WIP: Add DifferentialEquation: API for Bayesian inference of ODEs #3578
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* stabilize covariance * add release note * fix test
* Fix typos in docstrings. Fix some minor wording errors, but mostly fixed formatting issues. * Update sphinx configuration. Updated to make a deprecation warning go away. This should not change the behavior at all. * Update MultiTrace docs. Minor typo fixes and added MultiTrace attributes section. * Fix RST issues in documentation. * Remove obsolete file. The `getting_started.rst` file does not yield output that is linked into the docs. Instead, the index.rst file directly links to the pages once linked from getting_started.
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Dpananos
changed the title
Added @pytest.mark.xfail(condition=(theano.config.floatX == "float32"), reason="Fails on float32")
Adding dectorator actually made coverage worse.
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Please add tests to ensure ValueErrors are being raised when expected :) |
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Thanks for the catch @canyon289! Added the tests and will push later today. |
please remember to resolve the respective discussions |
| def _simulate(self, parameters): | ||
| # Initial condition comprised of state initial conditions and raveled | ||
| # sensitivity matrix | ||
| y0 = np.concatenate([ parameters[self.n_odeparams:] , self._sens_ic]) |
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Our pylint settings are actually quite permissive when it comes to spaces. There are several empty lines, or spaces missing around operators
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In many places, PyMC3 uses the test_value stuff to make sanity checks. Can we support this also for ODEs? (forgot to hit finish review button...)
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Can you show me an example?
* move smc from step_methods to its own family * black * update notebooks * add release note and fix lint * add release note and fix lint * minor fix docstring * reorder arguments and minor fix docstring
Clean up docstring for `sample`.
* stabilize covariance * add release note * fix test
* Fix typos in docstrings. Fix some minor wording errors, but mostly fixed formatting issues. * Update sphinx configuration. Updated to make a deprecation warning go away. This should not change the behavior at all. * Update MultiTrace docs. Minor typo fixes and added MultiTrace attributes section. * Fix RST issues in documentation. * Remove obsolete file. The `getting_started.rst` file does not yield output that is linked into the docs. Instead, the index.rst file directly links to the pages once linked from getting_started.
Added @pytest.mark.xfail(condition=(theano.config.floatX == "float32"), reason="Fails on float32")
Adding dectorator actually made coverage worse.
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Will repoen another PR once I fix some more issues. |
This is a work in progress, and a part of Google Summer of Code 2019.
This PR adds:
odesubmodule, which containsDifferntialEquation, the main tool for doing inference with ODEs.Unit tests for
odeA Notebook showcasing how to use
DifferentialEquationin a couple of examples.As this is a work in progress, comments are much appreciated.