`BridgeStan`: Efficient in-memory access to the methods of a Stan model

<h2>What's Changed</h2> <ul> <li>Update stanc to version 2.33.1 by @WardBrian in https://github.com/roualdes/bridgestan/pull/181</li> <li>Fix memory leak in <code>log_density(propto=True)</code> by @WardBrian in https://github.com/roualdes/bridgestan/pull/180</li> <li>Python: Move all metadata to pyproject.toml by @WardBrian in https://github.com/roualdes/bridgestan/pull/177</li> <li>Python: Issue warning when re-loading the same module by @WardBrian in https://github.com/roualdes/bridgestan/pull/178</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/roualdes/bridgestan/compare/v2.2.1...v2.2.2</p>If you use this software, please cite our article in the Journal of Open Source Software

A data management infrastructure for the integration of imaging and omics data in life sciences

BACKGROUND: As technical developments in omics and biomedical imaging increase the throughput of data generation in life sciences, the need for information systems capable of managing heterogeneous digital assets is increasing. In particular, systems supporting the findability, accessibility, interoperability, and reusability (FAIR) principles of scientific data management. RESULTS: We propose a Service Oriented Architecture approach for integrated management and analysis of multi-omics and biomedical imaging data. Our architecture introduces an image management system into a FAIR-supporting, web-based platform for omics data management. Interoperable metadata models and middleware components implement the required data management operations. The resulting architecture allows for FAIR management of omics and imaging data, facilitating metadata queries from software applications. The applicability of the proposed architecture is demonstrated using two technical proofs of concept and a use case, aimed at molecular plant biology and clinical liver cancer research, which integrate various imaging and omics modalities. CONCLUSIONS: We describe a data management architecture for integrated, FAIR-supporting management of omics and biomedical imaging data, and exemplify its applicability for basic biology research and clinical studies. We anticipate that FAIR data management systems for multi-modal data repositories will play a pivotal role in data-driven research, including studies which leverage advanced machine learning methods, as the joint analysis of omics and imaging data, in conjunction with phenotypic metadata, becomes not only desirable but necessary to derive novel insights into biological processes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04584-3

pymc-devs/pymc: v5.8.2

What's Changed Bugfixes Fix bug in compute_log_likelihood when variable has dims without coords by @jaharvey8 in https://github.com/pymc-devs/pymc/pull/6882 Full Changelog: https://github.com/pymc-devs/pymc/compare/v5.8.1...v5.8.

pymc-devs/pymc: v5.9.2

<p><!-- Release notes generated using configuration in .github/release.yml at main --></p> <h2>What's Changed</h2> <h3>New Features </h3> <ul> <li>Recognize alternative form of sigmoid in logprob inference by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6978</li> <li>Allow IntervalTransform to handle dynamic infinite bounds by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/7001</li> </ul> <h3>Bugfixes </h3> <ul> <li>Fix compute_test_value error when creating observed variables by @vandalt in https://github.com/pymc-devs/pymc/pull/6982</li> <li>Fix memory leak in logp of transformed variables by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6991</li> </ul> <h3>Documentation </h3> <ul> <li>fix typo in notebook about Distribution Dimensionality by @nicrie in https://github.com/pymc-devs/pymc/pull/7005</li> </ul> <h3>Maintenance </h3> <ul> <li>Add more missing functions to math module by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6979</li> </ul> <h2>New Contributors</h2> <ul> <li>@vandalt made their first contribution in https://github.com/pymc-devs/pymc/pull/6982</li> <li>@nicrie made their first contribution in https://github.com/pymc-devs/pymc/pull/7005</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/pymc-devs/pymc/compare/v5.9.1...v5.9.2</p&gt

pymc-devs/pymc: v5.9.1

<p><!-- Release notes generated using configuration in .github/release.yml at main --></p> <h2>What's Changed</h2> <h3>New Features </h3> <ul> <li>Allow batched parameters in MvNormal and MvStudentT distributions by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6897</li> <li>Logprob derivation of Max for Discrete IID distributions by @Dhruvanshu-Joshi in https://github.com/pymc-devs/pymc/pull/6790</li> <li>Support logp derivation of <code>power(base, rv)</code> by @LukeLB in https://github.com/pymc-devs/pymc/pull/6962</li> </ul> <h3>Bugfixes </h3> <ul> <li>Make <code>Model.str_repr</code> robust to variables without monkey-patch by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6942</li> <li>Fix bug in GP Periodic and WrappedPeriodic kernel full method by @lucianopaz in https://github.com/pymc-devs/pymc/pull/6952</li> <li>Fix rejection-based truncation of scalar variables by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6923</li> </ul> <h3>Documentation </h3> <ul> <li>Add expression for NegativeBinomial variance by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6957</li> </ul> <h3>Maintenance </h3> <ul> <li>Add constant and observed data to nutpie idata by @Y0dler in https://github.com/pymc-devs/pymc/pull/6943</li> <li>Improve multinomial moment by @aerubanov in https://github.com/pymc-devs/pymc/pull/6933</li> <li>Fix HurdleLogNormal Docstring by @amcadie in https://github.com/pymc-devs/pymc/pull/6958</li> <li>Use numpy testing utilities instead of custom close_to* by @erik-werner in https://github.com/pymc-devs/pymc/pull/6961</li> <li>Include more PyTensor functions in math module by @jaharvey8 in https://github.com/pymc-devs/pymc/pull/6956</li> <li>Improve blackjax sampling integration by @junpenglao in https://github.com/pymc-devs/pymc/pull/6963</li> </ul> <h2>New Contributors</h2> <ul> <li>@Y0dler made their first contribution in https://github.com/pymc-devs/pymc/pull/6943</li> <li>@amcadie made their first contribution in https://github.com/pymc-devs/pymc/pull/6958</li> <li>@erik-werner made their first contribution in https://github.com/pymc-devs/pymc/pull/6961</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/pymc-devs/pymc/compare/v5.9.0...v5.9.1</p&gt

pymc-devs/pymc: v5.10.0

<p><!-- Release notes generated using configuration in .github/release.yml at main --></p> <h2>What's Changed</h2> <h3>Major Changes </h3> <ul> <li>ChiSquared now returns a Gamma random variable by @wd60622 in https://github.com/pymc-devs/pymc/pull/7007</li> <li>Remove several deprecated model properties and deprecate new ones by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/7033</li> <li>Bump Pytensor dependency to <code>>=2.18.1,<2.19</code> by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/7020</li> </ul> <h3>New Features </h3> <ul> <li>Default <code>moment</code> for <code>CustomDist</code> provided with a <code>dist</code> function by @aerubanov in https://github.com/pymc-devs/pymc/pull/6873</li> </ul> <h3>Documentation </h3> <ul> <li>Fix docs formatting in <code>shape_utils</code> by @kataev in https://github.com/pymc-devs/pymc/pull/7025</li> </ul> <h3>Maintenance </h3> <ul> <li>Update CODE_OF_CONDUCT.md by @fonnesbeck in https://github.com/pymc-devs/pymc/pull/7012</li> <li>Update devcontainer by @maresb in https://github.com/pymc-devs/pymc/pull/7017</li> <li>Merge redundant code across <code>logprob</code>, <code>pytensorf</code> and <code>distributions/transform</code> by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6976</li> <li>Use PyTensor StudentT RV by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/7028</li> <li>Update GOVERNANCE.md by @canyon289 in https://github.com/pymc-devs/pymc/pull/7031</li> </ul> <h2>New Contributors</h2> <ul> <li>@kataev made their first contribution in https://github.com/pymc-devs/pymc/pull/7025</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/pymc-devs/pymc/compare/v5.9.2...v5.10.0</p&gt

pymc-devs/pymc: v5.10.1

<p><!-- Release notes generated using configuration in .github/release.yml at main --></p> <h2>What's Changed</h2> <h3>New Features </h3> <ul> <li>Implement periodic kernel for HSGP by @theorashid in https://github.com/pymc-devs/pymc/pull/6877</li> </ul> <h3>Bugfixes </h3> <ul> <li>Avoid inplace mutation in <code>replace_rvs_by_values</code> by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/7055</li> </ul> <h3>Documentation </h3> <ul> <li>Reorganize docs API entries by @kataev in https://github.com/pymc-devs/pymc/pull/7030</li> <li>Remove message about JAX not being supported on Windows in installation instructions by @jackhenderson101 in https://github.com/pymc-devs/pymc/pull/7039</li> </ul> <h3>Maintenance </h3> <ul> <li>Better float32 sampling support for TruncatedNormal by @JasonTam in https://github.com/pymc-devs/pymc/pull/7026</li> </ul> <h2>New Contributors</h2> <ul> <li>@jackhenderson101 made their first contribution in https://github.com/pymc-devs/pymc/pull/7039</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/pymc-devs/pymc/compare/v5.10.0...v5.10.1</p&gt

pymc-devs/pymc: v5.8.1

What's Changed New Features Logprob derivation for Min of continuous IID variables by @Dhruvanshu-Joshi in https://github.com/pymc-devs/pymc/pull/6846 Derive logprob for exp2, log2, log10, log1p, expm1, log1mexp, log1pexp (softplus), and sigmoid transformations by @LukeLB in https://github.com/pymc-devs/pymc/pull/6826 ### Bugfixes Fix wrong ZeroSumNormal logp expression by @lucianopaz in https://github.com/pymc-devs/pymc/pull/6872 Fix bug in univariate Ordered and SumTo1 transform logp by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6903 ### Documentation Link to updated PyMC port of DBDA in README by @cluhmann in https://github.com/pymc-devs/pymc/pull/6890 ### Maintenance Reject logp derivation of binary operations with broadcasted measurable input by @shreyas3156 in https://github.com/pymc-devs/pymc/pull/6893 Cast ZeroSumNormal shape operations to config.floatX by @thomasjpfan in https://github.com/pymc-devs/pymc/pull/6889 Bump docker/build-push-action from 4.1.1 to 4.2.1 by @dependabot in https://github.com/pymc-devs/pymc/pull/6900 Bump pytensor by @ricardoV94 in https://github.com/pymc-devs/pymc/pull/6910 Full Changelog: https://github.com/pymc-devs/pymc/compare/v5.8.0...v5.8.