PyPI deployment now active + documentation updates

What's Changed

• Update installation instructions in light of working PyPI deployment by @WillJRoper in #839
• Added version 3.13 to testing suite by @WillJRoper in #838

Full Changelog: v0.8.4-beta...v0.8.5-beta

v0.8.4-beta

Still debugging the deployment but maybe there now.

What's Changed

• Pipeline instrument arguments by @christopherlovell in #836
• Modifications to make the pip deployment (hopefully) work by @WillJRoper in #837

Full Changelog: v0.8.3-beta...v0.8.4-beta

v0.8.3-beta

More deployment testing (this time with a small change associated)

What's Changed

• Remove requirement for intrinsic to have non-zero escape fraction by @christopherlovell in #835

Full Changelog: v0.8.2-beta...v0.8.3-beta

v0.8.2-beta

Testing deployment again

Full Changelog: v0.8.1-beta...v0.8.2-beta

v0.8.1-beta

We need twine in the workflow to deploy... this might qualify as the smallest change between releases ever!

Transformations and PyPi Deployment

What's Changed

• Fix extinction wavelength limits by @aswinpvijayan in #829
• Switching to a Box server and using a yaml file for file locations by @WillJRoper in #830
• Moving dense_basis install to an optional dependency by @WillJRoper in #831
• Adding a "weighting variable" to a Grid by @WillJRoper in #812
• Simplifies the unit system by introducing "unit categories" by @WillJRoper in #826
• Attenuation operation generalised to Transformation (+ butterfly effect) by @WillJRoper in #827
• Adding a deployment workflow by @WillJRoper in #833

Full Changelog: v0.7.0-beta...v0.8.0-beta

v0.7.0-beta (introduced velocity shift + pre EmissionModel change checkpoint)

What's Changed

• Introduce a decorator for handling expected units by @WillJRoper in #737
• Integrating imaging into EmissionModel framework (+abstract base class) by @WillJRoper in #750
• Making Grid.get_grid_point safer by @WillJRoper in #752
• BUGFIX: Fixing line unpacking when no lines can be made by @WillJRoper in #754
• BUGFIX: Handling empty list attributes in TableFormatter by @WillJRoper in #751
• Introducing the instrument module by @WillJRoper in #753
• Remove the check for the grid to be associated with a line emitting region to allow the use of generic grids by @stephenmwilkins in #760
• Fix for periodic boundary by @aswinpvijayan in #764
• Generalise ionising photon calculation to arrays by @stephenmwilkins in #761
• Scale BH spectra by the bolometric_luminosity by @stephenmwilkins in #762
• Add dense basis method by @christopherlovell in #622
• Update particle_spectra_with_shift.c by @marcoleonardi97 in #768
• Update property_funcs.h by @marcoleonardi97 in #769
• Update property_funcs.c by @marcoleonardi97 in #770
• Update property_funcs.h by @marcoleonardi97 in #771
• Allow the loading of a Flares master file without abundances by @sophie-newman in #772
• using correct redshift from eagle header, plus bug in particle dust calculation by @aswinpvijayan in #773
• Quarantining dense_basis import to avoid print by @WillJRoper in #774
• Update sfzh.c by @marcoleonardi97 in #775
• Update integrated_line.c by @marcoleonardi97 in #776
• Update integrated_spectra.c by @marcoleonardi97 in #777
• Update particle_line.c by @marcoleonardi97 in #778
• Update particle_spectra.c by @marcoleonardi97 in #779
• Update particle_spectra_with_shift.c by @marcoleonardi97 in #780
• Update particle_spectra_with_shift.c by @marcoleonardi97 in #781
• Update particle_spectra_with_shift.c by @marcoleonardi97 in #782
• Add index for CAMELS Swift-EAGLE by @christopherlovell in #784
• Fix parametric young stars by @christopherlovell in #718
• Updating workflow versioning across the board by @WillJRoper in #786
• Giving filters.py some TLC by @WillJRoper in #785
• Some fixes for image creation with EmissionModels by @WillJRoper in #787
• Small fixes to the documentation by @sophie-newman in #788
• Vel shift spectra marco by @marcoleonardi97 in #783
• Cleaning up Morphology classes and streamlining the Sersic implementation by @WillJRoper in #755
• Add option to do metal free cloudy runs by @aswinpvijayan in #795
• Load eagle by @aswinpvijayan in #794
• Fixing lyman alpha escape fraction application by @WillJRoper in #789
• Giving the docs some TLC by @WillJRoper in #796
• Fixing limit_to argument in imaging methods by @WillJRoper in #797
• Vel shift spectra marco by @marcoleonardi97 in #790
• Update particle_spectra.c by @marcoleonardi97 in #799
• BUGFIX: Fixing the accepts decorator for list/tuple args by @WillJRoper in #800
• Update SVO load to check units on transmission by @christopherlovell in #792
• Introducing the Pipeline replacement by @WillJRoper in #763
• Fix unit error in filters.py to address PR 802 by @alex-rawlings in #803
• Automatically calculate the extent when plotting a map by @WillJRoper in #805
• Added photon energies as spectra coordinate by @WillJRoper in #807
• Including test data download in readme by @WillJRoper in #808
• Fully implementing Line fluxes by @WillJRoper in #806
• Fixed MPI heading level in pipeline docs by @WillJRoper in #809
• Always scale by the initial mass when initialising a parametric Stars object by @WillJRoper in #810
• Updating grid axes to work for old and new grids by @WillJRoper in #811
• Introducing velocity shifts in particle spectra (Will's modified version) by @WillJRoper in #804
• Adding some tests for emissions by @WillJRoper in #814
• Refining instantaneous SFH and metallicity distributions (+ SFH and Z Dist helpers) by @WillJRoper in #817
• Add ISM grain type from cloudy by @aswinpvijayan in #816
• Added a safety check for covering fractions exceeding unity by @WillJRoper in #813
• Added the ability to blend lines based on wavelength bins by @WillJRoper in #815
• Some Quality of Life improvements to the Template by @WillJRoper in #819
• Simplified the CAMELS data download by @WillJRoper in #824
• Added utility function for generating smoothing lengths by @WillJRoper in #822
• Refining examples and handling some default argument oddities by @WillJRoper in #820
• Folded the velocity shift flag into EmissionModels by @WillJRoper in #823

New Contributors

• @marcoleonardi97 made their first contribution in #768
• @alex-rawlings made their first contribution in #803

Full Changelog: v0.6.0-beta...v0.7.0-beta

Emission models, optimisations and various bugfixes

This tag serves as an intermediate tag including lots of bug fixes and improvements to the spectra generation using EmissionModel templates.

Note, that this tag should be used if you have any scripts that don't use units for all applicable inputs. After this tag, the version on main will require all applicable arguments to be passed with units.

For a full summary of the changes see the changelog below.

What's Changed

• Emission templating docs by @christopherlovell in #653
• Introducing EmissionModels and docs rework (Using dependency injection for spectra generation) by @WillJRoper in #624
• Removing automatic bolometric luminosity calculation by @WillJRoper in #662
• Enabling the discarding of spectra for memory savings by @WillJRoper in #661
• Implemented methods to return "Characteristic radii" by @WillJRoper in #656
• Ensuring emissions aren't prematurely deleted by @WillJRoper in #666
• Remove multiple returns for non-reprocessed grid in PacmanEmission by @WillJRoper in #669
• Added an escape fractionless PacmanEmission called ScreenEmission by @WillJRoper in #673
• Improved the emission model docs to include emitter info and parameter overides by @WillJRoper in #667
• Introduced tau conversions. by @AdrienFAVDASH in #676
• Added some extra defaults and controls to the installation process by @WillJRoper in #663
• Fixed assignment of dust emission and total spectra by @WillJRoper in #665
• Swift eagle loader by @christopherlovell in #660
• Removed conflicting Quantites from an Sed by @WillJRoper in #664
• Added a method to explicitly list spectra to save by @WillJRoper in #674
• Fix parametric young stars masks by @christopherlovell in #668
• Fix doc build example failures by @christopherlovell in #678
• BUGFIX: Fixed a bad error in line attenuation by @WillJRoper in #679
• BUGFIX: Ensuring a Grid always contains attributes even if they are None by @WillJRoper in #680
• Removing passing a FilterCollection to a Grid to limit wavelengths. by @aswinpvijayan in #682
• Introduced helper methods for clearing out emissions on a Galaxy and components by @WillJRoper in #675
• Optimisation and refactor of LOS calculations by @WillJRoper in #684
• BUGFIX: Ensure masked lines remain the same shape. by @WillJRoper in #687
• BUGFIX: Removed broken args when compiling without openmp by @WillJRoper in #688
• Introduced ability to get limit test data downloads by @WillJRoper in #685
• BUGFIX: Fixed PacmanEmission intrinsic model by @WillJRoper in #690
• Changed nebular nomenclature to birth to be more accurate in BimodalPacmanEmission by @WillJRoper in #691
• Grid age lookup table implementation by @christopherlovell in #694
• Replace equivalent_width attribute with method by @stephenmwilkins in #696
• Fix age lookup by @christopherlovell in #697
• Small fixes by @christopherlovell in #692
• Age grid updates and check added by @christopherlovell in #698
• Updating lines structure in the grid to give correct continua by @WillJRoper in #693
• Fixed deprecated arguments by @WillJRoper in #701
• Update parametric SFH models by @stephenmwilkins in #700
• Introduces threading in imaging module by @WillJRoper in #703
• Introducing an aperture method for an Image by @WillJRoper in #705
• Clearer photometry naming convention by @WillJRoper in #704
• Overlooked some places deprecation was needed and fixed typo in warning by @WillJRoper in #706
• BUGFIX: Stars.generate_particle_line didn't handle entirely masked out arrays properly by @WillJRoper in #707
• Introduced rotation methods for particles and galaxies by @WillJRoper in #708
• BUGFIX: Cautionary tale in using ones in tests (aperture fix) by @WillJRoper in #709
• lnu_to_fnu was missing from the conversions module by @WillJRoper in #710
• dust_to_metal_vijayan19 wouldn't necessarily update the dust masses by @WillJRoper in #711
• BUGFIX: Fixes various bugs when using a template by @WillJRoper in #712
• Making per particle spectra an emission model attribute not a method choice by @WillJRoper in #714
• Ensuring Synthesizer behaves predictably for galaxy with empty components by @WillJRoper in #713
• BUGFIX: Better handling of operation errors, NaNs, templates and optical depth fix by @WillJRoper in #715
• fix astrid mass scaling, other small fixes to load_data by @christopherlovell in #716
• Introduce a fallback data mirror on dropbox to get around server failures (until we find a better host) by @WillJRoper in #722
• Handle sed objects with ndim > 2 by @christopherlovell in #717
• Switching to a limitless bandwidth dropbox by @WillJRoper in #723
• Removing redundant coordinate shift in imaging by @WillJRoper in #721
• BUGFIX: apply_filter could cause divide by zero errors by @WillJRoper in #720
• Small fix for Filter.find_filter to ensure unit consistency by @WillJRoper in #719
• Adjusting plot size to avoid overlapping models in galaxy spectra docs by @WillJRoper in #724
• BUGFIX: Fixing Grid.get_spectra edge case by @WillJRoper in #727
• Catching more errors in downloads and redirecting to dropbox by @WillJRoper in #730
• Ensuring unit consistency in Emission generators by @WillJRoper in #725
• Fixing some Unified AGN bugs by @stephenmwilkins in #731
• Added a timeout for the primary data server to stop wait time by @WillJRoper in #740
• BUGFIX: Fixed mask behind the scenes mask generation for parametric BlackHole line generation by @WillJRoper in #738
• added nbh property to parametric blackholes by @stephenmwilkins in #743
• Add bolometric luminosity as property by @stephenmwilkins in #742
• Fix blackhole line bugs by @stephenmwilkins in #744
• Fixing the scaling in Unified AGN by @stephenmwilkins in #748
• Added luminosity function integration test by @christopherlovell in #741

New Contributors

• @AdrienFAVDASH made their first contribution in #676

Full Changelog: v0.5.0-beta...v0.6.0-beta

Pre-EmissionModel checkpoint

This is a checkpoint release. After this the process of getting spectra will be simplified by the introduction of EmissionModels, this will be a large breaking change that will render any non-updated pipelines unusable. To continue running those pipelines, this tag should be used.

Primarily this release introduces shared memory parallelism in spectra generation, updates to line emission, miscellaneous updates to documentation and workflows, and a number of small bug fixes. In addition lots of ground work has been put into the final release at this point with the next releases being smaller in scope and more converged on the final release version.

What's Changed

• Minor updates to lines by @stephenmwilkins in #546
• Fix unit conversion during PhotometryCollection intialisation by @WillJRoper in #558
• Fix bug where filter_codes aren't updated during ImageCollection addition by @WillJRoper in #556
• Cleaning up our dependencies by @WillJRoper in #554
• Test multiple python versions by @WillJRoper in #545
• Update conf.py by @christopherlovell in #559
• Giving grid.py some TLC by @WillJRoper in #565
• fixed issues with masks by @stephenmwilkins in #570
• Load FLARES now loads stellar smoothing lengths by @WillJRoper in #577
• changed instances of metals to metallicities by @aswinpvijayan in #579
• Added a function to visualise a spectra as a rainbow by @stephenmwilkins in #583
• add nebular continuum method on stellar component by @christopherlovell in #580
• Ensure filter resampling on new filter collection by @christopherlovell in #593
• fixing BlueTides ages bug (yrs --> Myrs) (fresh clone with pre-commit hook) by @sabrinastronomy in #594
• Add cloudy23 by @stephenmwilkins in #533
• Introduced a warnings module with a deprecation function and decorator by @WillJRoper in #586
• Fix dust bugs by @christopherlovell in #592
• Fixing docs build warnings and errors by @WillJRoper in #595
• Added an interactive grid explorer by @stephenmwilkins in #547
• Removed outdated tests/examples by @WillJRoper in #596
• Remove LineRatios, add line_ratios sub-module, and fix id bug by @stephenmwilkins in #552
• Implement particle based line emission and misc fixes by @WillJRoper in #599
• More intuitive multi-line Line objects (e.g. doublets). by @WillJRoper in #601
• Unknown pleasures by @stephenmwilkins in #609
• Particle line fix by @stephenmwilkins in #604
• added method on stars to generate attenuated spectra and produce summed Lines and LineCollections by @stephenmwilkins in #611
• Fix masking for particle_spectra_screen method by @stephenmwilkins in #615
• Raise warning when particle arrays empty and setting stars or gas to none by @christopherlovell in #619
• moved verbose to init, added more warnings by @aswinpvijayan in #625
• Simplifies Filter.apply_filter slightly by @WillJRoper in #629
• Added method for loading TNG data by @christopherlovell in #631
• Fix typo, add docs in TNG load data method by @christopherlovell in #632
• Added Filter.str by @WillJRoper in #633
• Made sure Filters are loaded from a HDF5 file cleanly by @WillJRoper in #634
• Converted prints to warnings by @WillJRoper in #636
• Script for reading eagle data into synthesizer by @aswinpvijayan in #628
• Setting DTM=0.3 for None cases by @aswinpvijayan in #641
• Moved intergrate_particle_spectra to component level by @WillJRoper in #635
• remove default IGM attenuation in get_fnu method by @christopherlovell in #642
• Fix dtype issue for age calculations by @christopherlovell in #643
• Los orientation by @aswinpvijayan in #644
• Implementing errors and malloc checks in C extensions, improving setup.py by @WillJRoper in #637
• Adds a plotting script for interfacing with valgrind and profiling scripts by @WillJRoper in #646
• Some much needed clean up and abstraction in the extensions by @WillJRoper in #647
• Introduced internal shared memory parallelism in spectra extensions with OpenMP by @WillJRoper in #648
• Documentation update by @christopherlovell in #600
• Switching to "more accurate" interpolation in terms of log metallicity by @WillJRoper in #651
• Swap integration routines by @christopherlovell in #544
• Option to add enchancement of IR luminosity due to CMB heating by @aswinpvijayan in #574

Full Changelog: v0.4.0-beta...v0.5.0-beta

Imaging improvements, apertures, `Grid` truncation, and development QOL

This release includes:

• Introduction of a PhotometryCollection for manipulating photometry.
• Complete rewrite of the imaging functionality improving flexibility.
• Particle based objects can now be masked using spatial apertures.
• Parametric young populations have been introduced.
• Filter objects (and collections) now initialise their wavelength arrays smartly and the ability to unify a Grid and FilterCollection has been implemented (allowing unification in both directions depending on the user's focus).
• Grids can now be truncated to useful wavelength ranges to limit memory usage.
• Linting and formatting is now done with ruff.
• Developers can now use a pre-commit hook to ensure their code is formatted correctly.