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Reorganize docs API entries #7030

Merged
merged 6 commits into from
Nov 29, 2023
Merged

Reorganize docs API entries #7030

merged 6 commits into from
Nov 29, 2023

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kataev
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@kataev kataev commented Nov 23, 2023

What is this PR about?
Hello, while making previous PR i found what some modules doesn't import at all:

WARNING: [autosummary] failed to import pymc.constant_fold.
Possible hints:
* AttributeError: module 'pymc' has no attribute 'constant_fold'
* ModuleNotFoundError: No module named 'pymc.constant_fold'
* ImportError:
WARNING: [autosummary] failed to import pymc.math.det.
Possible hints:
* AttributeError: module 'pymc.math' has no attribute 'det'
* ModuleNotFoundError: No module named 'pymc.math.det'; 'pymc.math' is not a package
* ImportError:
WARNING: [autosummary] failed to import pymc.math.extract_diag.
Possible hints:
* ModuleNotFoundError: No module named 'pymc.math.extract_diag'; 'pymc.math' is not a package
* AttributeError: module 'pymc.math' has no attribute 'extract_diag'
* ImportError:
WARNING: [autosummary] failed to import pymc.math.matrix_dot.
Possible hints:
* ModuleNotFoundError: No module named 'pymc.math.matrix_dot'; 'pymc.math' is not a package
* ImportError:
* AttributeError: module 'pymc.math' has no attribute 'matrix_dot'
WARNING: [autosummary] failed to import pymc.math.trace.
Possible hints:
* ImportError:
* AttributeError: module 'pymc.math' has no attribute 'trace'
* ModuleNotFoundError: No module named 'pymc.math.trace'; 'pymc.math' is not a package
WARNING: [autosummary] failed to import pymc.model.core.model_to_networkx.
Possible hints:
* AttributeError: module 'pymc.model.core' has no attribute 'model_to_networkx'
* ModuleNotFoundError: No module named 'pymc.model.core.model_to_networkx'; 'pymc.model.core' is not a package
* ImportError:

Extension error (sphinx.ext.autosummary):

So i am looked in history and found what they removed long ago.

Bugfixes

  • Fixes misspel in import shim around transforms.sum_to_1

Documentation

  • Less errors while docs build

📚 Documentation preview 📚: https://pymc--7030.org.readthedocs.build/en/7030/

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codecov bot commented Nov 23, 2023

Codecov Report

Merging #7030 (4cd807c) into main (ec70d86) will increase coverage by 4.25%.
Report is 7 commits behind head on main.
The diff coverage is 100.00%.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #7030      +/-   ##
==========================================
+ Coverage   87.91%   92.16%   +4.25%     
==========================================
  Files         101      101              
  Lines       16849    16827      -22     
==========================================
+ Hits        14812    15509     +697     
+ Misses       2037     1318     -719     
Files Coverage Δ
pymc/distributions/transforms.py 98.48% <100.00%> (+15.90%) ⬆️

... and 7 files with indirect coverage changes

Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com>
@@ -13,8 +13,6 @@ This submodule contains functions for MCMC and forward sampling.
sample_prior_predictive
sample_posterior_predictive
sample_posterior_predictive_w
sampling.jax.sample_blackjax_nuts
sampling.jax.sample_numpyro_nuts
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Did these go somewhere else?

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You right, problem was in sampling.jax which doesn't import.
I split tables a little bit.

@twiecki twiecki merged commit 005ba5f into pymc-devs:main Nov 29, 2023
22 checks passed
LukeLB pushed a commit to LukeLB/pymc that referenced this pull request Nov 29, 2023
Update CODE_OF_CONDUCT.md

Changed contact email

ChiSquared now returns a Gamma random variable (pymc-devs#7007)

Update devcontainer (pymc-devs#7017)

* Update dev container on release and schedule

* Use latest version of upstream dev container image

* Remove pre-commit cache hack

* Add Jupyter extension to container

Rename RVTransform to Transform

Remove duplicate ChainTransform

Move ZeroSumTransform methods inside respective class

Remove deprecated function rvs_to_value_vars

Merge functionality of pytensorf and logprob/utils

Also fixes circular imports

Deprecate unused function walk_model

update theme (pymc-devs#7018)

* update theme version

* update conf.py

Fix docs formatting in `shape_utils` (pymc-devs#7025)

* Small docs update shape_utils.py

Fix docs markup

* Update to_tuple docs shape_utils.py

* Types

---------

Co-authored-by: Denis Kataev <denis.a.kataev+git@gmail.com>

Use PyTensor StudentT RV

Update GOVERNANCE.md (pymc-devs#7031)

* Update GOVERNANCE.md

* Update GOVERNANCE.md

Co-authored-by: Purna Chandra Mansingh <purnachandramansingh135@gmail.com>

---------

Co-authored-by: Purna Chandra Mansingh <purnachandramansingh135@gmail.com>

Remove deprecated model methods

Deprecate Model.model property

Deprecate pytensor_config

Bump Pytensor dependency to >=2.18.1,<2.19

Better float32 sampling support for TruncatedNormal (pymc-devs#7026)

* manually inv transform; force rng same type

* always upcast f64 and downcast to dtype of param

* add comment

* use class attr dtype

* need else stmt for dtype

* actually no need to downcast in this method

* rm unused import

Another small fixes in docs and imports (pymc-devs#7030)

* Remove old import from autosummary doc pages

* Fix small error

* Correct place for model_to_networkx & model_to_graphviz

* Correct currentmodule source for pytensorf.rst

* Update docs/source/api/model/core.rst

Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com>

* Fix sampling & jax docs imports

---------

Co-authored-by: Denis Kataev <denis.a.kataev+git@gmail.com>
Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com>

Update installation instructions to remove incompatibility of JAX on Windows
@ricardoV94 ricardoV94 changed the title Another small fixes in docs and imports Reorganize docs API entries Dec 10, 2023
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3 participants