Refactor `make_source_function` into solver #3177

hmperk18 · 2025-07-07T20:00:54Z

📝 Description

Type: 🎢 infrastructure

Reorganizing the formal integral make_source_function function into a solver class and adds testing to the computed values.

Also, repairs the cuda tests/benchmarks that were broken in PR #3181.

How did you test these changes?

Testing pipeline - on m2 macbook and moria
Other method (describe)

Requires tardis-regression-data PR#61.

tardis-bot · 2025-07-07T20:02:11Z

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tardis-bot · 2025-07-07T20:02:35Z

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Hi human,
I ran ruff on the latest commit (378f47f).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

Details

4948	       	[ ] syntax-error
25	E902   	[ ] io-error
23	I001   	[*] unsorted-imports
21	F401   	[*] unused-import
16	G004   	[ ] logging-f-string
12	W605   	[*] invalid-escape-sequence
11	D202   	[*] blank-line-after-function
10	W291   	[ ] trailing-whitespace
10	RET505 	[*] superfluous-else-return
 8	W293   	[*] blank-line-with-whitespace
 4	B011   	[ ] assert-false
 4	PT015  	[ ] pytest-assert-always-false
 3	F821   	[ ] undefined-name
 3	NPY201 	[ ] numpy2-deprecation
 2	D406   	[*] missing-new-line-after-section-name
 1	E402   	[ ] module-import-not-at-top-of-file
 1	E701   	[ ] multiple-statements-on-one-line-colon
 1	E712   	[ ] true-false-comparison
 1	E722   	[ ] bare-except
 1	W292   	[*] missing-newline-at-end-of-file
 1	B019   	[ ] cached-instance-method
 1	B020   	[ ] loop-variable-overrides-iterator
 1	C416   	[ ] unnecessary-comprehension
 1	D407   	[*] missing-dashed-underline-after-section
 1	D411   	[*] no-blank-line-before-section
 1	D412   	[*] blank-lines-between-header-and-content
 1	N999   	[ ] invalid-module-name
 1	PERF102	[ ] incorrect-dict-iterator
 1	PERF403	[ ] manual-dict-comprehension
 1	RET506 	[*] superfluous-else-raise
 1	S604   	[ ] call-with-shell-equals-true
 1	TRY300 	[ ] try-consider-else
 1	UP004  	[*] useless-object-inheritance
Found 5118 errors.
[*] 97 fixable with the `--fix` option (15 hidden fixes can be enabled with the `--unsafe-fixes` option).

Complete output(might be large):

Details

benchmarks/spectrum_formal_integral.py:5:1: I001 [*] Import block is un-sorted or un-formatted
benchmarks/spectrum_formal_integral.py:26:5: B019 Use of `functools.lru_cache` or `functools.cache` on methods can lead to memory leaks
tardis/energy_input/GXPacket.py:1:1: N999 Invalid module name: 'GXPacket'
tardis/energy_input/GXPacket.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/GXPacket.py:41:16: UP004 [*] Class `GXPacket` inherits from `object`
tardis/energy_input/GXPacket.py:75:9: D407 [*] Missing dashed underline after section ("Returns")
tardis/energy_input/GXPacket.py:75:9: D406 [*] Section name should end with a newline ("Returns")
tardis/energy_input/GXPacket.py:202:13: F821 Undefined name `get_chain_decay_power_per_ejectamass`
tardis/energy_input/GXPacket.py:203:17: F821 Undefined name `inventory`
tardis/energy_input/decay_radiation.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/energy_source.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/energy_source.py:96:11: E712 Avoid equality comparisons to `True`; use `check:` for truth checks
tardis/energy_input/energy_source.py:112:16: C416 Unnecessary list comprehension (rewrite using `list()`)
tardis/energy_input/energy_source.py:198:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/energy_input/gamma_ray_packet_source.py:1:25: F401 [*] `astropy.units` imported but unused
tardis/energy_input/gamma_ray_packet_source.py:294:53: F821 Undefined name `positronium_continuum`
tardis/energy_input/gamma_ray_transport.py:231:9: PERF403 Use a dictionary comprehension instead of a for-loop
tardis/energy_input/gamma_ray_transport.py:456:39: PERF102 When using only the values of a dict use the `values()` method
tardis/energy_input/main_gamma_ray_loop.py:166:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:167:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:211:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:234:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:235:17: G004 Logging statement uses f-string
tardis/energy_input/main_gamma_ray_loop.py:295:17: G004 Logging statement uses f-string
tardis/energy_input/tests/conftest.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/energy_input/tests/conftest.py:16:12: S604 Function call with truthy `shell` parameter identified, security issue
tardis/energy_input/tests/test_gamma_ray_channel.py:119:9: B020 Loop control variable `isotope_dict` overrides iterable it iterates
tardis/energy_input/tests/test_gamma_ray_grid.py:12:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_grid.py:12:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_grid.py:18:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_grid.py:18:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:16:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:16:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:22:5: PT015 Assertion always fails, replace with `pytest.fail()`
tardis/energy_input/tests/test_gamma_ray_interactions.py:22:12: B011 Do not `assert False` (`python -O` removes these calls), raise `AssertionError()`
tardis/energy_input/tests/test_gamma_ray_packet_source_minimal.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/transport/GXPacket.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/transport/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/transport/tests/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/energy_input/util.py:409:5: RET505 [*] Unnecessary `elif` after `return` statement
tardis/energy_input/util.py:420:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/energy_input/util.py:422:5: D411 [*] Missing blank line before section ("Parameters")
tardis/io/model/parse_mass_fraction_configuration.py:4:25: F401 [*] `astropy.units` imported but unused
tardis/io/util.py:20:20: F401 [*] `tardis.__version__` imported but unused
tardis/model/matter/composition.py:173:9: RET505 [*] Unnecessary `else` after `return` statement
tardis/model/matter/decay.py:101:21: G004 Logging statement uses f-string
tardis/model/matter/decay.py:104:17: G004 Logging statement uses f-string
tardis/simulation/base.py:245:17: G004 Logging statement uses f-string
tardis/simulation/base.py:418:13: G004 Logging statement uses f-string
tardis/simulation/base.py:519:13: G004 Logging statement uses f-string
tardis/simulation/base.py:599:13: G004 Logging statement uses f-string
tardis/simulation/base.py:604:13: G004 Logging statement uses f-string
tardis/simulation/base.py:655:13: TRY300 Consider moving this statement to an `else` block
tardis/simulation/base.py:657:26: G004 Logging statement uses f-string
tardis/spectrum/formal_integral/base.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/base.py:3:24: F401 [*] `scipy.sparse` imported but unused
tardis/spectrum/formal_integral/base.py:4:31: F401 [*] `scipy.sparse.linalg` imported but unused
tardis/spectrum/formal_integral/base.py:8:33: F401 [*] `tardis.constants` imported but unused
tardis/spectrum/formal_integral/base.py:38:9: RET506 [*] Unnecessary `else` after `raise` statement
tardis/spectrum/formal_integral/base.py:115:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/formal_integral.py:5:31: F401 [*] `scipy.interpolate.interp1d` imported but unused
tardis/spectrum/formal_integral/formal_integral.py:81:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/formal_integral_cuda.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/formal_integral_cuda.py:85:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral/formal_integral_cuda.py:124:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral/formal_integral_numba.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/formal_integral_numba.py:29:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral/formal_integral_numba.py:59:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral/formal_integral_numba.py:134:12: NPY201 `np.trapz` will be removed in NumPy 2.0. Use `numpy.trapezoid` on NumPy 2.0, or ignore this warning on earlier versions.
tardis/spectrum/formal_integral/source_function.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/source_function.py:16:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/source_function.py:28:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/source_function.py:151:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/source_function.py:232:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/source_function.py:280:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/source_function.py:310:9: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/spectrum/formal_integral/source_function.py:322:5: D412 [*] No blank lines allowed between a section header and its content ("Attributes")
tardis/spectrum/formal_integral/source_function.py:322:5: D406 [*] Section name should end with a newline ("Attributes")
tardis/spectrum/formal_integral/tests/test_cuda_formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/tests/test_formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/tests/test_formal_integral.py:7:55: F401 [*] `tardis.transport.montecarlo.configuration.montecarlo_globals` imported but unused
tardis/spectrum/formal_integral/tests/test_formal_integral.py:13:27: F401 [*] `tardis.spectrum.formal_integral.formal_integral_cuda.calculate_p_values` imported but unused
tardis/spectrum/formal_integral/tests/test_formal_integral.py:14:5: F401 [*] `tardis.spectrum.formal_integral.formal_integral_cuda.intensity_black_body_cuda` imported but unused
tardis/spectrum/formal_integral/tests/test_numba_formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral/tests/test_numba_formal_integral.py:8:61: F401 [*] `tardis.spectrum.formal_integral.formal_integral.FormalIntegrator` imported but unused
tardis/spectrum/formal_integral/tests/test_numba_formal_integral.py:47:16: NPY201 `np.trapz` will be removed in NumPy 2.0. Use `numpy.trapezoid` on NumPy 2.0, or ignore this warning on earlier versions.
tardis/tests/test_tardis_full_formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/tests/test_tardis_full_formal_integral.py:3:17: F401 [*] `numpy` imported but unused
tardis/transport/montecarlo/base.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/transport/montecarlo/base.py:10:56: F401 [*] `tardis.opacities.continuum.continuum_state.ContinuumState` imported but unused
tardis/transport/montecarlo/base.py:12:5: F401 [*] `tardis.opacities.opacity_state.OpacityState` imported but unused
tardis/transport/montecarlo/packet_source.py:246:9: RET505 [*] Unnecessary `else` after `return` statement
tardis/util/base.py:188:20: NPY201 `np.trapz` will be removed in NumPy 2.0. Use `numpy.trapezoid` on NumPy 2.0, or ignore this warning on earlier versions.
tardis/util/base.py:339:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/util/base.py:513:5: E722 Do not use bare `except`
tardis/util/base.py:621:5: RET505 [*] Unnecessary `elif` after `return` statement
tardis/visualization/plot_util.py:54:5: RET505 [*] Unnecessary `else` after `return` statement
tardis/visualization/tests/test_plot_util.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/visualization/widgets/tests/test_line_info.py:10:1: E402 Module level import not at top of file
tardis/workflows/high_energy/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/high_energy/tests/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/high_energy/tests/conftest.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/high_energy/tests/test_tardis_he_workflow.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/simple_tardis_workflow.py:249:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:466:17: G004 Logging statement uses f-string
tardis/workflows/tardis_he_workflow.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/workflows/tardis_he_workflow.py:2:17: F401 [*] `numpy` imported but unused
tardis/workflows/tardis_he_workflow.py:4:25: F401 [*] `astropy.units` imported but unused
tardis/workflows/tardis_he_workflow.py:5:29: F401 [*] `astropy.constants` imported but unused
tardis/workflows/tardis_he_workflow.py:8:47: F401 [*] `tardis.energy_input.energy_source.get_nuclear_lines_database` imported but unused
tardis/workflows/tardis_he_workflow.py:72:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:84:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:93:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:103:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:107:90: W291 Trailing whitespace
tardis/workflows/tardis_he_workflow.py:112:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:127:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:134:1: W293 [*] Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:139:1: W293 Blank line contains whitespace
tardis/workflows/tardis_he_workflow.py:169:44: W291 [*] Trailing whitespace
tardis/workflows/tardis_he_workflow.py:170:54: W291 [*] Trailing whitespace
tardis/workflows/tardis_he_workflow.py:193:34: W292 [*] No newline at end of file
Found 123 errors.
[*] 68 fixable with the `--fix` option (15 hidden fixes can be enabled with the `--unsafe-fixes` option).

wkerzendorf · 2025-07-07T20:36:45Z

in this PR - can you make a sub package called formal integral.

hmperk18 · 2025-07-07T20:41:26Z

in this PR - can you make a sub package called formal integral.

Yep, I have the formal integral separated into a different package here in PR #3172. I can make this one rely on that. I was intending on blending them after #3172 was merged. I will double check everything there and make it not a draft.

codecov · 2025-07-07T21:09:09Z

Codecov Report

❌ Patch coverage is 84.83412% with 32 lines in your changes missing coverage. Please review.
✅ Project coverage is 71.72%. Comparing base (95358ad) to head (378f47f).
⚠️ Report is 17 commits behind head on master.

Files with missing lines	Patch %	Lines
...formal_integral/tests/test_cuda_formal_integral.py	10.00%	27 Missing ⚠️
...s/spectrum/formal_integral/formal_integral_cuda.py	50.00%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3177      +/-   ##
==========================================
+ Coverage   69.96%   71.72%   +1.75%     
==========================================
  Files         244      248       +4     
  Lines       17296    17359      +63     
==========================================
+ Hits        12102    12450     +348     
+ Misses       5194     4909     -285

☔ View full report in Codecov by Sentry.
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Rodot- · 2025-07-14T18:27:26Z

tardis/spectrum/formal_integral/source_function.py

+        source_level_idx = ma_int_data.source_level_idx.values
+        destination_level_idx = ma_int_data.destination_level_idx.values
+
+    # if transport.line_interaction_type == "macroatom":


You could make line_interaction_type a default kwarg passed to this function that the Solver class could then pass when performing calculations

tardis/spectrum/formal_integral/formal_integral_solver.py

andrewfullard · 2025-07-16T13:07:07Z

tardis/spectrum/formal_integral/source_function.py

+        self.line_interaction_type = line_interaction_type
+
+
+    def solve(self, sim_state, opacity_state, transport_state, atomic_data, levels):


The atomic_data should be part of the init, because it does not change between runs of the solver. levels is also part of the atomic data, so that doesn't need to be a separate argument.

when I use atomic_data.levels instead of plasma.levels I get an error with the size of dataframes when computing e_dot_u. I moved the atomic_data but left the levels where they are for now

tardis/spectrum/formal_integral/source_function.py

tardis/spectrum/formal_integral/tests/test_cuda_formal_integral.py

benchmarks/spectrum_formal_integral.py

atharva-2001 · 2025-08-06T13:44:49Z

tardis/tests/test_tardis_full_formal_integral.py

        expected = regression_data.sync_ndarray(luminosity.cgs.value)
        expected = u.Quantity(expected, "erg /s")
-        assert_quantity_allclose(luminosity, expected)
+        assert_quantity_allclose(luminosity, expected, rtol=1e-11, atol=0*u.erg/u.s)


Why is this needed? Sorry if this has been asked before

for all the tests we do - we always want to make sure to know exactly the tolerance.

tardis/spectrum/formal_integral/tests/test_source_function.py

Co-authored-by: Jing Lu <[email protected]>

tardis/spectrum/formal_integral/tests/test_source_function.py

wkerzendorf

etst

Adjusting tolerances Co-authored-by: Joshua Shields <[email protected]> Co-authored-by: Jack O’Brien <[email protected]> Co-authored-by: Jing Lu <[email protected]> Co-authored-by: Wolfgang Kerzendorf <[email protected]>

tardis/spectrum/formal_integral/tests/test_source_function.py

jvshields

Atols I think we always want to be 0.

tardis/spectrum/formal_integral/tests/test_source_function.py

Co-authored-by: Jing Lu <[email protected]>

…tolerance

Co-authored-by: Joshua Shields <[email protected]> Co-authored-by: Jack O'Brien <[email protected]> Co-authored-by: Jing Lu <[email protected]>

tardis-bot and others added 3 commits January 4, 2021 00:07

Update CHANGELOG.md [skip ci]

063a761

cherry picked initial source function solver

8401eae

use the new functions in make_source function

ef3bf92

solve now computes and returns the make_source_function parameters

d256988

update formal integral to use source function solver

85cbe49

tests all pass

6d77079

hmperk18 added 2 commits July 9, 2025 10:50

Merge branch 'master' into source-function-solver

060ed73

use SourceFunctionSolver in formal_integral

688e61f

hmperk18 self-assigned this Jul 11, 2025

hmperk18 added 3 commits July 14, 2025 09:28

Merge branch 'master' into source-function-solver

5ed2b65

initial tests

83deb89

use dataclass for source function results

995ba71

Rodot- reviewed Jul 14, 2025

View reviewed changes

hmperk18 added 2 commits July 14, 2025 14:32

Merge branch 'main' into source-function-solver

db3f6da

clean up comments/docstrings and finalize tests

141dd55

hmperk18 marked this pull request as ready for review July 14, 2025 21:09

hmperk18 mentioned this pull request Jul 14, 2025

add regression data for source function tests tardis-sn/tardis-regression-data#59

Merged

hmperk18 requested review from andrewfullard and wkerzendorf July 14, 2025 21:13

hmperk18 and others added 2 commits July 14, 2025 16:17

Merge branch 'master' into source-function-solver

e4adae3

fix tests

d37e9b2

hmperk18 mentioned this pull request Jul 16, 2025

Refactor FormalIntegral(s) into solver #3195

Closed

3 tasks

andrewfullard requested changes Jul 16, 2025

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hmperk18 added 2 commits July 16, 2025 09:38

rm formal integral solver - should be in different pr

02a93df

move sourcefunction methods and fix full_cuda test

1d5bef5

Rodot- self-requested a review August 5, 2025 19:35

rename and move more things around

84da32a

wkerzendorf reviewed Aug 5, 2025

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ruff and respond to comments

2553d17

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andrewfullard requested review from andrewfullard, atharva-2001, jvshields and wkerzendorf August 6, 2025 13:03

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jvshields and others added 3 commits August 6, 2025 11:04

Update tardis/spectrum/formal_integral/tests/test_source_function.py

8e4eeaa

Co-authored-by: Jing Lu <[email protected]>

Update tardis/spectrum/formal_integral/tests/test_source_function.py

ab9b752

Co-authored-by: Jing Lu <[email protected]>

Update tardis/spectrum/formal_integral/tests/test_source_function.py

ead381b

Co-authored-by: Jing Lu <[email protected]>

wkerzendorf reviewed Aug 6, 2025

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jvshields and others added 3 commits August 6, 2025 11:23

Update tardis/spectrum/formal_integral/tests/test_source_function.py

d64ad32

Co-authored-by: Jing Lu <[email protected]>

Refactor tests in test_source_function.py to use consistent relative …

1148e30

…tolerance

removed new-line

378f47f

Co-authored-by: Joshua Shields <[email protected]> Co-authored-by: Jack O'Brien <[email protected]> Co-authored-by: Jing Lu <[email protected]>

jvshields approved these changes Aug 6, 2025

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andrewfullard approved these changes Aug 6, 2025

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andrewfullard requested review from DeerWhale, atharva-2001 and wkerzendorf August 6, 2025 18:29

andrewfullard merged commit 20e253f into tardis-sn:master Aug 6, 2025
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		self.line_interaction_type = line_interaction_type


		def solve(self, sim_state, opacity_state, transport_state, atomic_data, levels):

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Refactor make_source_function into solver #3177

Refactor make_source_function into solver #3177

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Refactor `make_source_function` into solver #3177

Refactor `make_source_function` into solver #3177

hmperk18 commented Jul 7, 2025 •

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