Tests Plasma Using Syrupy #2413

atharva-2001 · 2023-09-19T14:27:21Z

📝 Description

This PR has my extensions inside fixtures in the main conftest.py. It uses those fixtures to generate the snapshot_np and snapshot_pd fixtures in the plasma conftest.py file.
Until the Syrupy devs complete their PR syrupy-project/syrupy#816 to allow sending kwargs to custom extensions, we are stuck with fixed functions like assert_allclose for NumPy and Pandas. However I have sent them an example and asked them for a workaround. The snapshots are saved in a separate plasma directory.

TODO-

Remove parameters from test func definitions
Change lockfiles
Push data for all plasma tests
Make all checks pass (docstr fails)

📌 Resources

Examples, notebooks, and links to useful references.

Plasma data pull request- tardis-sn/tardis-regressions#1

🚦 Testing

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I updated the documentation according to my changes
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atharva-2001 · 2023-09-20T11:54:02Z

All the data which was generated(for test plasma complete at the moment)-
https://github.com/atharva-2001/tardis-refdata/tree/syrupy_plasma/syrupy_data

tardis_env3.yml

tardis/conftest.py

tardis/plasma/tests/test_complete_plasmas.py

jvshields · 2023-09-20T14:37:30Z

Needs an updated lockfile so that the tests don't break, and should remove the redundant assert statements in many tests. Other than that, it looks good to me!

codecov · 2023-09-29T08:07:12Z

Codecov Report

Merging #2413 (8a156df) into master (f89e125) will decrease coverage by 0.13%.
Report is 13 commits behind head on master.
The diff coverage is 77.27%.

❗ Current head 8a156df differs from pull request most recent head 36bf454. Consider uploading reports for the commit 36bf454 to get more accurate results

@@            Coverage Diff             @@
##           master    #2413      +/-   ##
==========================================
- Coverage   66.94%   66.82%   -0.13%     
==========================================
  Files         153      154       +1     
  Lines       13621    13651      +30     
==========================================
+ Hits         9119     9122       +3     
- Misses       4502     4529      +27

Files	Coverage Δ
tardis/plasma/tests/test_hdf_plasma.py	`91.42% <100.00%> (-3.31%)`	⬇️
tardis/plasma/tests/test_nlte_excitation.py	`100.00% <100.00%> (ø)`
tardis/plasma/tests/test_nlte_solver.py	`100.00% <100.00%> (ø)`
tardis/plasma/tests/test_plasma_contiuum.py	`100.00% <100.00%> (ø)`
tardis/plasma/tests/test_plasma_vboundary.py	`100.00% <100.00%> (ø)`
...s/plasma/tests/test_tardis_model_density_config.py	`100.00% <100.00%> (ø)`
...dis/montecarlo/montecarlo_numba/formal_integral.py	`54.43% <66.66%> (+0.11%)`	⬆️
tardis/io/atom_data/base.py	`91.62% <50.00%> (-0.84%)`	⬇️
tardis/plasma/properties/atomic.py	`85.60% <33.33%> (-0.62%)`	⬇️
tardis/plasma/tests/test_complete_plasmas.py	`96.59% <82.35%> (-0.47%)`	⬇️
... and 2 more

... and 1 file with indirect coverage changes

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andrewfullard · 2023-09-29T12:26:55Z

tardis/plasma/tests/test_nlte_excitation.py

-    )
+    # TODO: allow rtol=1e-6
+    assert snapshot_np == np.array(actual_rate_matrix)
+    # assert_allclose(


Does assert_allclose not work with the snapshot?

I'd have to create another snapshot fixture to get that to work. Does assert_almostequal not fulfill the needs?

The Syrupy devs are working on another PR which would enable the functionality to do this-
syrupy-project/syrupy#816

That's good, but this functionality is critical for our tests. I'm concerned about the timeline for the syrupy updates in this case.

I asked them, would let you know in sometime.

tardis-bot · 2023-10-02T13:17:19Z

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

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.github/workflows/tests.yml

andrewfullard · 2023-10-02T14:44:04Z

.github/workflows/tests.yml

+      - name: Clone tardis-sn/tardis-regressions
+        uses: actions/checkout@v4
+        with:
+          repository: atharva-2001/tardis-regressions


When will this be changed to the "official" repository?

I was thinking to change this once everything else is done.

tardis/plasma/tests/test_hdf_plasma.py

tardis/plasma/tests/test_nlte_excitation.py

andrewfullard · 2023-10-02T14:53:59Z

tardis/plasma/tests/test_nlte_solver.py

-        [0.0, 1.0, 0.0, 1.0, 2.0, -1.0],
-    ]
-    assert_almost_equal(actual_jacobian_matrix, desired_jacobian_matrix)
+    # TODO: allow for assert_almost_equal


I think if I understand correctly, assert_allclose is good enough

andrewfullard

Looks good to me! Time for the last bit of cleanup.

…ackets

andrewfullard · 2023-10-13T13:09:49Z

Why are tests failing now?

andrewfullard · 2023-10-18T15:53:05Z

Why are tests failing now?

Ah I see, because this is using the slightly outdated env without syrupy in

andrewfullard

great work atharva!

atharva-2001 · 2023-10-18T16:10:16Z

great work atharva!

Thank you so much! I might need to rebase this once #2441 is merged

atharva-2001 · 2023-10-23T03:46:30Z

Looks like since no merge conflicts are visible- this can be merged.
We can also merge the regressions PR if we want to see tests pass.
tardis-sn/tardis-regressions#1

andrewfullard · 2023-10-23T12:35:52Z

Tests complaining about no syrupy package in the env

atharva-2001 · 2023-11-01T11:36:59Z

Tests complaining about no syrupy package in the env

It's because the latest cache is not used. The cache is just ~400 MBs, I deleted them and the tests are now passing.

* 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]>

atharva-2001 added work in progress 🚧 testing 🚦 labels Sep 19, 2023

atharva-2001 marked this pull request as ready for review September 20, 2023 11:44

atharva-2001 requested review from epassaro, wkerzendorf and andrewfullard September 20, 2023 11:44

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andrewfullard self-requested a review September 20, 2023 14:59

atharva-2001 force-pushed the syrupy_plasma branch 2 times, most recently from ce094ad to af3ae92 Compare September 22, 2023 12:51

atharva-2001 mentioned this pull request Sep 29, 2023

Slash Command Update Syrupy Regression Data #2423

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atharva-2001 added 11 commits October 2, 2023 18:23

Add syrupy classes to conftest

a9afe7d

Add syrupy to env file

7c54354

Another folder for syrupy data

4cdca78

Save as npy instead of txt

e31de7a

Use syrupy fixtures

f0d06ab

Different assertion functions for pandas dataframes and series

f56055b

Zeta data fix

26c7b49

Blackify

f51eead

Blackify conftest

b331690

test_hdf_plasmas using syrupy

f464f3e

Install syrupy with conda

9384794

atharva-2001 added build-docs and removed restructure labels Oct 2, 2023

atharva-2001 requested review from andrewfullard and jvshields October 2, 2023 13:15

Merge remote-tracking branch 'upstream/master' into syrupy_plasma

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atharva-2001 added 2 commits October 3, 2023 13:20

remove commented out fixtures which are not used anywhere

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docs code render fix

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atharva-2001 force-pushed the syrupy_plasma branch from bbc056d to 99c8810 Compare October 3, 2023 08:31

andrewfullard previously approved these changes Oct 3, 2023

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tests final cleanup

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renaming files, yet to deal with ambr snapshot extension and curly br…

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atharva-2001 dismissed andrewfullard’s stale review via c093b3c October 11, 2023 09:57

renaming snapshots

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Tests Plasma Using Syrupy #2413

Tests Plasma Using Syrupy #2413

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Tests Plasma Using Syrupy #2413

Tests Plasma Using Syrupy #2413

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atharva-2001 commented Sep 19, 2023 • edited Loading

📝 Description

📌 Resources

🚦 Testing

☑️ Checklist

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