restructure of geometry #2422

wkerzendorf · 2023-09-28T19:32:25Z

No description provided.

wkerzendorf · 2023-09-30T01:22:54Z

It's draft for now but good to follow

tardis/model/geometry/tests/test_radial1d.py

tardis/model/geometry/radial1d.py

tardis/model/geometry/tests/test_radial1d.py

tardis/model/base.py

andrewfullard · 2023-10-04T18:46:26Z

tardis/model/geometry/radial1d.py

-        self.v_inner = v_inner
-        self.v_outer = v_outer
+    DEFAULT_VELOCITY_UNIT = u.km / u.s
+    DEFAULT_DISTANCE_UNIT = u.km


Not u.cm?

I think setting the defaults to be cgs makes most sense

atharva-2001 · 2023-10-09T09:34:05Z

Might be helpful- rebasing this or merging the master branch with this would disable code coverage workflow from checking on tests, so it would fail only when necessary.

Rodot- · 2023-10-09T22:52:06Z

tardis/model/base.py

            t_radiative = t_radiative[
-                self.v_boundary_inner_index
-                + 1 : self.v_boundary_outer_index
+                self.geometry.v_inner_boundary_index


Change v_inner_boundary_index to inner_boundary_index

can we make that an issue for now?

Rodot- · 2023-10-09T22:53:44Z

tardis/model/geometry/radial1d.py

+        )
+
+    @property
+    def v_outer_boundary_index(self):


Change name to outer_boundary_index

same as above.

codecov · 2023-10-10T03:52:40Z

Codecov Report

Merging #2422 (64a4266) into master (aea441c) will increase coverage by 0.16%.
Report is 6 commits behind head on master.
The diff coverage is 90.87%.

❗ Current head 64a4266 differs from pull request most recent head 9c680a8. Consider uploading reports for the commit 9c680a8 to get more accurate results

@@            Coverage Diff             @@
##           master    #2422      +/-   ##
==========================================
+ Coverage   66.94%   67.11%   +0.16%     
==========================================
  Files         153      155       +2     
  Lines       13621    13706      +85     
==========================================
+ Hits         9119     9199      +80     
- Misses       4502     4507       +5

Files	Coverage Δ
tardis/grid/base.py	`86.53% <ø> (ø)`
tardis/io/model/hdf.py	`100.00% <ø> (ø)`
tardis/io/model/model_reader.py	`33.09% <100.00%> (ø)`
tardis/io/model_reader.py	`0.00% <ø> (ø)`
tardis/io/tests/test_model_reader.py	`98.91% <100.00%> (ø)`
tardis/model/geometry/tests/test_radial1d.py	`100.00% <100.00%> (ø)`
tardis/model/tests/test_base.py	`100.00% <100.00%> (ø)`
tardis/model/tests/test_csvy_model.py	`97.29% <ø> (ø)`
tardis/montecarlo/base.py	`87.28% <100.00%> (ø)`
...dis/montecarlo/montecarlo_numba/tests/test_base.py	`97.36% <ø> (ø)`
... and 15 more

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

tardis/model/base.py

andrewfullard · 2023-10-10T20:47:39Z

tardis/model/base.py


    @property
    def r_middle(self):
        return 0.5 * self.r_inner + 0.5 * self.r_outer

    @property
    def velocity(self):
+        velocity = self.geometry.v_outer_active.copy()
+        return velocity.insert(0, self.geometry.v_inner_active[0])


Another early return

will clean up.

tardis/model/tests/test_base.py

andrewfullard · 2023-10-10T21:08:16Z

tardis/montecarlo/montecarlo_numba/tests/test_base.py

@@ -33,6 +33,7 @@ def test_montecarlo_main_loop(
    config_montecarlo_1e5_verysimple.montecarlo.no_of_virtual_packets = 0
    config_montecarlo_1e5_verysimple.montecarlo.iterations = 1
    config_montecarlo_1e5_verysimple.plasma.line_interaction_type = "macroatom"
+


not sure what you mean by this.

andrewfullard · 2023-10-10T21:08:38Z

tardis/montecarlo/montecarlo_numba/tests/test_vpacket.py

@@ -66,7 +66,8 @@ def test_trace_vpacket_within_shell(
    )

    npt.assert_almost_equal(tau_trace_combined, 8164850.891288479)
-    npt.assert_almost_equal(distance_boundary, 843684056256104.1)
+    # changed from almost equal to allclose. Now seems to work.


I assume you don't know why

no - you think it's fine?

Presumably it is related to the data types. The comment is fine anyway

tardis/simulation/tests/test_simulation.py

* 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]>

restructure of geometry

314cf30

wkerzendorf requested review from andrewfullard and atharva-2001 September 30, 2023 01:22

wkerzendorf added 2 commits October 4, 2023 12:17

add radial1d boundary logic

d353133

black format

2475551

wkerzendorf commented Oct 4, 2023

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tardis/model/geometry/tests/test_radial1d.py Show resolved Hide resolved

andrewfullard reviewed Oct 4, 2023

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wkerzendorf added 4 commits October 4, 2023 13:41

several fixes

e6d1697

fix epsilon

3c53cda

add testing of boundaries

6dce2b4

change the r_inner_active

1fdcea8

andrewfullard reviewed Oct 4, 2023

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andrewfullard reviewed Oct 4, 2023

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wkerzendorf added 3 commits October 7, 2023 17:14

first integration with from_config working

56e9da5

hunting down density indexing bug

f6743d7

all model tests (without csvy) pass

b55b21d

wkerzendorf added 2 commits October 9, 2023 13:04

more fixes

ed978d9

fix of model to simulation_state

cae9c19

Rodot- reviewed Oct 9, 2023

View reviewed changes

wkerzendorf added 3 commits October 9, 2023 19:01

fix inner boundary packet error

d829e73

fix some leftovers

9592a97

final fix for csvy

4da6869

blackify

f381d2e

andrewfullard reviewed Oct 10, 2023

View reviewed changes

wkerzendorf added 3 commits October 10, 2023 20:11

restructure to readers and remove some leftover code

e59741d

further cleanup

a42dd55

first start of the restructure

3288c6c

add comment about removing quantitiness

518a8f9

andrewfullard self-requested a review October 11, 2023 20:59

add velocity check

c78b6de

andrewfullard previously approved these changes Oct 11, 2023

View reviewed changes

add new abundance functions

006ca9d

wkerzendorf dismissed andrewfullard’s stale review via 006ca9d October 12, 2023 13:05

remove default units

9c680a8

andrewfullard requested review from Rodot- and andrewfullard October 13, 2023 13:07

andrewfullard approved these changes Oct 13, 2023

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Rodot- approved these changes Oct 19, 2023

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andrewfullard merged commit 1503684 into tardis-sn:master Oct 19, 2023
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restructure of geometry #2422

restructure of geometry #2422

wkerzendorf commented Sep 28, 2023

wkerzendorf commented Sep 30, 2023

andrewfullard Oct 4, 2023

wkerzendorf Oct 10, 2023

andrewfullard Oct 11, 2023

atharva-2001 commented Oct 9, 2023

Rodot- Oct 9, 2023

wkerzendorf Oct 10, 2023

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restructure of geometry #2422

restructure of geometry #2422

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