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Restructure/estimators#2500

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wkerzendorf wants to merge 199 commits intotardis-sn:mastertardis-sn/tardis:masterfrom wkerzendorf:restructure/estimatorswkerzendorf/tardis:restructure/estimatorsCopy head branch name to clipboard

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Commits on Sep 28, 2023

• restructure of geometry

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Commits on Oct 4, 2023

• add radial1d boundary logic

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• black format

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• several fixes

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• fix epsilon

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• add testing of boundaries

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• change the r_inner_active

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Commits on Oct 7, 2023

• first integration with from_config working

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Commits on Oct 8, 2023

• hunting down density indexing bug

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• all model tests (without csvy) pass

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Commits on Oct 9, 2023

• more fixes

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• fix of model to simulation_state

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• fix inner boundary packet error

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Commits on Oct 10, 2023

• fix some leftovers

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• final fix for csvy

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• blackify

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Commits on Oct 11, 2023

• restructure to readers and remove some leftover code

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• further cleanup

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• first start of the restructure

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• add comment about removing quantitiness

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• add velocity check

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Commits on Oct 12, 2023

• add new abundance functions

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• remove default units

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• add new matter module

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• several restructures. move decay from io to tardis/model/matter

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Commits on Oct 13, 2023

• mid restructure

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Commits on Oct 20, 2023

• slow progress on abundance refactor

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Commits on Oct 22, 2023

• include effective_element_masses

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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Commits on Nov 2, 2023

• further updates

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• fix of csvy readers

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Commits on Nov 4, 2023

• last fixes to custom abundance widget

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Commits on Nov 5, 2023

• restructuring the radiation field

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• some cleanup

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• Merge branch 'restructure/abundance' into restructure/radiation_field

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• cleanup

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• further cleanup

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• Merge branch 'restructure/abundance' into restructure/radiation_field

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• clearnup

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Commits on Nov 6, 2023

• changes

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Commits on Nov 8, 2023

• remove matter base.py

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• removing matter

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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Commits on Nov 10, 2023

• Fix zero division handling in normalize_trans_probs (which breaks to_hdf)

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• Use correct references_idx for levels

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• Convert probabilities to float64

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Commits on Nov 20, 2023

• fixed last tests

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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• first commit for regression_data

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• Merge branch 'restructure/abundance' into restructure/radiation_field

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• add several parsers

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• add composition

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• remove isotopemassfractions

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• some small fixes

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• Merge branch 'restructure/abundance' into restructure/radiation_field

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• fixed w, t_rad to dilution_factor, t_radiative

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• add setters for w, t_rad

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Commits on Nov 21, 2023

• several fixes for instantiating the right t_rads.

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• add the from_config atom_data

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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• fixing model.ipynb

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• Merge branch 'restructure/abundance' into restructure/radiation_field

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• fix some more tests

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• start of montecarlo restructure

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Commits on Nov 22, 2023

• large scale changes

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Commits on Nov 23, 2023

• further disentangling state and solver

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• fix tests

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• fix some of the issues wdigets

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• assert mass fractions positive.

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• update estimators

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• add packet collection

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• move spectrum to mct_state

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• add radiation_field_state

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• Merge branch 'restructure/radiation_field' into restructure/transport_solver

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Commits on Nov 24, 2023

• Refactor packet initialization in

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• Update model_nparray_attrs in test_base.py and fix

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• Fix temperature assertion in

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Commits on Nov 26, 2023

• Fix Integrator

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• Fix SDEC plot for MCTState

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• Fix variable names in transport module

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Commits on Nov 27, 2023

• Refactor the to_hdf code.

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• Refactor Monte Carlo transport solver

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• Fix isotope mass fraction typo and t_radiatve duplicate definition

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• Document remove functionality for effective element masses

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• Fix variable name in

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• Refactor test names and variable names in

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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Commits on Nov 28, 2023

• restructuring montecarlo state

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Commits on Nov 29, 2023

• Refactor gamma ray simulation setup and test

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• fix gamma ray tests

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• Add model_isotope_time_0 property to abundances

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• Add test for montecarlo main loop with vpacket

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• Refactor config_reader and config_validator

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• Fix model_isotope_time_0 property in

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• Refactor simulation module to use pathlib

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• remove bad comment and refactor with ruff

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• Fix variable name in test_simulation_state_mass()

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• Fix unit conversion in calculate_cell_masses

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• Fix logger debug message in CSV reader and update

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• black formatting

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• Refactor code to use composition variable in

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Commits on Nov 30, 2023

• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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• Refactor imports in atom_web_download.py and

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Commits on Dec 4, 2023

• fix for documentation not builiding

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• add fix for model_isotope_time_0

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• fix grid test

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• restructure the grid

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• final change

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• Merge branch 'restructure/abundance' into restructure/radiation_field

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• add stuff

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• add vpacket_log

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• transfer over to VPacketCollection constructor

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• Refactor model_reader.py and shell_info.py

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• Update damping constants and variable names

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• Refactor vpacket tracking in montecarlo_radial1d

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• fix w in several places in tardis

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• slowly fixing radiation_field changes

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• fixing montecarlo tests

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• Merge remote-tracking branch 'origin/restructure/radiation_field' into restructure/radiation_field

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• slowly fixing vpacket_tracker

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• last fix

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• change hdf from model to simulation_state

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• fixing model->simulation-state

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• Merge remote-tracking branch 'upstream/master' into restructure/radiation_field

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• Fix model_reader.py imports and formatting issues

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• Refactor variable names for clarity and

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• Update variable names in model.ipynb

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• Update variable name for average temperature

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Commits on Dec 5, 2023

• Merge branch 'restructure/radiation_field' into restructure/transport_solver

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• Fix file paths in test_grid.py, test_base.py,

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• Fix transport dictionary comparison

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Commits on Dec 7, 2023

• Merge branch 'restructure/radiation_field' into tests/regression_data

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Commits on Dec 9, 2023

• Implement regression data configurations

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• Refactor snapshot fixtures and add regression data

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Commits on Dec 10, 2023

• Update to new testing framework

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• Merge remote-tracking branch 'origin/restructure/radiation_field' into tests/regression_data

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• Refactor imports and fixtures in conftest.py and

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• Make regression-data optional

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• Fix regression data synchronization in plasma

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• Refactor variable names in model reader and

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• Refactor store_model_to_hdf to

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Commits on Dec 11, 2023

• Refactor HDF file handling and model reader

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• add docstr

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• Merge branch 'restructure/radiation_field' into tests/regression_data

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• Merge branch 'tests/regression_data' into restructure/transport_solver

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• Merge branch 'restructure/transport_solver' into restructure/separate_transport_state

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• Merge remote-tracking branch 'upstream/master' into tests/regression_data

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• Remove syrupy_extensions.py

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Commits on Dec 14, 2023

• Refactor code and remove unused imports and

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Commits on Dec 15, 2023

• Merge remote-tracking branch 'upstream/master' into restructure/transport_solver

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• Fix test_base and test_simulation

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• Merge branch 'restructure/transport_solver' into restructure/separate_transport_state

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• setting up regression with github actions

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Commits on Dec 16, 2023

• Update LFS cache IDs for refdata and regression

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• Fix test_montecarlo_radial1d function

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• Update sync_hdf_store method in RegressionData class

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• Refactor test_base.py for improved accuracy and precision

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• update docstrings

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• Merge branch 'tests/regression_data' into restructure/transport_solver

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Commits on Dec 20, 2023

• Refactor transport state access in test_base.py

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• Fix warnings and add HDF output in sdec_plot.ipynb and cleanup regression_data.py

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Commits on Dec 21, 2023

• Update demo.hdf file

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Commits on Dec 24, 2023

• Fix negative values in last_interaction_types

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• Update URL for atomic data repository

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• Refactor code for improved readability and maintainability

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• Refactor code to remove unnecessary array conversion

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• Refactor code to remove unnecessary conversion to numpy array in test_hdf_scalars

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• Merge branch 'tests/regression_data' into restructure/transport_solver

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• Merge remote-tracking branch 'upstream/pr/2469' into restructure/estimators

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