Add solver to callback call #215

LeonStadelmann · 2025-04-21T14:58:16Z

No description provided.

LeonStadelmann · 2025-04-21T15:00:22Z

on_train_end is currectly not utilized anywhere, so I only edited on_log_iteration for each callback.

codecov · 2025-04-21T15:38:03Z

Codecov Report

Attention: Patch coverage is 63.63636% with 8 lines in your changes missing coverage. Please review.

Project coverage is 81.85%. Comparing base (4970ad4) to head (b6c0bdb).
Report is 47 commits behind head on main.

Files with missing lines	Patch %	Lines
src/cellflow/training/_callbacks.py	46.66%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #215      +/-   ##
==========================================
+ Coverage   81.35%   81.85%   +0.49%     
==========================================
  Files          38       38              
  Lines        2564     2546      -18     
  Branches      329      320       -9     
==========================================
- Hits         2086     2084       -2     
+ Misses        334      327       -7     
+ Partials      144      135       -9

Files with missing lines	Coverage Δ
src/cellflow/training/_trainer.py	`98.30% <100.00%> (+0.05%)`	⬆️
src/cellflow/training/_callbacks.py	`65.10% <46.66%> (+0.91%)`	⬆️

... and 3 files with indirect coverage changes

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src/cellflow/training/_callbacks.py

MUCDK · 2025-04-22T13:43:55Z

src/cellflow/training/_callbacks.py

@@ -477,6 +492,8 @@ def on_train_end(self, valid_data, pred_data) -> dict[str, Any]:
            Validation data in nested dictionary format with same keys as ``pred_data``
        pred_data: dict
            Predicted data in nested dictionary format with same keys as ``valid_data``
+        solver
+            OTFM/GENOT solver with a conditional velocity field.


please link to classes

MUCDK · 2025-04-22T13:44:07Z

src/cellflow/training/_callbacks.py

@@ -452,6 +460,8 @@ def on_log_iteration(
            Validation data in nested dictionary format with same keys as ``pred_data``
        pred_data
            Predicted data in nested dictionary format with same keys as ``valid_data``
+        solver
+            OTFM/GENOT solver with a conditional velocity field.


please link to classes

MUCDK · 2025-04-22T13:48:40Z

src/cellflow/training/_callbacks.py

@@ -176,6 +180,7 @@ def on_log_iteration(
        self,
        validation_data: dict[str, dict[str, ArrayLike]],
        predicted_data: dict[str, dict[str, ArrayLike]],
+        _,


please add typing, i.e. the two solver classes

MUCDK · 2025-04-22T13:48:44Z

src/cellflow/training/_callbacks.py

@@ -248,6 +253,7 @@ def on_log_iteration(
        self,
        validation_data: dict[str, dict[str, ArrayLike]],
        predicted_data: dict[str, dict[str, ArrayLike]],
+        _,


please add typing, i.e. the two solver classes

MUCDK · 2025-04-22T13:48:47Z

src/cellflow/training/_callbacks.py

@@ -305,6 +311,7 @@ def on_log_iteration(
        self,
        validation_data: dict[str, dict[str, ArrayLike]],
        predicted_data: dict[str, dict[str, ArrayLike]],
+        _,


please add typing, i.e. the two solver classes

what I mean is _: _otfm.OTFlowMatching | _genot.GENOT

MUCDK

Please also adapt at_train_end.

Please also introduce a test which tests for some custom callback using the solver.

Maybe a good use case would be compute two predictions when having stochastic mode, i.e. passing to different keys to predict, and report the gene-wise difference in the mean .

MUCDK · 2025-05-05T13:22:36Z

tests/trainer/test_trainer.py

+        pass
+
+    def on_log_iteration(self, validation_data, predicted_data, solver):
+        pred_1 = solver.predict(x_test, cond)


That's almost great!

Please make sure to provide a random key during initialisation, and then split the key into three keys, for 1) overriding self.key, and the other two for passing to solver.predict, as if you do not pass the key, predict will automatically select the learnt mean , thus you will get the same result.

I understand the purpose of the two keys that are passed to solver.predict, but could you please explain again why we need to override self.key?

if it always utilizes the same self.key, it will generate the same random noise. this is because split(key_0, 2) always returns the same two keys.

tests/trainer/test_trainer.py

MUCDK

see comments.

MUCDK · 2025-05-07T12:34:15Z

One thing I had missed so far is that we need to pass the ValidationData as well to on_log_iteration etc., not only the solver!

for more information, see https://pre-commit.ci

MUCDK · 2025-05-13T07:25:23Z

src/cellflow/training/_callbacks.py

@@ -246,8 +265,10 @@ def __init__(

    def on_log_iteration(
        self,
+        _source_data: dict[str, dict[str, ArrayLike]],


why _source_data, and not source_data?

here it'd better to absorb it actually.

MUCDK · 2025-05-13T07:26:30Z

src/cellflow/training/_callbacks.py

        validation_data: dict[str, dict[str, ArrayLike]],
        predicted_data: dict[str, dict[str, ArrayLike]],
+        _solver: _otfm.OTFlowMatching | _genot.GENOT,


absorb _solver

MUCDK

Looks good, thanks!

The only thing I'm wondering about now is the naming in on_log_iteration, etc.

maybe source_val_data, true_val_data, pred_val_data?

commit 56888eb Merge: d169628 9068a93 Author: Selman Özleyen <32667648+selmanozleyen@users.noreply.github.com> Date: Fri Jun 13 12:03:07 2025 +0200 Merge pull request #235 from theislab/feature/predict_batch Feature and Speedup: `predict_batch` commit d169628 Merge: f6cdf17 801adf0 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri Jun 13 11:28:18 2025 +0200 Merge pull request #239 from theislab/feature/ooc-dataloading Feature: Out of Core Dataloading Option commit 801adf0 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 15:31:53 2025 +0200 add return types commit 6d44054 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:56:48 2025 +0200 update error message commit 3bda128 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:56:20 2025 +0200 document better commit de3b6ee Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 11:51:03 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 8f18574 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:50:55 2025 +0200 remove unused fixture commit 8e808a9 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 11:17:33 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 67e64e1 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:17:22 2025 +0200 add tests commit ab95081 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 12:08:48 2025 +0200 throw error when there isn't any valid indices commit 9068a93 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 09:38:43 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit d65151a Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:38:34 2025 +0200 When using PredictionSampler we can't use batched mode commit bb941ea Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:33:45 2025 +0200 clarify documentation that this requires same number of cells commit 7461dc3 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sun Jun 1 16:07:15 2025 +0200 Fix type error commit 04566e7 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Tue May 27 17:11:02 2025 +0200 Replace tree map commit 4a9bbcd Merge: 855c5d9 f6cdf17 Author: LeonStadelmann <169152764+LeonStadelmann@users.noreply.github.com> Date: Tue May 27 16:58:19 2025 +0200 Merge branch 'main' into feature/predict_batch commit f6cdf17 Merge: b4b7c96 70766f5 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 27 09:10:57 2025 +0200 Merge pull request #246 from theislab/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit b4b7c96 Merge: 7a69c5d b67804f Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 27 09:10:36 2025 +0200 Merge pull request #245 from theislab/feature/stochastic_to_cellflow_class pass rng from cellflow.predict commit 70766f5 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 26 18:56:02 2025 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.4 → v2.0.0-beta.5](biomejs/pre-commit@v2.0.0-beta.4...v2.0.0-beta.5) - [github.com/tox-dev/pyproject-fmt: v2.5.1 → v2.6.0](tox-dev/pyproject-fmt@v2.5.1...v2.6.0) - [github.com/astral-sh/ruff-pre-commit: v0.11.10 → v0.11.11](astral-sh/ruff-pre-commit@v0.11.10...v0.11.11) commit b67804f Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Mon May 26 11:03:13 2025 +0200 fix callback/ commit b9bc6c2 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Mon May 26 09:04:25 2025 +0200 pass rng from cellflow.predict commit 7a69c5d Merge: ce064e3 50a3cc8 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:17:03 2025 +0200 Merge pull request #238 from theislab/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit ce064e3 Merge: 6cb5540 b6c0bdb Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:14:53 2025 +0200 Merge pull request #215 from theislab/add/solver_callback Add solver to callback call commit 6cb5540 Merge: 0dbf90f 83db489 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:05:14 2025 +0200 Merge pull request #233 from theislab/tutorial/combosciplex add combosciplex commit 0dbf90f Merge: d8ae659 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:04:55 2025 +0200 Merge pull request #244 from theislab/tests/find_failing2 deprecation python 3.10 commit 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 15:42:55 2025 +0200 enable all tests commit 83db489 Merge: 63c4966 d8ae659 Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 23 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<leonstadlmnn@gmail.com> Date: Thu May 1 16:16:21 2025 +0200 Rename flow commit ac8d073 Merge: 5327a05 4970ad4 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 16:14:11 2025 +0200 Merge branch 'main' into add/solver_callback commit 5327a05 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 12:37:09 2025 +0200 Added test for custom callbacks commit e650031 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu Apr 24 18:09:57 2025 +0200 Add typing and solver for on_train_end commit 5e18f6e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Mon Apr 21 16:57:33 2025 +0200 Add solver to callback call

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pre-commit.com hooks for more information, see https://pre-commit.ci commit d65151a Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:38:34 2025 +0200 When using PredictionSampler we can't use batched mode commit bb941ea Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:33:45 2025 +0200 clarify documentation that this requires same number of cells commit 7461dc3 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sun Jun 1 16:07:15 2025 +0200 Fix type error commit 04566e7 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Tue May 27 17:11:02 2025 +0200 Replace tree map commit 4a9bbcd Merge: 855c5d9 f6cdf17 Author: LeonStadelmann <169152764+LeonStadelmann@users.noreply.github.com> Date: Tue May 27 16:58:19 2025 +0200 Merge branch 'main' into feature/predict_batch commit f6cdf17 Merge: b4b7c96 70766f5 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 27 09:10:57 2025 +0200 Merge pull request #246 from 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<dominik.klein@helmholtz-munich.de> Date: Mon May 26 09:04:25 2025 +0200 pass rng from cellflow.predict commit 7a69c5d Merge: ce064e3 50a3cc8 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:17:03 2025 +0200 Merge pull request #238 from theislab/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit ce064e3 Merge: 6cb5540 b6c0bdb Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:14:53 2025 +0200 Merge pull request #215 from theislab/add/solver_callback Add solver to callback call commit 6cb5540 Merge: 0dbf90f 83db489 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:05:14 2025 +0200 Merge pull request #233 from theislab/tutorial/combosciplex add combosciplex commit 0dbf90f Merge: d8ae659 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:04:55 2025 +0200 Merge pull request #244 from theislab/tests/find_failing2 deprecation python 3.10 commit 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 15:42:55 2025 +0200 enable all tests commit 83db489 Merge: 63c4966 d8ae659 Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 23 15:29:53 2025 +0200 Merge branch 'main' into tutorial/combosciplex commit 63c4966 Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 23 15:22:53 2025 +0200 add combosciplex commit 855c5d9 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:59:56 2025 +0200 revert duplicate removal commit 235bc0e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:03:43 2025 +0200 emove duplicate commit 24ade1e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:01:31 2025 +0200 Add testing for genot predict commit 340b696 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 12:23:15 2025 +0200 only enable test_cellflow_with_validation commit 9dfcd18 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 11:50:27 2025 +0200 skip some tests again commit f481dac Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:38:10 2025 +0200 enable more tests again commit 6bb6550 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:27:57 2025 +0200 deprecate 3.10 commit 8e8d2ad Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:26:24 2025 +0200 deprecate 3.10 commit 11d2f55 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:24:35 2025 +0200 deprecate 3.10 commit 459f435 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:22:14 2025 +0200 enable some more tests commit 0b56b4c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:05:24 2025 +0200 skip more tests commit 2e7aac9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 09:48:30 2025 +0200 skip more tests commit d8ae659 Merge: 70eec9a f3c840c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 16:27:36 2025 +0200 Merge pull request #241 from theislab/fix/tokenattention fix TokenAttention commit 0da9154 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 16:25:26 2025 +0200 skip more tests commit 7de55b3 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 15:06:36 2025 +0200 skip more tests commit 6e266a2 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu May 22 11:17:07 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 7840c80 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 13:16:42 2025 +0200 skip gene emb tests commit f3c840c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 08:41:30 2025 +0200 update scvi dependency commit fd76f07 Author: selmanozleyen <syozleyen@gmail.com> Date: Wed May 21 13:15:15 2025 +0200 add genot commit e97edd2 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Wed May 21 12:41:07 2025 +0200 Handle empty input commit 454734e Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 19:31:39 2025 +0200 revert previous precommit changes commit 0884a8b Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 17:17:10 2025 +0200 fix tests commit 186bcaa Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 15:35:46 2025 +0200 fix tests commit c5c0494 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 15:30:09 2025 +0200 fix TokenAttention commit 1e585cd Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue May 20 10:46:42 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 5dc4a54 Author: selmanozleyen <syozleyen@gmail.com> Date: Tue May 20 12:45:24 2025 +0200 support both dataloaders commit dd098fa Author: selmanozleyen <syozleyen@gmail.com> Date: Tue May 20 11:21:35 2025 +0200 init commit 50a3cc8 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 19 18:57:43 2025 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.3 → v2.0.0-beta.4](biomejs/pre-commit@v2.0.0-beta.3...v2.0.0-beta.4) - [github.com/astral-sh/ruff-pre-commit: v0.11.9 → v0.11.10](astral-sh/ruff-pre-commit@v0.11.9...v0.11.10) commit 2ccb43d Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sun May 18 12:33:32 2025 +0200 Add batched predict test commit 10edee2 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sat May 17 20:11:45 2025 +0200 Adjust docs commit b6c0bdb Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sat May 17 17:42:27 2025 +0200 fix docs commit 021aff0 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu May 15 12:42:30 2025 +0200 update implementation so that two functions predict and predict batch are unified commit 6bdbf5c Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue May 13 16:24:30 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit db6dc69 Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 18:20:22 2025 +0200 needs testing commit a3c43d3 Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 18:00:26 2025 +0200 condition keys left to add commit 03dfb2b Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 17:50:41 2025 +0200 init commit f1e8704 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 12 11:24:11 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit facf52d Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Mon May 12 13:23:52 2025 +0200 Added source data parameter + stochastic test commit 04a1d2c Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 9 13:35:02 2025 +0200 add combosciplex commit 54e2386 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 16:16:21 2025 +0200 Rename flow commit ac8d073 Merge: 5327a05 4970ad4 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 16:14:11 2025 +0200 Merge branch 'main' into add/solver_callback commit 5327a05 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 12:37:09 2025 +0200 Added test for custom callbacks commit e650031 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu Apr 24 18:09:57 2025 +0200 Add typing and solver for on_train_end commit 5e18f6e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Mon Apr 21 16:57:33 2025 +0200 Add solver to callback call Revert "resolve comments" This reverts commit 1429cab. Revert "Revert "resolve comments"" This reverts commit 6f0d747. Revert "Squashed commit of the following:" This reverts commit d850771.

…aframe Iterations (#240) * init * add tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * resolve comments * Squashed commit of the following: commit 56888eb Merge: d169628 9068a93 Author: Selman Özleyen <32667648+selmanozleyen@users.noreply.github.com> Date: Fri Jun 13 12:03:07 2025 +0200 Merge pull request #235 from theislab/feature/predict_batch Feature and Speedup: `predict_batch` commit d169628 Merge: f6cdf17 801adf0 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri Jun 13 11:28:18 2025 +0200 Merge pull request #239 from theislab/feature/ooc-dataloading Feature: Out of Core Dataloading Option commit 801adf0 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 15:31:53 2025 +0200 add return types commit 6d44054 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:56:48 2025 +0200 update error message commit 3bda128 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:56:20 2025 +0200 document better commit de3b6ee Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 11:51:03 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 8f18574 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:50:55 2025 +0200 remove unused fixture commit 8e808a9 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 11:17:33 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 67e64e1 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:17:22 2025 +0200 add tests commit ab95081 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 12:08:48 2025 +0200 throw error when there isn't any valid indices commit 9068a93 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 09:38:43 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit d65151a Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:38:34 2025 +0200 When using PredictionSampler we can't use batched mode commit bb941ea Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:33:45 2025 +0200 clarify documentation that this requires same number of cells commit 7461dc3 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sun Jun 1 16:07:15 2025 +0200 Fix type error commit 04566e7 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Tue May 27 17:11:02 2025 +0200 Replace tree map commit 4a9bbcd Merge: 855c5d9 f6cdf17 Author: LeonStadelmann <169152764+LeonStadelmann@users.noreply.github.com> Date: Tue May 27 16:58:19 2025 +0200 Merge branch 'main' into feature/predict_batch commit f6cdf17 Merge: b4b7c96 70766f5 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 27 09:10:57 2025 +0200 Merge pull request #246 from theislab/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit b4b7c96 Merge: 7a69c5d b67804f Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 27 09:10:36 2025 +0200 Merge pull request #245 from theislab/feature/stochastic_to_cellflow_class pass rng from cellflow.predict commit 70766f5 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 26 18:56:02 2025 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.4 → v2.0.0-beta.5](biomejs/pre-commit@v2.0.0-beta.4...v2.0.0-beta.5) - [github.com/tox-dev/pyproject-fmt: v2.5.1 → v2.6.0](tox-dev/pyproject-fmt@v2.5.1...v2.6.0) - [github.com/astral-sh/ruff-pre-commit: v0.11.10 → v0.11.11](astral-sh/ruff-pre-commit@v0.11.10...v0.11.11) commit b67804f Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Mon May 26 11:03:13 2025 +0200 fix callback/ commit b9bc6c2 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Mon May 26 09:04:25 2025 +0200 pass rng from cellflow.predict commit 7a69c5d Merge: ce064e3 50a3cc8 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:17:03 2025 +0200 Merge pull request #238 from theislab/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit ce064e3 Merge: 6cb5540 b6c0bdb Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:14:53 2025 +0200 Merge pull request #215 from theislab/add/solver_callback Add solver to callback call commit 6cb5540 Merge: 0dbf90f 83db489 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:05:14 2025 +0200 Merge pull request #233 from theislab/tutorial/combosciplex add combosciplex commit 0dbf90f Merge: d8ae659 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:04:55 2025 +0200 Merge pull request #244 from theislab/tests/find_failing2 deprecation python 3.10 commit 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 15:42:55 2025 +0200 enable all tests commit 83db489 Merge: 63c4966 d8ae659 Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 23 15:29:53 2025 +0200 Merge branch 'main' into tutorial/combosciplex commit 63c4966 Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 23 15:22:53 2025 +0200 add combosciplex commit 855c5d9 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:59:56 2025 +0200 revert duplicate removal commit 235bc0e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:03:43 2025 +0200 emove duplicate commit 24ade1e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:01:31 2025 +0200 Add testing for genot predict commit 340b696 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 12:23:15 2025 +0200 only enable test_cellflow_with_validation commit 9dfcd18 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 11:50:27 2025 +0200 skip some tests again commit f481dac Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:38:10 2025 +0200 enable more tests again commit 6bb6550 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:27:57 2025 +0200 deprecate 3.10 commit 8e8d2ad Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:26:24 2025 +0200 deprecate 3.10 commit 11d2f55 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:24:35 2025 +0200 deprecate 3.10 commit 459f435 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:22:14 2025 +0200 enable some more tests commit 0b56b4c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:05:24 2025 +0200 skip more tests commit 2e7aac9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 09:48:30 2025 +0200 skip more tests commit d8ae659 Merge: 70eec9a f3c840c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 16:27:36 2025 +0200 Merge pull request #241 from theislab/fix/tokenattention fix TokenAttention commit 0da9154 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 16:25:26 2025 +0200 skip more tests commit 7de55b3 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 15:06:36 2025 +0200 skip more tests commit 6e266a2 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu May 22 11:17:07 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 7840c80 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 13:16:42 2025 +0200 skip gene emb tests commit f3c840c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 08:41:30 2025 +0200 update scvi dependency commit fd76f07 Author: selmanozleyen <syozleyen@gmail.com> Date: Wed May 21 13:15:15 2025 +0200 add genot commit e97edd2 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Wed May 21 12:41:07 2025 +0200 Handle empty input commit 454734e Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 19:31:39 2025 +0200 revert previous precommit changes commit 0884a8b Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 17:17:10 2025 +0200 fix tests commit 186bcaa Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 15:35:46 2025 +0200 fix tests commit c5c0494 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 15:30:09 2025 +0200 fix TokenAttention commit 1e585cd Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue May 20 10:46:42 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 5dc4a54 Author: selmanozleyen <syozleyen@gmail.com> Date: Tue May 20 12:45:24 2025 +0200 support both dataloaders commit dd098fa Author: selmanozleyen <syozleyen@gmail.com> Date: Tue May 20 11:21:35 2025 +0200 init commit 50a3cc8 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 19 18:57:43 2025 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.3 → v2.0.0-beta.4](biomejs/pre-commit@v2.0.0-beta.3...v2.0.0-beta.4) - [github.com/astral-sh/ruff-pre-commit: v0.11.9 → v0.11.10](astral-sh/ruff-pre-commit@v0.11.9...v0.11.10) commit 2ccb43d Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sun May 18 12:33:32 2025 +0200 Add batched predict test commit 10edee2 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sat May 17 20:11:45 2025 +0200 Adjust docs commit b6c0bdb Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sat May 17 17:42:27 2025 +0200 fix docs commit 021aff0 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu May 15 12:42:30 2025 +0200 update implementation so that two functions predict and predict batch are unified commit 6bdbf5c Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue May 13 16:24:30 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit db6dc69 Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 18:20:22 2025 +0200 needs testing commit a3c43d3 Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 18:00:26 2025 +0200 condition keys left to add commit 03dfb2b Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 17:50:41 2025 +0200 init commit f1e8704 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 12 11:24:11 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit facf52d Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Mon May 12 13:23:52 2025 +0200 Added source data parameter + stochastic test commit 04a1d2c Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 9 13:35:02 2025 +0200 add combosciplex commit 54e2386 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 16:16:21 2025 +0200 Rename flow commit ac8d073 Merge: 5327a05 4970ad4 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 16:14:11 2025 +0200 Merge branch 'main' into add/solver_callback commit 5327a05 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 12:37:09 2025 +0200 Added test for custom callbacks commit e650031 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu Apr 24 18:09:57 2025 +0200 Add typing and solver for on_train_end commit 5e18f6e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Mon Apr 21 16:57:33 2025 +0200 Add solver to callback call * Revert "resolve comments" This reverts commit 1429cab. * Revert "Revert "resolve comments"" This reverts commit 6f0d747. * Revert "Squashed commit of the following:" This reverts commit d850771. * fix TokenAttention * fix tests * fix tests * revert previous precommit changes * update scvi dependency * skip gene emb tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * skip more tests * skip more tests * skip more tests * skip more tests * enable some more tests * deprecate 3.10 * deprecate 3.10 * deprecate 3.10 * enable more tests again * skip some tests again * only enable test_cellflow_with_validation * enable all tests * add combosciplex * add combosciplex * Add solver to callback call * Add typing and solver for on_train_end * Added test for custom callbacks * Rename flow * Added source data parameter + stochastic test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix docs * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.3 → v2.0.0-beta.4](biomejs/pre-commit@v2.0.0-beta.3...v2.0.0-beta.4) - [github.com/astral-sh/ruff-pre-commit: v0.11.9 → v0.11.10](astral-sh/ruff-pre-commit@v0.11.9...v0.11.10) * pass rng from cellflow.predict * fix callback/ * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.4 → v2.0.0-beta.5](biomejs/pre-commit@v2.0.0-beta.4...v2.0.0-beta.5) - [github.com/tox-dev/pyproject-fmt: v2.5.1 → v2.6.0](tox-dev/pyproject-fmt@v2.5.1...v2.6.0) - [github.com/astral-sh/ruff-pre-commit: v0.11.10 → v0.11.11](astral-sh/ruff-pre-commit@v0.11.10...v0.11.11) * init * support both dataloaders * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * throw error when there isn't any valid indices * add tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unused fixture * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * document better * update error message * add return types * init * condition keys left to add * needs testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update implementation so that two functions predict and predict batch are unified * Adjust docs * Add batched predict test * Handle empty input * add genot * Add testing for genot predict * emove duplicate * revert duplicate removal * Replace tree map * Fix type error * clarify documentation that this requires same number of cells * When using PredictionSampler we can't use batched mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * init add tests [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci resolve comments Squashed commit of the following: commit 56888eb Merge: d169628 9068a93 Author: Selman Özleyen <32667648+selmanozleyen@users.noreply.github.com> Date: Fri Jun 13 12:03:07 2025 +0200 Merge pull request #235 from theislab/feature/predict_batch Feature and Speedup: `predict_batch` commit d169628 Merge: f6cdf17 801adf0 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri Jun 13 11:28:18 2025 +0200 Merge pull request #239 from theislab/feature/ooc-dataloading Feature: Out of Core Dataloading Option commit 801adf0 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 15:31:53 2025 +0200 add return types commit 6d44054 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:56:48 2025 +0200 update error message commit 3bda128 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:56:20 2025 +0200 document better commit de3b6ee Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 11:51:03 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 8f18574 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:50:55 2025 +0200 remove unused fixture commit 8e808a9 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 11:17:33 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 67e64e1 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 13:17:22 2025 +0200 add tests commit ab95081 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 12:08:48 2025 +0200 throw error when there isn't any valid indices commit 9068a93 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu Jun 12 09:38:43 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit d65151a Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:38:34 2025 +0200 When using PredictionSampler we can't use batched mode commit bb941ea Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu Jun 12 11:33:45 2025 +0200 clarify documentation that this requires same number of cells commit 7461dc3 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sun Jun 1 16:07:15 2025 +0200 Fix type error commit 04566e7 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Tue May 27 17:11:02 2025 +0200 Replace tree map commit 4a9bbcd Merge: 855c5d9 f6cdf17 Author: LeonStadelmann <169152764+LeonStadelmann@users.noreply.github.com> Date: Tue May 27 16:58:19 2025 +0200 Merge branch 'main' into feature/predict_batch commit f6cdf17 Merge: b4b7c96 70766f5 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 27 09:10:57 2025 +0200 Merge pull request #246 from theislab/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit b4b7c96 Merge: 7a69c5d b67804f Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 27 09:10:36 2025 +0200 Merge pull request #245 from theislab/feature/stochastic_to_cellflow_class pass rng from cellflow.predict commit 70766f5 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 26 18:56:02 2025 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.4 → v2.0.0-beta.5](biomejs/pre-commit@v2.0.0-beta.4...v2.0.0-beta.5) - [github.com/tox-dev/pyproject-fmt: v2.5.1 → v2.6.0](tox-dev/pyproject-fmt@v2.5.1...v2.6.0) - [github.com/astral-sh/ruff-pre-commit: v0.11.10 → v0.11.11](astral-sh/ruff-pre-commit@v0.11.10...v0.11.11) commit b67804f Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Mon May 26 11:03:13 2025 +0200 fix callback/ commit b9bc6c2 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Mon May 26 09:04:25 2025 +0200 pass rng from cellflow.predict commit 7a69c5d Merge: ce064e3 50a3cc8 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:17:03 2025 +0200 Merge pull request #238 from theislab/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate commit ce064e3 Merge: 6cb5540 b6c0bdb Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:14:53 2025 +0200 Merge pull request #215 from theislab/add/solver_callback Add solver to callback call commit 6cb5540 Merge: 0dbf90f 83db489 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:05:14 2025 +0200 Merge pull request #233 from theislab/tutorial/combosciplex add combosciplex commit 0dbf90f Merge: d8ae659 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 17:04:55 2025 +0200 Merge pull request #244 from theislab/tests/find_failing2 deprecation python 3.10 commit 69327d9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 15:42:55 2025 +0200 enable all tests commit 83db489 Merge: 63c4966 d8ae659 Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 23 15:29:53 2025 +0200 Merge branch 'main' into tutorial/combosciplex commit 63c4966 Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 23 15:22:53 2025 +0200 add combosciplex commit 855c5d9 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:59:56 2025 +0200 revert duplicate removal commit 235bc0e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:03:43 2025 +0200 emove duplicate commit 24ade1e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Fri May 23 14:01:31 2025 +0200 Add testing for genot predict commit 340b696 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 12:23:15 2025 +0200 only enable test_cellflow_with_validation commit 9dfcd18 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 11:50:27 2025 +0200 skip some tests again commit f481dac Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:38:10 2025 +0200 enable more tests again commit 6bb6550 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:27:57 2025 +0200 deprecate 3.10 commit 8e8d2ad Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:26:24 2025 +0200 deprecate 3.10 commit 11d2f55 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:24:35 2025 +0200 deprecate 3.10 commit 459f435 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:22:14 2025 +0200 enable some more tests commit 0b56b4c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 10:05:24 2025 +0200 skip more tests commit 2e7aac9 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Fri May 23 09:48:30 2025 +0200 skip more tests commit d8ae659 Merge: 70eec9a f3c840c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 16:27:36 2025 +0200 Merge pull request #241 from theislab/fix/tokenattention fix TokenAttention commit 0da9154 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 16:25:26 2025 +0200 skip more tests commit 7de55b3 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 15:06:36 2025 +0200 skip more tests commit 6e266a2 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu May 22 11:17:07 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 7840c80 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 13:16:42 2025 +0200 skip gene emb tests commit f3c840c Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Thu May 22 08:41:30 2025 +0200 update scvi dependency commit fd76f07 Author: selmanozleyen <syozleyen@gmail.com> Date: Wed May 21 13:15:15 2025 +0200 add genot commit e97edd2 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Wed May 21 12:41:07 2025 +0200 Handle empty input commit 454734e Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 19:31:39 2025 +0200 revert previous precommit changes commit 0884a8b Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 17:17:10 2025 +0200 fix tests commit 186bcaa Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 15:35:46 2025 +0200 fix tests commit c5c0494 Author: Dominik Klein <dominik.klein@helmholtz-munich.de> Date: Tue May 20 15:30:09 2025 +0200 fix TokenAttention commit 1e585cd Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue May 20 10:46:42 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 5dc4a54 Author: selmanozleyen <syozleyen@gmail.com> Date: Tue May 20 12:45:24 2025 +0200 support both dataloaders commit dd098fa Author: selmanozleyen <syozleyen@gmail.com> Date: Tue May 20 11:21:35 2025 +0200 init commit 50a3cc8 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 19 18:57:43 2025 +0000 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/biomejs/pre-commit: v2.0.0-beta.3 → v2.0.0-beta.4](biomejs/pre-commit@v2.0.0-beta.3...v2.0.0-beta.4) - [github.com/astral-sh/ruff-pre-commit: v0.11.9 → v0.11.10](astral-sh/ruff-pre-commit@v0.11.9...v0.11.10) commit 2ccb43d Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sun May 18 12:33:32 2025 +0200 Add batched predict test commit 10edee2 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sat May 17 20:11:45 2025 +0200 Adjust docs commit b6c0bdb Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Sat May 17 17:42:27 2025 +0200 fix docs commit 021aff0 Author: selman.ozleyen <syozleyen@gmail.com> Date: Thu May 15 12:42:30 2025 +0200 update implementation so that two functions predict and predict batch are unified commit 6bdbf5c Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue May 13 16:24:30 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit db6dc69 Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 18:20:22 2025 +0200 needs testing commit a3c43d3 Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 18:00:26 2025 +0200 condition keys left to add commit 03dfb2b Author: selman.ozleyen <syozleyen@gmail.com> Date: Tue May 13 17:50:41 2025 +0200 init commit f1e8704 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon May 12 11:24:11 2025 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit facf52d Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Mon May 12 13:23:52 2025 +0200 Added source data parameter + stochastic test commit 04a1d2c Author: Dominik Klein <domin.klein@gmail.com> Date: Fri May 9 13:35:02 2025 +0200 add combosciplex commit 54e2386 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 16:16:21 2025 +0200 Rename flow commit ac8d073 Merge: 5327a05 4970ad4 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 16:14:11 2025 +0200 Merge branch 'main' into add/solver_callback commit 5327a05 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu May 1 12:37:09 2025 +0200 Added test for custom callbacks commit e650031 Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Thu Apr 24 18:09:57 2025 +0200 Add typing and solver for on_train_end commit 5e18f6e Author: LeonStadelmann <leonstadlmnn@gmail.com> Date: Mon Apr 21 16:57:33 2025 +0200 Add solver to callback call Revert "resolve comments" This reverts commit 1429cab. Revert "Revert "resolve comments"" This reverts commit 6f0d747. Revert "Squashed commit of the following:" This reverts commit d850771. * add dask as dependency to see which tests fail * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * submit working version * remove get_condition_old * also remove function itself * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * partially working version * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * version closest to working so far * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * passes except condition_data * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * some state * save state before working on changing something * precommit * all works except condition_data * working version with models * change assert * all tests pass * format * format * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix primary_items * fix tests * all tests pass * fix the primary_group arg * remove assertion * remove some files * cleanup * format * fix not handling condition_id * add pyproject * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add the old function properly in the tests * skip some tests on CI * remove pertpy from main dependencies and pin the version of pertpy * try to fix the issue with ubuntu * undo pertpy pinning * try to fix yaml files * reduce the number of slow cis * add pyarrpw for dask dataframes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add import error message to check what really is the problem with pertpy * modify dependency list until statsmodels/statsmodels#9584 is fixed * fix scipy thing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reduce the size of the model in test cases * Refactor/get cond data rewrite (#254) * save state * a bit more tidying * save state * add primary group to docstring * Revert "add import error message to check what really is the problem with pertpy" This reverts commit 2062f4c. * revert * revert train argument * fix the bizzare bug * make test_cellflow models even smaller * remove is conditional * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Dominik Klein <dominik.klein@helmholtz-munich.de> Co-authored-by: Dominik Klein <domin.klein@gmail.com> Co-authored-by: LeonStadelmann <leonstadlmnn@gmail.com>

Add solver to callback call

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LeonStadelmann requested a review from MUCDK April 21, 2025 14:58

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LeonStadelmann added 4 commits April 24, 2025 18:09

Add typing and solver for on_train_end

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Added test for custom callbacks

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Merge branch 'main' into add/solver_callback

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Rename flow

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LeonStadelmann and others added 2 commits May 12, 2025 13:23

Added source data parameter + stochastic test

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LeonStadelmann requested a review from MUCDK May 12, 2025 15:38

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fix docs

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MUCDK approved these changes May 23, 2025

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MUCDK merged commit ce064e3 into main May 23, 2025
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MUCDK deleted the add/solver_callback branch May 23, 2025 15:14

Add solver to callback call #215

Add solver to callback call #215

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