Update from develop

[PabloCorcho]

No description provided.

[Copilot]

Pull request overview

This PR appears to be a broad “sync from develop” update that modernizes BESTA’s fitting/sampling infrastructure (new sampler support, likelihood backends, LOSVD refactor), expands pipeline execution capabilities (batch/parallel runs), and updates tests/docs accordingly.

Changes:

• Adds a modern PyMC sampler integration and associated tests.
• Refactors spectral/photometric likelihood evaluation (new pipeline_modules/likelihoods.py) and updates multiple pipeline modules to use inverse-variance workflows and reusable LOSVD kernels.
• Enhances pipeline orchestration and post-processing utilities (BatchPipeline, results I/O helpers, autocorrelation tools), with documentation + CI test coverage updates.

Reviewed changes

Copilot reviewed 36 out of 37 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tutorials/fit_redshift/fit_jwst_redshift.ipynb	Adds pickle security warning and minor tutorial guidance updates.
tests/test_run.py	Updates config section naming for dust attenuation.
tests/test_pymc_sampler.py	Adds smoke/integration tests for the new PyMC sampler.
tests/test_postprocessing.py	Switches results reading to besta.io.read_results_file.
tests/test_pipeline.py	Adds BatchPipeline tests and updates pipeline imports.
tests/test_pipeline_module.py	Updates dust section naming used in DataBlock.
tests/test_likelihoods.py	Adds tests validating likelihood backend selection and correctness.
tests/test_kinematics.py	Adds unit tests for new pixel-kernel LOSVD and convolution helpers.
tests/test_grid.py	Removes MagTransform/CensoredSizeLikelihood references and updates tests accordingly.
tests/test_fitting_modules.py	Updates dust section naming and adds a __main__ runner.
src/besta/spectrum.py	Adds wavelength/velocity helpers, enriches emission-line outputs, and improves docstrings/comments.
src/besta/sfh.py	Adds transform-aware parameter bounds/monotonicity enforcement and fixes alpha parameter naming.
src/besta/samplers/pymc_sampler.py	Introduces a PyMC-based CosmoSIS sampler implementation.
src/besta/samplers/init.py	Exports the new PyMC sampler.
src/besta/postprocess.py	Adds autocorrelation tooling, burn-in support, and moves results I/O to besta.io.
src/besta/pipeline.py	Improves error handling, fixes config update logic, and adds BatchPipeline parallel runner support.
src/besta/pipeline_modules/spectra_redshift_fit.py	Speeds up redshift scan with numba + adds table-based persistence for z profiles.
src/besta/pipeline_modules/sfh_photometry_grid.py	Passes likelihood kind explicitly for photometry.
src/besta/pipeline_modules/sfh_photometry_emu.py	Passes likelihood kind explicitly for photometry.
src/besta/pipeline_modules/likelihoods.py	New backend-selectable likelihood implementations (NumPy/Numba).
src/besta/pipeline_modules/galaxy_spectra.py	Refactors to reusable LOSVD kernels and new likelihood plumbing.
src/besta/pipeline_modules/galaxy_photometry.py	Passes likelihood kind explicitly for photometry.
src/besta/pipeline_modules/full_spectral_fit.py	Refactors to reusable LOSVD kernels, new dust section naming, and new likelihood plumbing.
src/besta/pipeline_modules/base_module.py	Introduces likelihood_kind/method, ivar plumbing, non-finite handling, and LOSVD kernel preparation.
src/besta/kinematics.py	Major refactor to pixel-kernel classes with caching + updated convolution helpers.
src/besta/io.py	Enhances results-file parsing, adds burn-in helpers, and table format utilities.
src/besta/grid/transforms.py	Removes MagTransform; improves LinearStandardiser naming/docs.
src/besta/grid/prob.py	Refactors numba imports, prior normalization, and removes CensoredSizeLikelihood.
src/besta/grid/grid.py	Refactors imports and internal boundary helper naming.
src/besta/grid/binning.py	Fixes JSON key stability for tuple keys with robust parsing/serialization.
requirements.txt	Unpins numpy and explicitly includes numba.
README.md	Expands installation and contribution documentation.
docs/source/manager.rst	Documents BatchPipeline usage patterns.
docs/source/grid.rst	Expands/clarifies grid-based inference docs.
docs/source/configuration.rst	Adds maxlike/emcee config examples.
docs/requirements.txt	Unpins numpy for docs builds.
.github/workflows/test.yml	Broadens pytest invocation to tests/test_*.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.