Remove joint logprob test 6619 #1
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* Clean up MANIFEST.in * Remove useless option from setup.py * Exclude tests from package discovery * Make get_data not look at local files anymore This seems to be a relic of the past when `tests/data` contained data files. It is not the case anymore.
Most of the IR logprob rewrites require a PreserveRVMappings feature in the fgraph. The rewrite responsible to introduce IR in the inner graph of Scan was not adding this feature. In addition, find_measurable_scans, was bailing out when there were MesurableVariable nodes that were not outputs, even if these were being used by downstream nodes as the source of measurability.
* initial gitpod instructions * update url * spelling * more instructions on gitpod * new line at end of file * fix trailing whitespace * fix trailing whitespace * fix trailing whitespace * fix wording * try image * try sphinx image code * add link format * add link format * add link format * add link format * try html for image Co-authored-by: Ben Mares <[email protected]> * add blank line * try image code * spacing, fix commit errors * backticks * try image option again * terminal instructions * clarify instructions * fix image agai * fix precommit spacing errors * try admonition * try double indent * resize image * pre-commit error * add workspace image * clean up formatting * fix pre-commit error * fix pre-commit error * pre-commit error * use generic user name Co-authored-by: Ben Mares <[email protected]> * indent note Co-authored-by: Oriol Abril-Pla <[email protected]> * use console instead of bash for backticks content Co-authored-by: Oriol Abril-Pla <[email protected]> * indent list Co-authored-by: Oriol Abril-Pla <[email protected]> * verb grammar * use console instead of bash * clean up text * clean up text and formatting * indent * indent --------- Co-authored-by: Ben Mares <[email protected]> Co-authored-by: Oriol Abril-Pla <[email protected]>
* Adding dims parameter in Potential * Test case to check the dims in potential
* Remove spurious minus signs from the first two code examples in the Potential function * Shorten warning about applicability of Potential only to logp-based sampling
* Adding Mistplay image in the Readme * Adding Mistplay image in the Readme
* Fix `warn_treedepth` looking at the wrong stat * Add test for `warn_treedepth` function Closes pymc-devs#6587
* Reinstate nuts_kwargs in sample for passing arguments to numpyro * Removed redundant condition from if statement * Added sampler_kwargs * Rename sampler_kwargs; fix test failures * Ensure nuts_kwargs get passed to pymc nuts * Fix test_step_args failure * Moved numpyro test; use nuts_sampler_kwargs * Test failure fix * Fix docstrings for nuts/sampler kwargs; debugging target accept argument passing * Removed passing kwargs to external samplers; only nuts_sampler_kwargs for clarity * Revert nuts_kwargs to nuts * Fix failures in test_mcmc_external * Revert argument parameterization * Update pymc/sampling/mcmc.py Apply suggested nuts_sampler_kwarg docstring change Co-authored-by: Thomas Wiecki <[email protected]> --------- Co-authored-by: Thomas Wiecki <[email protected]>
Note that adding a nan switch to the icdf expression of discrete variables, prevents the returned dtype to be the same as the original distribution. There is no integer nan!
…eping their interdependencies intact
) * Remove auto argument from Deterministic * Add missing arguments in the deterministic docstring as per numpydoc style guide * Add missing arguments in the Potential docstring * Add spaces around colons --------- Co-authored-by: Michael Osthege <[email protected]>
* add HSGP implementation * Extend Covariances to support power spectral densities --------- Co-authored-by: Michael Osthege <[email protected]>
This utility can find RVs in inner graphs
…#6604) * Add definition of B in documentation for Beta dist * Define B in Beta distribution and link Wikipedia.
Also updates the sphinx cap to match the one from the theme, which is more realistic. I haven't tried but doubt our doc build would still work with sphinx 1.5
* It works with nested RNGs * It raises error if RNG used in SymbolicRandomVariable is not given an update * It raises warning if same RNG is used in multiple nodes
The default use of `check_parameters` indicates that an expression can be replaced by -inf, if the constraints aren't met. Instead, if `can_be_replaced_by_ninf=False`, sampling would fail for negative tau/sigma. To avoid this, the conversion now returns the right value for positive tau or sigma, but negative images if the inputs were negative. The methods that then validate the paramters (such as logp, logcdf, random), can later catch this.
* Added ICDF for the continuous exponential distribution. * Removed redundant out of bounds parameter tests.
* ⬆️ UPGRADE: Autoupdate pre-commit config --------- Co-authored-by: pymc-bot <[email protected]>
* config.yml file >>> add welcome bot links * Update links to contributing guide --------- Co-authored-by: Oriol Abril-Pla <[email protected]>
Introduced in 433703ab0156c88de4eb3b180ea85ec21dd3e3fb
Co-authored-by: Ricardo Vieira <[email protected]>
* Also remove the experimental warning when using CustomSymbolicDists
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