Migration to depthcharge v0.4.8 #350

andradesalazar · 2024-07-01T18:59:16Z

This version of Casanovo is now based on depthcharge v0.4.8 instead of v.0.2.3.

wfondrie

Thank you for this excellent PR 🎉

As a note for others, PR also adds a few features and changes some functionality. Some that I noticed:

Checkpoints now have useful file names.
Early stopping can be enabled.
The learning rate is logged.
Model precision can now be changed.
Various gradient things (clipping and such) can be configured. These are very useful for stability.

I've requested a few, mostly small changes. The biggest thing we need to address now are updates to the unit tests, so that all of our CI checks pass.

@wsnoble, @bittremieux, @melihyilmaz - with as big of a change as this is, you should all take it for a spin and make sure we didn't miss anything!

casanovo/data/ms_io.py

casanovo/config.yaml

casanovo/denovo/dataloaders.py

casanovo/denovo/model_runner.py

pyproject.toml

andradesalazar · 2024-07-29T16:26:26Z

Hi @wfondrie ,

thanks for the comments :)

are you taking care of the updates to the unit tests, so that the CI checks pass or is it better if I have a look?

I think the documentation probably needs to be updated a bit, as well as the download of the latest weights for prediction, as the old ones are not compatible anymore.

Best,
Daniela

bittremieux · 2024-07-29T18:11:44Z

I think the documentation probably needs to be updated a bit, as well as the download of the latest weights for prediction, as the old ones are not compatible anymore.

Yes, we'll cut a new release v5.x.x for this implementation, as these are some breaking changes. We'll have to train a new model, but with the new major version the downloading code won't get confused.

are you taking care of the updates to the unit tests, so that the CI checks pass or is it better if I have a look?

Some of the first fixes might be relatively straightforward, with some renamed modules that have to be updated in the unit tests. If you have some bandwidth to look at it, feel free to do so.

Lilferrit · 2024-09-18T21:38:21Z

casanovo/denovo/model_runner.py

+        # Configure early stopping
+        if config.early_stopping_patience is not None:
+            self.callbacks.append(
+                EarlyStopping(


Removing for now. This will be introduced back into casanovo/dev by a future pr if it is decided to introduce early stopping functionality into the mainline casanovo release.

Lilferrit · 2024-09-18T21:38:56Z

casanovo/denovo/model_runner.py

+        # Configure learning rate monitor
+        if config.tb_summarywriter is not None:
+            self.callbacks.append(
+                LearningRateMonitor(logging_interval="step", log_momentum=True)


Same thing here, removing for now as this will be reintroduced in an open pr.

tests/unit_tests/test_unit.py

casanovo/data/ms_io.py

Lilferrit · 2024-10-02T00:09:23Z

tests/unit_tests/test_unit.py

-    assert os.path.basename(mgf_small.name) not in out_writer._run_map
-    assert os.path.abspath(mgf_small.name) in out_writer._run_map
+    assert mgf_small.name in out_writer._run_map
+    assert os.path.abspath(mgf_small.name) not in out_writer._run_map


I updated this test to reflect the current behavior of MztabWriter, but it might be worth looking into we want to change the behavior of MztabWriter, especially if depthcharge is updated to include the full path in the spectrum dataloaders.

Lilferrit · 2024-10-02T20:58:29Z

It looks like there might be a bug in Spec2Pep._finish_beams where beams that have not been predicted to end aren't checked for early termination due to exceeding the precursor m/z tolerance if the tokenizer doesn't have any residues with negative mass.

Particularly, this loop

for aa in ([None] if finished_beams[i] else aa_neg_mass_idx):

that does the early termination check is never entered if the beam isn't finished and there is nothing in aa_neg_mass_idx.

Lilferrit · 2024-10-02T21:09:34Z

I've initialized the model's tokenizer with the residues from the tiny config as a work around to get the test_beam_search_decode test to run as we look into potential fixes, assuming this actually is a bug.

bittremieux · 2024-10-03T07:26:55Z

Yes, from a quick check I think you're right.

In the current version, there's always at least None included for no AAs with a negative mass. This is missing in the changed version.

Lilferrit · 2024-10-07T23:26:13Z

tests/unit_tests/test_unit.py

    beam = model.n_beams  # S
-    model.decoder.reverse = True


It doesn't look like the current PeptideDecoder supports the reverse option.

bittremieux · 2024-10-08T00:09:58Z

The tests still seem to fail on GitHub, in contrast to the latest commit message. @Lilferrit is this expected behavior?

Lilferrit · 2024-10-08T00:16:02Z

Best I can tell looking at the GitHub actions logs, the reason the tests fail on GitHub is due to the Pylance hf_converter keyword issue in Depthcharge. The test do pass in my local environment, but I manually downgraded Pylance to v0.15.0. Should I update Casanovo's pyproject.toml to require Pylance v0.15.0? That should solve the issue with the tests not passing on GitHub.

bittremieux · 2024-10-08T02:07:34Z

Yes. And also make an issue and link it to the one in DepthCharge to track this.

codecov · 2024-10-08T02:31:34Z

Codecov Report

Attention: Patch coverage is 93.42105% with 15 lines in your changes missing coverage. Please review.

Project coverage is 88.85%. Comparing base (0f06ac9) to head (943dda4).

Files with missing lines	Patch %	Lines
casanovo/denovo/model_runner.py	90.00%	7 Missing ⚠️
casanovo/denovo/dataloaders.py	92.85%	4 Missing ⚠️
casanovo/denovo/model.py	94.73%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #350      +/-   ##
==========================================
- Coverage   94.37%   88.85%   -5.53%     
==========================================
  Files          13       14       +1     
  Lines        1102     1202     +100     
==========================================
+ Hits         1040     1068      +28     
- Misses         62      134      +72

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Lilferrit · 2024-10-08T02:35:54Z

Yes. And also make an issue and link it to the one in DepthCharge to track this.

Done, all of the test on GitHub pass now, and seem to run faster than they have historically as well.

Lilferrit · 2024-11-21T01:11:58Z

I overwrote the previous merge with dev with the latest rebase to make the diff more representative of any new functionality.

bittremieux changed the base branch from main to dev July 2, 2024 06:33

bittremieux linked an issue Jul 3, 2024 that may be closed by this pull request

Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo #337

Open

wfondrie self-requested a review July 27, 2024 06:24

wfondrie requested changes Jul 27, 2024

View reviewed changes

andradesalazar requested a review from wfondrie July 29, 2024 16:21

Lilferrit mentioned this pull request Aug 13, 2024

Eliminate evaluate Command #359

Merged

This was referenced Aug 22, 2024

ValueError upon unexpected scan title format #354

Open

Flexible format for scan titles #369

Draft

Lilferrit reviewed Sep 18, 2024

View reviewed changes

tests/unit_tests/test_unit.py Show resolved Hide resolved

Lilferrit reviewed Sep 30, 2024

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casanovo/data/ms_io.py Show resolved Hide resolved

Lilferrit reviewed Oct 2, 2024

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Lilferrit reviewed Oct 7, 2024

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Lilferrit requested a review from bittremieux October 7, 2024 23:27

Lilferrit linked an issue Oct 14, 2024 that may be closed by this pull request

Use lightning.pytorch.loggers.TensorBoardLogger for tensorboard logging. #382

Open

wfondrie mentioned this pull request Oct 24, 2024

m/z and intensity embedding #394

Closed

bittremieux mentioned this pull request Oct 28, 2024

PeptideDecoder #395

Closed

Daniela Klaproth-Andrade added 2 commits November 19, 2024 12:57

migration to depthcharge v0.4.8

6826a1c

shuffling training set by default

8c8dc61

Lilferrit added 21 commits November 19, 2024 13:09

spectrum id unit tests

3d1c20f

integration test fix

3ec8d7c

model prediction io flow fixes

9b8efea

PyLightning logging refactor

47df27e

mgf file reader title field formatting

45b3e26

integration tests fix

a1b42af

integration tests

261f63c

test_initialize_model fix

e3e8456

test_save_and_load_weights fix

0fb6692

test_save_and_load_weights_deprecated fix

5594bf8

test_evaluate fix, evaluate unnanotated peak file error handling

7bd2b5e

test_evaluate fix, evaluate unnanotated peak file error handling

d178860

test_eval_metrics fix

340695a

test_spectrum_id tests fix

e4d93f9

unit tests fixes

eb4af71

teast_beam_search_decode fix

2a946c2

negative residue work around

17bc3a2

depthcharge upgrade - all unit tests pass

7d789a7

pylance depthcharge compatability fix

c1ca436

removed scans field from dataloaders

2d539fd

non db functionality working

6ab3397

Lilferrit force-pushed the dev_latest_depthcharge branch from 943dda4 to 6ab3397 Compare November 21, 2024 01:10

Lilferrit added 7 commits November 25, 2024 16:38

import orders, CasanovoDB psm batching

9dc293f

CasanovoDB unit tests

051a82a

no batch made edge case

8ebb55a

mass caclulation

a6a2db8

CasanovoDB mass mod fixes

d3cd392

remove unsqueeze batch method

113c879

reduced test epochs from 20 to 15

54366a5

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Migration to depthcharge v0.4.8 #350

Migration to depthcharge v0.4.8 #350

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Migration to depthcharge v0.4.8 #350

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Migration to depthcharge v0.4.8 #350

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