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Test on Python 3.12 #87

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wants to merge 12 commits into from
Closed

Test on Python 3.12 #87

wants to merge 12 commits into from

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ziw-liu
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@ziw-liu ziw-liu commented Jun 12, 2024 •
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#69 rebooted.

@ziw-liu ziw-liu mentioned this pull request Jun 12, 2024
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@ziw-liu ziw-liu requested a review from edyoshikun June 12, 2024 22:37
@ziw-liu ziw-liu added maintenance Maintenance work CI Continuous integration labels Jun 12, 2024
@ziw-liu ziw-liu mentioned this pull request Jun 12, 2024
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@edyoshikun
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Thanks for fixing my failed attempt to merge things.

I still get the error:

Traceback (most recent call last):
  File "/hpc/mydata/eduardo.hirata/.conda/envs/py312/bin/viscy", line 5, in <module>
    from viscy.cli.cli import main
  File "/hpc/mydata/eduardo.hirata/repos/viscy/viscy/cli/cli.py", line 13, in <module>
    from viscy.light.engine import VSUNet
  File "/hpc/mydata/eduardo.hirata/repos/viscy/viscy/light/engine.py", line 9, in <module>
    from matplotlib.cm import get_cmap
ImportError: cannot import name 'get_cmap' from 'matplotlib.cm' (/hpc/mydata/eduardo.hirata/.conda/envs/py312/lib/python3.12/site-packages/matplotlib/cm.py)

edyoshikun and others added 7 commits June 12, 2024 15:46
@edyoshikun @ziw-liu
checkpoint as a model config parameter for warmup cosine learning rat…
41b9d10 
…es (#66)

* adding chkpt path optional to configfile to use warmup cosine learning rate

* fixing the loading of weights

* remove additional blank

---------

Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
@ziw-liu @edyoshikun
Masked autoencoder pre-training for virtual staining models (#67)
f924cbc 
* refactor data loading into its own module

* update type annotations

* move the logging module out

* move old logging into utils

* rename tests to match module name

* bump torch

* draft fcmae encoder

* add stem to the encoder

* wip: masked stem layernorm

* wip: patchify masked features for linear

* use mlp from timm

* hack: POC training script for FCMAE

* fix mask for fitting

* remove training script

* default architecture

* fine-tuning options

* fix cli for finetuning

* draft combined data module

* fix import

* manual validation loss reduction

* update linting
new black version has different rules

* update development guide

* update type hints

* bump iohub

* draft ctmc v1 dataset

* update tests

* move test_data

* remove path conversion

* configurable normalizations (#68)

* inital commit adding the normalization.

* adding dataset_statistics to each fov to facilitate the configurable augmentations

* fix indentation

* ruff

* test preprocessing

* remove redundant field

* cleanup

---------

Co-authored-by: Ziwen Liu <ziwen.liu@czbiohub.org>

* fix ctmc dataloading

* add example ctmc v1 loading script

* changing the normalization and augmentations default from None to empty list.

* invert intensity transform

* concatenated data module

* subsample videos

* livecell dataset

* all sample fields are optional

* fix multi-dataloader validation

* lint

* fixing preprocessing for varying array shapes (i.e aics dataset)

* update loading scripts

* fix CombineMode

* compose normalizations for predict and test stages

* black

* fix normalization in example config

* fix collate when multi-sample transform is not used

* ddp caching fixes

* fix caching when using combined loader

* move log values to GPU before syncing
Lightning-AI/pytorch-lightning#18803

* removing normalize_source from configs.

* typing fixes

* fix test data path

* fix test dataset

* add docstring for ConcatDataModule

* format

---------

Co-authored-by: Eduardo Hirata-Miyasaki <edhiratam@gmail.com>
@ziw-liu @edyoshikun
filter empty detections (#74)
23689e6
@ziw-liu @edyoshikun
Add CITATION.cff (#79)
f954554 
* add CITATION.cff

* fix matplotlib 3.9.0 breakage
@ziw-liu @edyoshikun
Fix 3D to 2D prediction with UNeXt2 model (#80)
eeb8ce2 
* shuffle head

* use shuffle head for 2.1D

* use the same head for 2d and 2d output

* update script

* rename 2.1D to 2.2D

* fix reference

* remove unused module
@ziw-liu @edyoshikun
2D FCMAE (#71)
897a0b6 
* refactor data loading into its own module

* update type annotations

* move the logging module out

* move old logging into utils

* rename tests to match module name

* bump torch

* draft fcmae encoder

* add stem to the encoder

* wip: masked stem layernorm

* wip: patchify masked features for linear

* use mlp from timm

* hack: POC training script for FCMAE

* fix mask for fitting

* remove training script

* default architecture

* fine-tuning options

* fix cli for finetuning

* draft combined data module

* fix import

* manual validation loss reduction

* update linting
new black version has different rules

* update development guide

* update type hints

* bump iohub

* draft ctmc v1 dataset

* update tests

* move test_data

* remove path conversion

* configurable normalizations (#68)

* inital commit adding the normalization.

* adding dataset_statistics to each fov to facilitate the configurable augmentations

* fix indentation

* ruff

* test preprocessing

* remove redundant field

* cleanup

---------

Co-authored-by: Ziwen Liu <ziwen.liu@czbiohub.org>

* fix ctmc dataloading

* add example ctmc v1 loading script

* changing the normalization and augmentations default from None to empty list.

* invert intensity transform

* concatenated data module

* subsample videos

* livecell dataset

* all sample fields are optional

* fix multi-dataloader validation

* lint

* fixing preprocessing for varying array shapes (i.e aics dataset)

* update loading scripts

* fix CombineMode

* always use untrainable head for FCMAE

* move log values to GPU before syncing
Lightning-AI/pytorch-lightning#18803

* custom head

* ddp caching fixes

* fix caching when using combined loader

* compose normalizations for predict and test stages

* black

* fix normalization in example config

* fix normalization in example config

* prefetch more in validation

* fix collate when multi-sample transform is not used

* ddp caching fixes

* fix caching when using combined loader

* typing fixes

* fix test dataset

* fix invert transform

* add ddp prepare flag for combined data module

* remove redundant operations

* filter empty detections

* pass trainer to underlying data modules in concatenated

* hack: add test dataloader for LiveCell dataset

* test datasets for livecell and ctmc

* fix merge error

* fix merge error

* fix mAP default for over 100 detections

* bump torchmetric

* fix combined loader training for virtual staining task

* fix non-combined data loader training

* add fcmae to graph script

* fix type hint

* format

* add back convolutiuon option for fcmae head

---------

Co-authored-by: Eduardo Hirata-Miyasaki <edhiratam@gmail.com>
@ziw-liu @edyoshikun
Rename UNeXt2 (#84)
e6c6dfb 
* rename file

* rename the architecture

* fix merge
@ziw-liu
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ziw-liu commented Jun 12, 2024

Closing for #88

@ziw-liu ziw-liu closed this Jun 12, 2024
@ziw-liu ziw-liu deleted the python312 branch June 12, 2024 22:57
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