Ci/update refdata ga #41
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* 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
* 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
* Possible fix for prerelease workflow * Fix double @ symbol * Changed to v2
* Pin setuptools_scm to v6 * Fix typo
* 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]>
Automated changes for pre-release 2022.11.17
Automated changes for post-release 2022.11.17
Automated changes for pre-release 2022.11.20
* 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 on rate_matrix * changed the np arange to use 0 instead of 0.0
* 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
* solved KN ZetaData issue * KN missing Zeta fixed * mailmap changed
Automated changes for pre-release 2022.12.11
Automated changes for post-release 2022.12.12
…ardis-sn#2170) * Add missing __init__.py files to transport subpackage * Add missing __init__.py file to geometry subpackage
Automated changes for pre-release 2022.12.25
Automated changes for post-release 2022.12.26
Automated changes for pre-release 2023.01.08
Automated changes for post-release 2023.01.11
adding nlte_atom_data to be downloaded
* 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]>
* 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]>
* checking if the object has the attribute decode * fixed another decode issue
* 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 tests
Automated changes for pre-release 2023.02.05
Automated changes for post-release 2023.02.06
* Add test for versioning info * Add version string to simulation objects * Add name to mailmap * Add another alias to mailmap
Automated changes for pre-release 2023.02.12
Automated changes for post-release 2023.02.16
Automated changes for pre-release 2023.02.19
* 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
Automated changes for post-release 2023.02.20
…on (tardis-sn#2214) * Correct the description of 'no_of_packets' in Monte Carlo Configuration * Added a simple description
Automated changes for pre-release 2023.02.26
Automated changes for post-release 2023.02.27
* 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]>
Download atom data from the function
Use gh CLI to approve pull requests; use new token
* Refresh packet progress bar after every iteration * Udpdated .mailmap * Reformatted with black
Automated changes for pre-release 2023.03.20
Automated changes for post-release 2023.03.20
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