Develop #38
Merged
Develop #38
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Probably need some refactoring as currently it is close to unmaintainable.
Rename helical.py to base_models.py Move BaseTaskModel to base_models.py Move BaseModelProtocol to base_models.py
Notion leaderboard.
version of scipy 1.14.0. It seems like the anndata.X matrix was not converted into the desired np.array format but stayed as SparseCSRView.
bputzeys
commented
Jun 28, 2024
bputzeys
commented
Jun 28, 2024
| gitpython==3.1.43 | ||
| torch==2.3.0 | ||
| torchvision==0.18.0 | ||
| accelerate==0.29.3 | ||
| transformers==4.26.1 | ||
| loompy==3.0.7 | ||
| scib==1.1.5 | ||
| scikit-misc==0.3.1 |
There was a problem hiding this comment.
Fixed because 0.4.0 has an issue for apple silicon
has2k1/scikit-misc#37
bputzeys
commented
Jun 28, 2024
| @@ -3,13 +3,15 @@ pandas==2.2.2 | |||
| anndata==0.10.7 | |||
| numpy==1.26.4 | |||
| scikit-learn==1.2.2 | |||
| scipy==1.13.1 | |||
There was a problem hiding this comment.
Version 1.14.0 (which got released a few days ago) caused the following error:
data = scgpt.process_data(adata[:10])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "helical/helical/models/scgpt/model.py", line 203, in process_data
count_matrix = (adata.X if isinstance(adata.X, np.ndarray) else adata.X.A)
^^^^^^^^^
AttributeError: 'SparseCSRView' object has no attribute 'A'
maxiallard
approved these changes
Jun 30, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.