Fix bug in relativistic packet source #2453

chvogl · 2023-10-25T11:06:01Z

📝 Description

Type: 🪲 bugfix

#2366 broke the BlackBodySimpleSourceRelativistic by changing mus to nus. The packets source thus assigns frequencies between 0 and 1. This PR fixes this.

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chvogl · 2023-10-25T11:08:25Z

I still need to add tests for the relativistic packet source (to make sure something similar doesn't happen again).
I will remove the draft status afterwards.

codecov · 2023-10-25T11:16:25Z

Codecov Report

Merging #2453 (97d23ec) into master (cfce38d) will increase coverage by 0.12%.
The diff coverage is 100.00%.

❗ Current head 97d23ec differs from pull request most recent head 239f570. Consider uploading reports for the commit 239f570 to get more accurate results

@@            Coverage Diff             @@
##           master    #2453      +/-   ##
==========================================
+ Coverage   67.11%   67.23%   +0.12%     
==========================================
  Files         155      155              
  Lines       13707    13729      +22     
==========================================
+ Hits         9199     9231      +32     
+ Misses       4508     4498      -10

Files	Coverage Δ
tardis/montecarlo/packet_source.py	`86.00% <100.00%> (+10.00%)`	⬆️
tardis/montecarlo/tests/test_packet_source.py	`94.23% <100.00%> (+4.23%)`	⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

wkerzendorf · 2023-10-26T12:17:36Z

I still need to add tests for the relativistic packet source (to make sure something similar doesn't happen again). I will remove the draft status afterwards.

@atharva-2001 can help with syrupy

wkerzendorf · 2023-10-26T12:17:56Z

and my apologies - that was my bad

tardis/montecarlo/tests/test_packet_source.py

wkerzendorf · 2023-10-30T21:48:53Z

is this done?

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

chvogl · 2023-10-31T10:48:38Z

I think this should be good enough for now. The tests are not great but I think fixing the bug has priority.

jamesgillanders

The code looks good Christian! Some minor comments but probably related to my poor understanding as opposed to the PR...

tardis/montecarlo/tests/test_packet_source.py

jamesgillanders

I'm happy with this

andrewfullard · 2023-11-01T13:48:10Z

Merging this despite fails- OSX fails are HDF breaking, docstr-cov is not important.

* Allow Simulation Tests to Run Independently (tardis-sn#2407) * Modify test_packet_source.py so that sim and tardis/tests can run * remove BasePacketSource * format * Add docstrings * Pre-release 2023.09.17 (tardis-sn#2411) Automated changes for pre-release 2023.09.17 * upgrading env in 2022 (tardis-sn#2410) * fix several bugs related to upgrade * fix the get function in pandas * fixed several incompatibilities for new libraries * fixed up the changes in pandas testing and other reindexing issues * fix other bugs with new environment * blackify tardis * updated the conda-lock file * add lock files * update cache number * fix simulation tests * remove units for testing * blackify * Update tardis/visualization/tools/tests/test_sdec_plot.py good catch Co-authored-by: Atharva Arya <[email protected]> * add assert * reset caches --------- Co-authored-by: Atharva Arya <[email protected]> * In gamma ray code : Changed times to np.geomspace (tardis-sn#2415) * Changed times to np.geomspace * Added myself to mailmap * rename RadialModel1D to SimulationState (tardis-sn#2417) * rename RadialModel1D to SimulationState * black files * rename simulation_state2 (tardis-sn#2421) * fixup of many files to make them pass the tests * change model for typo * Ignore tests in docstr coverage (tardis-sn#2424) ignore tests in docstr coverage * Disabled formal integral for continuum interaction (tardis-sn#2426) Disabled formal integral Co-authored-by: Alexander Holas <alexander.holas@h-its> * add linelist exposure to atom data and reader, built on current (tardis-sn#2428) * add linelist exposure to atom data and reader, built on current * add josh to mailmap * Modified how setup input energy takes isotope name. Earlier it was ga… (tardis-sn#2425) Modified how setup input energy takes isotope name. Earlier it was gamma_ray_lines.Isotope * Added a function to calculate shell masses (tardis-sn#2434) * Added a function to calculate shell masses * Added a function to calculate shell masses * changed shell masses with the new function * Fix duplicate entries in continuum line list (tardis-sn#2443) * Workaround list access * Formatting * Added error if duplicate * Remove duplicates * Fix typo, add comment * Remove bandaid fix * Cleanup * More cleanup * Fix numba parallel issues (tardis-sn#2447) * Enabled parallel * Fix the mistake * Update docs * Change glob patterns in `setup.cfg` (tardis-sn#2441) * Fix package_data in setup.cfg, mainly io and viz * more folders * Test pip installation * Remove test step * Fix more folders * restructure of geometry (tardis-sn#2422) * restructure of geometry * add radial1d boundary logic * black format * several fixes * fix epsilon * add testing of boundaries * change the r_inner_active * first integration with `from_config` working * hunting down density indexing bug * all model tests (without csvy) pass * more fixes * fix of model to simulation_state * fix inner boundary packet error * fix some leftovers * final fix for csvy * blackify * restructure to readers and remove some leftover code * further cleanup * first start of the restructure * add comment about removing quantitiness * add velocity check * add new abundance functions * remove default units * Add FAQ section to documentation (tardis-sn#2450) * Add faq * Added Overview * Fix typo * Remove lock file creation from pre release workflow (tardis-sn#2432) * Install latest version of mamba * Unpin conda lock installatiion * Split lockfilee creation to separate workflow * change docs installation- put a warning for conda forge installation and comment out install from package * fix * delete create lockfiles * download llock file * Pre-release 2023.10.20 (tardis-sn#2452) Automated changes for pre-release 2023.10.20 * Add verbose assert to NLTE rate equation (tardis-sn#2457) * add verbose assert * formatting * Fix bug in relativistic packet source (tardis-sn#2453) * Fix bug in relativistic packet source * Add initial test for BlackBodySimpleSourceRelativistic * Remove incorrect docstring * Update tardis/montecarlo/tests/test_packet_source.py Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Update tardis/montecarlo/tests/test_packet_source.py Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Rename all occurences of blackbodysimplesourcerelativistic * Do not hardcore blackbody_simplesource_relativistic.beta --------- Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Enable nlte ionization as plasma component (tardis-sn#2458) * Rename nlte ion and electron * Enable NLTE * Fix typo * Add docs * Fix transitionprob dtype * dtype conversion * dtype for sparse matrix * Typing in numba * Fix test variable name * Add missing electron density case * Fix typo * Update docstr-cov.yml to fix failing action (tardis-sn#2462) * Update docstr-cov.yml to fix failing action * Explicitly install setuptools * NLTE Ionization solver polish (tardis-sn#2461) * assertion for first guess * Add checks to decay * Fix greater equal * Fix deprecated series index * Pre-release 2023.11.05 (tardis-sn#2466) Automated changes for pre-release 2023.11.05 * Tests Plasma Using Syrupy (tardis-sn#2413) * Add syrupy classes to conftest * Add syrupy to env file * Another folder for syrupy data * Save as npy instead of txt * Use syrupy fixtures * Different assertion functions for pandas dataframes and series * Zeta data fix * Blackify * Blackify conftest * test_hdf_plasmas using syrupy * Install syrupy with conda * Remove additional line adding syrupy as a plugin * Set update snapshots config option when generate reference is selected * Remove old refdata code from test plasmas complete * Create plasma conftest file * Text based snapshot fixture with custom location * Snapshot path * tardis regressions my fork * Refactor test_hdf_plasmas.py * Format using black * test nlte excitation using syrupy * nlte solver * plasma continuum * test tardis model density config * Lock files * Increase cache no * format using black * cleanup- sort dependencies, delete comments * Documentation to run these tests * remove commented out fixtures which are not used anywhere * docs code render fix * tests final cleanup * renaming files, yet to deal with ambr snapshot extension and curly brackets * renaming snapshots * Add comments * Add astropy import guard (tardis-sn#2470) * Add astropy import guard * mailmap * Reading in decay radiation data in atom data (tardis-sn#2471) * Reading in decay radiation data in atom data * Added docstring * Fixes the checksum * Pre-release 2023.11.26 (tardis-sn#2477) Automated changes for pre-release 2023.11.26 * Update plasma configuration documentation (tardis-sn#2459) * update plasma docs * Update mailmap * Fix typo * Add ruff rules and docs (tardis-sn#2478) * Add ruff rules and docs * Update pyproject.toml Co-authored-by: Wolfgang Kerzendorf <[email protected]> * rebuild docs --------- Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Decay energy chain (tardis-sn#2448) * Added a function to calculate shell masses * Added a function to calculate shell masses * changed shell masses with the new function * Changed mass fraction to masses in to_inventories() * Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Added a function to calculate total decays * Added a function to calculate energies from gamma rays and positrons. * added a function to calculate average energies of gamma rays and positrons * Added a fucntion to calculate each decay chain energies * Added dictionaries to handle multiple isotopes * Changed value to values * added tests for gamma_ray_transport * Added tests for calculating activity * Added test for activity * Added tests for two isotope * Changed Ni_isotope_mass * Added pytest paramterize * Added test for calculating shell masses * Ran test for checking activity of parent nuclide with analytical solution. * The function test_activity matches with the radioactivedecay output upto 14 decimal places. The Avogadro's number used in radioactivedecay is not from astropy. * Added tests for checking if iso_dict is returning the right key. * Added test for inventories dictionary. * Added a test to check if the calculate_average_energy function passes the right list ahead. * Added new function for testing energy budget from each decay chain. * Added a new function for energy per mass * Reading in decay radiation data in atom data * Add * Added tests for gamma ray transport. * Added tests for all functions for gamma_ray_transport. Added docstrings. * Changing decay energy chain * Added a function to get taus * Added tests for multiple isotopes * Fixes the test calculate shell masses with hand calculated values * Use Mamba instead of conda * Run asv for last 5 commits * Add pull request trigger temporarily * Reset --------- Co-authored-by: tardis-bot <[email protected]> Co-authored-by: Wolfgang Kerzendorf <[email protected]> Co-authored-by: Anirban <[email protected]> Co-authored-by: Alexander Holas <[email protected]> Co-authored-by: Alexander Holas <alexander.holas@h-its> Co-authored-by: Joshua Shields <[email protected]> Co-authored-by: Anirban <[email protected]> Co-authored-by: Christian Vogl <[email protected]> Co-authored-by: Andrew <[email protected]>

Fix bug in relativistic packet source

d038b63

chvogl added relativity bugfix 🪲 priority - medium labels Oct 25, 2023

chvogl requested review from wkerzendorf, andrewfullard and AlexHls October 25, 2023 11:06

chvogl marked this pull request as draft October 25, 2023 11:06

jamesgillanders self-requested a review October 27, 2023 22:14

chvogl added 2 commits October 30, 2023 22:15

Add initial test for BlackBodySimpleSourceRelativistic

723c094

Remove incorrect docstring

4829563

wkerzendorf reviewed Oct 30, 2023

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tardis/montecarlo/tests/test_packet_source.py Outdated Show resolved Hide resolved

wkerzendorf reviewed Oct 30, 2023

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tardis/montecarlo/tests/test_packet_source.py Outdated Show resolved Hide resolved

Update tardis/montecarlo/tests/test_packet_source.py

42c2c1f

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

chvogl marked this pull request as ready for review October 31, 2023 10:46

Update tardis/montecarlo/tests/test_packet_source.py

3b920d1

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

Rename all occurences of blackbodysimplesourcerelativistic

e9a5701

chvogl requested a review from wkerzendorf October 31, 2023 14:59

jamesgillanders reviewed Oct 31, 2023

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tardis/montecarlo/tests/test_packet_source.py Show resolved Hide resolved

Do not hardcore blackbody_simplesource_relativistic.beta

239f570

jamesgillanders approved these changes Oct 31, 2023

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andrewfullard approved these changes Nov 1, 2023

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andrewfullard merged commit 33bea12 into tardis-sn:master Nov 1, 2023
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Fix bug in relativistic packet source #2453

Fix bug in relativistic packet source #2453

chvogl commented Oct 25, 2023 •

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chvogl commented Oct 25, 2023

codecov bot commented Oct 25, 2023 •

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wkerzendorf commented Oct 26, 2023

wkerzendorf commented Oct 26, 2023

wkerzendorf commented Oct 30, 2023

chvogl commented Oct 31, 2023

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andrewfullard commented Nov 1, 2023

Fix bug in relativistic packet source #2453

Fix bug in relativistic packet source #2453

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chvogl commented Oct 25, 2023 • edited Loading

📝 Description

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🚦 Testing

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chvogl commented Oct 25, 2023

codecov bot commented Oct 25, 2023 • edited Loading

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wkerzendorf commented Oct 26, 2023

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andrewfullard commented Nov 1, 2023

chvogl commented Oct 25, 2023 •

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