented Apr 23, 2026

View reviewed changes

Comment thread docs/source/api/misc.rst

Comment thread docs/source/api/math.rst Outdated

Comment thread pymc/tuning/starting.py

jessegrabowski force-pushed the cleanup_namespace branch from 556c541 to 314d5ba Compare April 26, 2026 16:34

ricardoV94 commented Apr 26, 2026

View reviewed changes

Comment thread docs/source/api/misc.rst

Remove plots re-export into main namespace

af5bf64

jessegrabowski added 12 commits April 27, 2026 19:39

Remove remaining math functions from main namespace

1e52682

Revert removal of pm.compute_log_likelihood

d7a7ffc

Remove handler from root namespace

bb14656

Prevent leakage from sampling.forward and sampliong.mcmc into roo…

fb052e3

…t via `from sampling import *`

Add test to keep namespace tidy

8ddd71a

Add docs for stats submodule

fe7a38b

fix model_table import

c856cbb

Use literal re-export from forward and mcmc for type-checkers

1e05868

Document compute_log_likelihood in stats.rst (not misc.rst)

8bd4d82

Include test_root_namespace.py in test job

87f783f

Remove init from expected failures

b9d9ab4

Deprecation getter

75c7675

jessegrabowski force-pushed the cleanup_namespace branch from e6ae13e to 75c7675 Compare April 28, 2026 00:39

ricardoV94 commented Apr 28, 2026

View reviewed changes

Comment thread pymc/sampling/mcmc.py Outdated

jessegrabowski added 2 commits April 27, 2026 22:28

Update arviz references in api.rst

e73215c

Remove duplicated warning

6f7855c

aloctavodia reviewed Apr 28, 2026

View reviewed changes

Comment thread docs/source/api/stats.rst Outdated

Comment thread docs/source/api/stats.rst Outdated

Comment thread docs/source/api.rst Outdated

Comment thread docs/source/api.rst Outdated

ricardoV94 added 4 commits April 28, 2026 10:39

Automate math listing

72eeb9e

Add more exports to math.py

b2524d7

Update math.rst

b25f829

arviz_* fixes

7f53f23

ricardoV94 requested a review from OriolAbril April 28, 2026 09:10

sort all

efc6eaa

jessegrabowski approved these changes May 1, 2026

View reviewed changes

Only one warning

a9d4cc1

Conversation

ricardoV94 commented Oct 26, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

maresb commented Oct 26, 2023

Uh oh!

ricardoV94 commented Oct 26, 2023

Uh oh!

codecov Bot commented Oct 26, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

ColCarroll commented Oct 26, 2023

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

ricardoV94 Oct 26, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

twiecki commented Oct 26, 2023

Uh oh!

review-notebook-app Bot commented Apr 23, 2026

Uh oh!

jessegrabowski commented Apr 23, 2026

Uh oh!

read-the-docs-community Bot commented Apr 23, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Documentation build overview

Uh oh!

Uh oh!

Uh oh!

ricardoV94 commented Apr 23, 2026

Uh oh!

Uh oh!

Uh oh!

Uh oh!

jessegrabowski commented Apr 26, 2026

Uh oh!

ricardoV94 left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

jessegrabowski commented Apr 26, 2026

Uh oh!

ricardoV94 commented Apr 27, 2026

Uh oh!

jessegrabowski commented Apr 28, 2026

Uh oh!

Uh oh!

ricardoV94 commented Apr 28, 2026

Uh oh!

aloctavodia left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

ricardoV94 commented Apr 28, 2026

Uh oh!

aloctavodia commented Apr 28, 2026

Uh oh!

jessegrabowski commented May 1, 2026

ricardoV94 commented Oct 26, 2023 •

edited

Loading

codecov Bot commented Oct 26, 2023 •

edited

Loading

ricardoV94 Oct 26, 2023 •

edited

Loading

read-the-docs-community Bot commented Apr 23, 2026 •

edited

Loading