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Important miscellaneous v4 updates#4577

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Merged

brandonwillard merged 31 commits intopymc-devs:v4pymc-devs/pymc:v4from brandonwillard:fix-missing-valuesbrandonwillard/pymc:fix-missing-valuesCopy head branch name to clipboardMar 29, 2021

+1,547-1,465

Commits

Commits on Mar 27, 2021

• Rename Model.vars to Model.value_vars

  brandonwillard

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• Reintroduce the old Model.vars with a deprecation warning

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• Add value/rv variable maps to Model

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• Change no_transform_object sentinel to UNSET in pymc3.util

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Commits on Mar 28, 2021

• Move logp code into pymc3.distributions.logp and graph functions into pymc3.aesaraf

  brandonwillard

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• Remove build_named_node_tree and its helper functions

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• Move treelist and treedict to pymc3.util

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• Remove pymc3.model._walk_up_rv

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• Remove pymc3.model.as_iterargs

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• Move pymc3.model.all_continuous to pymc3.sampling

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• Move pymc3.model.pandas_to_array to pymc3.aesaraf

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• Rename pymc3.tests.test_model_utils to test_glm_utils

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• Rename pymc3.tests.test_models_linear to test_glm_linear

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• Add xfail to pymc3.tests.test_variational_inference

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• Remove remaining uses of Distribution.default

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• Remove Distribution.get_test_val and Distribution.getattr_value

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• Rename Model.test_point to Model.initial_point

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• Rename Model.check_test_point to Model.point_logps

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• Make pymc3.util.update_start_vals and check_start_vals Model methods

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• Re-enable pymc3.tests.test_util

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• Fix issue with single variable input to BlockedStep

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• Make GradientSharedStep a subclass of ArrayStepShared

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• Make initial_replacements argument in rvs_to_value_vars optional

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• Rename rv_ancestors to walk_model and add tests

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Commits on Mar 29, 2021

• Merge and improve apply_transforms and rvs_to_value_vars

  brandonwillard

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• Fix a NumPy non-tuple indexing deprecation warning in test_aesaraf

  brandonwillard

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• Convert and transform potentials in the log-likelihood

  brandonwillard

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• Finish refactoring BlockedStep.competence implementations

  brandonwillard

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• Fix RaveledVars and size-related issues in Metropolis and MLDA samplers

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• Seed flaky TestSamplePPC.test_deterministic_of_observed_modified_interface

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• Re-enable step method tests in pymc3.tests.test_step

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