Pymob

A simple useage example can be found in the documentation: https://pymob.readthedocs.io/en/latest/user_guide/quickstart.html

Details
* Merge dev into main from release 0.3.0 by flo-schu in https://github.com/flo-schu/pymob/pull/53
* Deploy documentation by flo-schu in https://github.com/flo-schu/pymob/pull/54
* Add a convenience method to traverse to the case studies directory fr… by flo-schu in https://github.com/flo-schu/pymob/pull/57
* Add parameter anaylsis to pymob by flo-schu in https://github.com/flo-schu/pymob/pull/58
* Implements pydantic for parsing and writing configuration files by flo-schu in https://github.com/flo-schu/pymob/pull/3
* write tests for the api by flo-schu in https://github.com/flo-schu/pymob/pull/62
* Add additional fixtures for different Simulation setup APIs by flo-schu in https://github.com/flo-schu/pymob/pull/63
* Implement a minimal simulation test by flo-schu in https://github.com/flo-schu/pymob/pull/66
* Implement scripting API for bufferGUTS by flo-schu in https://github.com/flo-schu/pymob/pull/67
* implement more flexible control over data dimensionality by flo-schu in https://github.com/flo-schu/pymob/pull/73


**Full Changelog**: https://github.com/flo-schu/pymob/compare/0.3.5...0.4.0

New features

* Implements parameter analysis methods developed in the reversible-damage project 58
* Minor fixes to case-study import functionality 58

Bugfixes

* Correct directory structure in documentation 58

**Full Changelog**: https://github.com/flo-schu/pymob/compare/0.3.4...0.3.5

New features

* implemens a convenience function to traverse the directory tree upwards until the case studies directory is encountered 57
* Updates workflow versions to avoid deprecation errors in the future 57


**Full Changelog**: https://github.com/flo-schu/pymob/compare/0.3.3...0.3.4

This is the first proper release of pymob. While it is still bumpy and the API will undergo breaking changes. It provides a package that is tested and documented in parts.

Merged pull requests:

* Conclude reversible damage project by flo-schu in https://github.com/flo-schu/pymob/pull/25

New Features

- **Simulation API Enhancements**
- Added `create_interpolation` method for datasets (commit hash: ade1bae)
- Introduced `load_functions` method to `SimulationBase` (commit hash: a087bec)
- Implemented `posterior_analysis` tools (commit hash: c89d2d6)
- Added `posterior_predictions` method for automatic generation of posterior predictions (commit hash: 571eeab)

- **Parameter Inference and Optimization**
- Implemented stochastic variational inference (SVI) for parameter estimation (commit hash: 6fc5e2b)
- Enabled bic to handle different posteriors (commit hash: e879221)
- Implemented log-likelihood computation from the probability model (commit hash: 90fec70)
- Added support for parallelization in posterior predictions (commit hash: 5db5788)

- **PyABC Integration**
- Improved compatibility with PyABC for test case studies (commit hash: be70fae)

Enhancements

- **Documentation**
- Expanded narrative documentation (commit hash: 12e158a)
- Enhanced case study documentation (commit hash: e7aab55)

- **Performance Improvements**
- Optimized chain concatenation for speed improvement (commit hash: fea8ec5)

Bug Fixes

- **General**
- Fixed various indexing bugs (commit hashes: 41fa4b2, a4cde74, 87f5822, 8f299de)
- Resolved import errors (commit hashes: 33aedaf, 8f1c195, 4cfed81)

- **Numpyro Backend**
- Fixed config bug (commit hash: e1fca53)
- Stabilized SVI with the `stable_update` option (commit hash: 8addd63)
- Fixed 2 indexing bugs (commit hash: b58d83e)
- Corrected error in prior specification (commit hash: 556bb73)

Miscellaneous

- **Testing and Quality Assurance**
- All tests are passing (commit hash: 139554d)
- Added new test scenarios (commit hashes: 69b4126, 7bfe7ca)
- Improved test coverage for various functionalities (commit hashes: c996dec, 5aa9f15, 92c2c7e)

- **Dependencies**
- Updated dependencies (commit hashes: 411831d, d15d766, 4941f2b)


**Full Changelog**: https://github.com/flo-schu/pymob/compare/0.3.0a5...0.3.0

This alpha release is associated with the **reversible-damage** project.

Features
- **Submit Script Update:**
- Updated the submit script to save log and error files in result folders. (Commit: `0aeac17`)

Bug Fixes
- **Fix Interactive Backend:**
- Fixed an issue with the interactive backend. (Commit: `35a00ab`)
- **Fix Test Case Study for PyABC:**
- Addressed a bug in PyABC related to the test case study. (Commit: `be70fae`, `be4b74d`)

Enhancements
- **Simulation Class Specification:**
- Enabled specification of the Simulation class in the config. (Commit: `818b1ff`)
- **Config File Improvements:**
- Added helpers for functional expression parsing and allowed specification of user-defined probability models in config files. (Commits: `5f0779b`, `f3a7cf9`)

New Features
- **Stochastic Variational Inference (SVI):**
- Implemented stochastic variational inference (SVI) in the NumPyro backend. (Commits: `ef09a09`, `6fc5e2b`)
- **Sample Adaptive MCMC Algorithm:**
- Implemented the sample adaptive MCMC algorithm. (Commit: `b723e9d`)

API Changes
- **Parameter Mapper:**
- Implemented a parameter mapper to sample from 1D distribution. (Commit: `9165a58`)
- **Stable API for Plotting:**
- Created a stable API for plotting posterior predictions. (Commit: `122e5ac`)
- **Array Parameters:**
- Implemented array parameters in the simulation. (Commit: `fdf7794`)

Configuration Updates
- **Config Settings:**
- Implemented various config settings for simulation and scenarios. (Commits: `5aa9f15`, `c610041`)

Miscellaneous
- **Todo Addition:**
- Added a todo. (Commit: `f65c6b9`)
- **Version Number Update:**
- Added version number to `__init__.py`. (Commit: `a3ae4da`)
- **Test Scenario Addition:**
- Added a new test scenario. (Commit: `69b4126`)

Documentation
- **Documentation Updates:**
- Improved and updated documentation. (Commits: `5f0779b`, `c610041`, `a3ae4da`)


**Full Changelog**: https://github.com/flo-schu/pymob/compare/0.3.0a3...0.3.0a5