Gamma ray spectra dep (#2793)

* Changed GX_packet to accommodate positron_fraction

* Added tardis like string

* Added positronium sampler

* Added time evolution of decays as the composition changes

* Added 3D Doppler function for all packets

* changed name of root to discriminant-helps in understanding

* Added sampling frequencies and positronium fraction

* Modified energy deposition

* Added tests and changed main loop

* Added changes to get deposition

* Modified how times and effective times are used

* Changed mailmap

* Black formatting

* changed GXpacket attribute

* Fixed test

* Added a note to change appending to dataframes

* Changed the positron fraction and updated with a function to extract packet info

* Black fixes

* Added black changes

* Added ToDo notes

* Added corrections to comments

* Comments addressed

* Added review suggestions and small changes to the GX packet

* Changes to conftest

* Changes to pair_creation_packet by adding time_start

* Removed not necessary comments

* Removed experimental features from this PR

* Changed name to time_start

* Refurbished the positronium sampling

* added a new array for getting energy in photons by area by time

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Co-authored-by: Anirban Dutta <duttaan2@moria.egr.msu.edu>

Updated packet_source to fix bug with BlackBodySimpleSource.create_pa… (

#2962)

Updated packet_source to fix bug with BlackBodySimpleSource.create_packets() not taking args or kwargs

Ensures consistency across codebase to ensure consistent codestyle (#…

…2951)

* for test

* Revert "for test"

This reverts commit 55a190d.

* @pytest.fixture -> @pytest.fixture()

* @pytest.fixture() to @pytest.fixture

* @fixture() to @fixture

Fix LFS sparse checkout (#2966)

* Change checkout methods for atom data

* Change checkout methods for atom data in action.yml

LFS Fixes typo fix

Fixes docs build error

V inner formal integral (#2800)

* Basic skeleton

* Lots of progress

Solvers pass info to each other
Simplified some parts

* Adds setup method, refactors some functions, removes unused items

* Move convergence setup to setup method

* Add docs notebook, fix a couple of errors

* Move setup to init

* Fix iteration and convergence

* Simplify spectrumsolver init

* Separate plasma "solver" and simulation state updates

* Simplify convergence solver setup with a dict.

* Minor formatting change

* Minor refactoring

* Fixes plasma update step

* Fixes loggers and progress bars

Also adds docstrings to methods. Updates some methods to use new functionality of the plasma. Adds requirements for the convergence plots (still broken)

* Fixes convergence plot rendering

* Fixes convergence plots in the final iteration

* black

* Simplify convergence plot updating

* Move logging handling to a separate class

* Add HDF output capability to solver

* Move more basic logging back into workflow

* Add not-converged error message

* Update notebook with export option

* Added simple base workflow and changed some verbiage

* Fix typo

* Moved solver workflow over to updated branch

* Added reprojection method for comparing arrays between iterations

* Updated schema and parser to add v_inner_boundary, added property to the model because it is named weirdly

* Added ntoebook for the IBVS workflow

* Updated workflow notebook to have correct convergence information, updated simple solver to properly set up the plasma with the new assembly

* Reduced size of overloaded functions to make them more in-line with the simple solver, updated simple solver to handle current tardis master branch

* cleared notebook outputs

* Updated notebook to use correctmethod

* Updated the docstrings

* removed unused imports

* Updated notebook to stop if converged

* Updated v_inner_solver to deal with detailed radiative rates types

* removed old comment

* Added docstrings, removed old comments

* Fixed typo

* Updated notebook to be more explicit

* removed old comment

* removed unused variable

* Changed the radiation_field to use the radiation field state properties with no explicit sovler method

* Added back radaition field to plasma solver in v_inner solver

* Added a solve opacity method

* Added docstring to solve_opacity method

* Fixed initializing opacity at the last iteration

* Added initial v_inner estimate in the __init__

* massively simplified the reproject method by just doing basic math

* added docstring describing the simplified reproject method so I don't forget why it works later

* Formatting error in doscstring

* Added nice logger output showing changes in geometry state

* Cleaned up the notebook a bit

* Updated the formal integral to handle changes in geometry

* Fixed the standard simulation solver

* Remove old files

* Fixes v_inner workflow

* Minor formatting changes

* Clean up confusing v_boundary_inner vs v_inner_boundary variable names

---------

Co-authored-by: Andrew Fullard <andrewgfullard@gmail.com>

Give tag in git cliff command (#2925)

Post-release 2024.12.29 (#2915)

Automated changes for post-release 2024.12.29

Post-release 2024.12.22 (#2909)

* Automated changes for post-release 2024.12.22

* Empty commit

---------

Co-authored-by: Atharva Arya <aryaatharva18@gmail.com>