* Adding rate matrix index (tardis-sn#2132)

* adding NlteIndexHelper class

* adding nlte_ionization_species to io/schemas/plasma.yml

* adding nlte_excitation_species to io/schemas/plasma.yml

* added nlte_ionization_species in assemble_plasma

* fixed the issue with getting nlte_ionization_species from config

* fixed transforming string from config to tuple for nlte ionization species

* ran black

* attempt of writing tests 1

* ran black

* test attempt 2

* black on test_hdf_plasma

* experimenting with revert

* attempt 3

* reverted tardis/plasma/tests/test_complete_plasmas.py

* reverted tardis/plasma/tests/test_hdf_plasma.py

* adding cofig for nlte

* adding fixture for tardis_cofig_verysimple_nlte

* added test_plasma_nlte_section_config

* ran black

* fixed the issue with the test, ran it locally

* ran black on necessary files

* updated description in schemas

* switching from nlte_ionization to be used from self

* ran black

* changed nlte_properties_new to nlte_solver_properties

* adding nlte_rate_equation_matrix.py

* reverting to previous commit

* Restructuring NumbaModel (tardis-sn#2136)

* Added NumbaRadial1DGeometry

* Added to_numba function

* Fixed incorrect naming of numba spec

* Updated docstring

* Updated to_numba docstring

* Updated docstring

* Updated numba model to contain only time explosion

* updated docstring formatting error

* Moved geometry to new geometry sub package

* Updated all functions where numba model was used

* Updated to specify units

* converting time_explosion to seconds specifically

* Added numba geometry fixture

* Updated tests to work with numba geometry

* Updated formatting

* Fixed issue with geometry initialization

* Fixed formatting

* Add missing cell to download atom data (tardis-sn#2146)

* Possible fix for prerelease workflow (tardis-sn#2127)

* Possible fix for prerelease workflow

* Fix double @ symbol

* Changed to v2

* Pin setuptools_scm to v6 (tardis-sn#2147)

* Pin setuptools_scm to v6

* Fix typo

* Adding nlte_rate_equation_solver.py (tardis-sn#2140)

* added nlte_rate_equation_matrix

* adding the rate_equation_matrix

* moved rate_matrix into a class NLTERateEquationSolver

* fixed a bug in rate_matrix_index, added an example for checking if rate matrix works properly

* changed the initial electron density for now

* added tests, fixed a small bug

* added some doctrings

* fixed a typo

* added some doctrings

* added some doctrings part 2

* added some docstrings part 3

* removed unnecessary import

* Update tardis/plasma/properties/nlte_rate_equation_solver.py

Co-authored-by: Christian Vogl <[email protected]>

* changed how atomic number is created from rate_matrix_index

* changed call of a function

* got rid of unnecessary if statement in set_nlte_ion_rate

* renamed last_row to charge_conservation_row

* switched 0, 1 to atomic_number and ion_number to make it more readable

* swtihed from rates to coefficients

* changed the matrix set up to only keep necessary row for nlte_ion

* ran black

* fixing some doctrings

* swtiched from using numbers to index names

* switched the return statement to NotImplementedError

* changed groupby from 0, 1 to atomic number, ion number

* fixed an issue in the test

* ran black

Co-authored-by: Christian Vogl <[email protected]>

* Set specific qgrid feedstock version (tardis-sn#2152)

* Pre-release 2022.11.17 (tardis-sn#2155)

Automated changes for pre-release 2022.11.17

* Post-release 2022.11.17 (tardis-sn#2156)

Automated changes for post-release 2022.11.17

* Pre-release 2022.11.20 (tardis-sn#2160)

Automated changes for pre-release 2022.11.20

* Fix relativistic packet initialization (tardis-sn#2159)

* Fix setting of full relativity flag

* Add relativistic packet source

Co-authored-by: Stuart Sim <[email protected]>

* Fix relativistic vpackets on inner boundary

Co-authored-by: Stuart Sim <[email protected]>

* Fixing typos for nlte ion (tardis-sn#2154)

* fixing typos on rate_matrix

* changed the np arange to use 0 instead of 0.0

* NLTE jacobian matrix (tardis-sn#2158)

* added jacobian matrix and deriv block functions

* added doctrings

* ran black

* switched from df to array

* added an initial test

* ran black

* reorganized the tests

* added doctrings

* added todo comments for future work

* ran black

* Kilonova missing zeta (tardis-sn#2150)

* solved KN ZetaData issue

* KN missing Zeta fixed

* mailmap changed

* Pre-release 2022.12.11 (tardis-sn#2172)

Automated changes for pre-release 2022.12.11

* Post-release 2022.12.12 (tardis-sn#2173)

Automated changes for post-release 2022.12.12

* Add missing __init__.py files to transport and geometry subpackages (tardis-sn#2170)

* Add missing __init__.py files to transport subpackage

* Add missing __init__.py file to geometry subpackage

* Pre-release 2022.12.25 (tardis-sn#2180)

Automated changes for pre-release 2022.12.25

* Post-release 2022.12.26 (tardis-sn#2182)

Automated changes for post-release 2022.12.26

* Pre-release 2023.01.08 (tardis-sn#2186)

Automated changes for pre-release 2023.01.08

* Post-release 2023.01.11 (tardis-sn#2188)

Automated changes for post-release 2023.01.11

* Downloading nlte_atom_data in ref data (tardis-sn#2187)

adding nlte_atom_data to be downloaded

* Adding nlte solver (tardis-sn#2171)

* adding solver part in the calculate method

* adding the objective function

* added the solution vector method

* final touches for the solver

* tests, attempt 1

* ran black

* fixed the issue with tests

* ran black

* added missing doctrings in the nlte_rate_equation_solver.py

* added doctrings to tests

* changed the test to explicitly calculate the lte solution ion number densities.

* ran black

* added the atom data file to download_reference_data.sh

* fixed download_reference_data.sh

* Revert "added the atom data file to download_reference_data.sh"

This reverts commit 58ce29e.

* got rid of index i, kept only shell

* switched DataFrame to pandas.DataFrame in the docstrings

* docstring bug fix

* got rid of the deepcopy of nlte atomic data file

* changed the number of shells to 5

* Update tardis/io/tests/data/tardis_configv1_nlte.yml

Co-authored-by: Christian Vogl <[email protected]>

* Update tardis/plasma/properties/nlte_rate_equation_solver.py

Co-authored-by: Christian Vogl <[email protected]>

* Update tardis/io/tests/data/tardis_configv1_nlte.yml

Co-authored-by: Christian Vogl <[email protected]>

* Update tardis/io/tests/data/tardis_configv1_nlte.yml

Co-authored-by: Christian Vogl <[email protected]>

* ran black

* Update tardis/plasma/properties/nlte_rate_equation_solver.py

Co-authored-by: Christian Vogl <[email protected]>

* Update tardis/plasma/tests/test_nlte_solver.py

Co-authored-by: Christian Vogl <[email protected]>

* restructured a summary in a docstring for the solution_vector_block

* ran black

* added the test for w=0 case

* Update tardis/plasma/properties/nlte_rate_equation_solver.py

Co-authored-by: Christian Vogl <[email protected]>

* Update tardis/plasma/properties/nlte_rate_equation_solver.py

Co-authored-by: Christian Vogl <[email protected]>

* Update tardis/plasma/tests/test_nlte_solver.py

Co-authored-by: Christian Vogl <[email protected]>

* fixed an issue in a docsting

* fixed an issue in a docsting

* removed a TODO comment

Co-authored-by: Christian Vogl <[email protected]>

* Rename T variables to temperature  (tardis-sn#2185)

* fixes tardis-sn#1600

* fixes tardis-sn#1600

* Update tardis/montecarlo/packet_source.py

Co-authored-by: Atharva Arya <[email protected]>

* fixes codestyle

* improve codestyle

* rename the function

* Update packet_source.py

* improve codequality

* add commit

* Update packet_source.py

Co-authored-by: Atharva Arya <[email protected]>

* Fixing test_store_runner_to_hdf (tardis-sn#2198)

* checking if the object has the attribute decode

* fixed another decode issue

* Reading nlte_excitation_species from config (tardis-sn#2195)

* implementing nlte_excitation

* ran black

* fixed a typo

* got rid of unnecessary lines

* rewrote tests

* made a change on assigning the config values to plasma properties

* fixed the tests

* Update tardis/io/tests/test_config_reader.py

Co-authored-by: Christian Vogl <[email protected]>

---------

Co-authored-by: Christian Vogl <[email protected]>

* Fix config reader tests (tardis-sn#2200)

Fix config tests

* Pre-release 2023.02.05 (tardis-sn#2205)

Automated changes for pre-release 2023.02.05

* Post-release 2023.02.06 (tardis-sn#2206)

Automated changes for post-release 2023.02.06

* Add version tag to simulation objects (tardis-sn#2190)

* Add test for versioning info

* Add version string to simulation objects

* Add name to mailmap

* Add another alias to mailmap

* Pre-release 2023.02.12 (tardis-sn#2208)

Automated changes for pre-release 2023.02.12

* Post-release 2023.02.16 (tardis-sn#2210)

Automated changes for post-release 2023.02.16

* Pre-release 2023.02.19 (tardis-sn#2211)

Automated changes for pre-release 2023.02.19

* Cache LFS objects in the tests workflow (tardis-sn#2194)

* Cache LFS objects (actions/checkout#165)

* Delete steps to see file size

Delete commented step which used to download LFS objects using the bash script

* Add lfs:false flag

* Add my username to .mailmap

* Cache hit and allow pytest to run all tests

* Do git lfs checkout if the cache key is found

* Post-release 2023.02.20 (tardis-sn#2213)

Automated changes for post-release 2023.02.20

* Correct the description of 'no_of_packets' in Monte Carlo Configuration (tardis-sn#2214)

* Correct the description of 'no_of_packets' in Monte Carlo Configuration

* Added a simple description

* Pre-release 2023.02.26 (tardis-sn#2222)

Automated changes for pre-release 2023.02.26

* Post-release 2023.02.27 (tardis-sn#2223)

Automated changes for post-release 2023.02.27

* Add docstrings to subpackages (tardis-sn#2204)

* add docstring to subpackage grid

* Add docstrings to subpackages

* Change comments to docstrings

* add docstrings to subpackages

* rename gui/__init__.py

* Reformat using black

* add contributor infos to mailmap file

* add extended summary to docstrings

* Add extended summary to plasma/properties

* Update tardis/io/parsers/__init__.py

Co-authored-by: Sona Chitchyan <[email protected]>

---------

Co-authored-by: kim <[email protected]>
Co-authored-by: Sona Chitchyan <[email protected]>

* Docs Fix: Download Atom Data in rpacket_tracking.ipynb (tardis-sn#2236)

Download atom data from the function

* Fix for automerge (tardis-sn#2242)

Use gh CLI to approve pull requests; use new token

* Fix for release dates (tardis-sn#2243)

* MonteCarlo packet progress bar completes to 100% (tardis-sn#2237)

* Refresh packet progress bar after every iteration

* Udpdated .mailmap

* Reformatted with black

* Fix team reviewers on workflows (tardis-sn#2246)

* Pre-release 2023.03.20 (tardis-sn#2247)

Automated changes for pre-release 2023.03.20

* Post-release 2023.03.20 (tardis-sn#2248)

Automated changes for post-release 2023.03.20

* Create new workflow

* Patch for arepo tests

* Restore deleted parameter

* Black format; Add missing skip reason

* Fix typo in comment

* Add more comments

* Create slash command dispatcher

* Changes to dispatcher

* Black format

---------

Co-authored-by: Sona Chitchyan <[email protected]>
Co-authored-by: Satwik Kambham <[email protected]>
Co-authored-by: Andrew <[email protected]>
Co-authored-by: Christian Vogl <[email protected]>
Co-authored-by: tardis-bot <[email protected]>
Co-authored-by: Stuart Sim <[email protected]>
Co-authored-by: gleck97 <[email protected]>
Co-authored-by: ABHISHEK PATIDAR <[email protected]>
Co-authored-by: Atharva Arya <[email protected]>
Co-authored-by: Kim <[email protected]>
Co-authored-by: Abhishek Patidar <[email protected]>
Co-authored-by: Le Truong <[email protected]>
Co-authored-by: kim <[email protected]>
Co-authored-by: Shreyas Singh <[email protected]>

Automated changes for pre-release 2023.02.26

Automated changes for pre-release 2023.02.26