AllenCell/serotiny issues and pull requests

#184 - feature/folder_dataloader

Pull Request - State: open - Opened by colobas almost 2 years ago - 1 comment

#183 - bugfix/suppress_bfio_output

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#182 - bugfix/mlflow_client_deprecated

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#181 - feature/accept-strings-or-ints-as-channels-in-omezarrreader

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#180 - bugfix/2d_slice

Pull Request - State: closed - Opened by benjijamorris about 2 years ago - 1 comment

#179 - convert to float before taking mean

Pull Request - State: closed - Opened by benjijamorris about 2 years ago - 1 comment

#178 - add key interpolation resolver

Pull Request - State: closed - Opened by benjijamorris about 2 years ago - 1 comment

#177 - feature/ome_zarr_reader

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#176 - release v1

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#175 - Revert "Bugfix/failing GitHub actions"

Pull Request - State: closed - Opened by colobas about 2 years ago

#174 - copy slice object before removing z dimension

Pull Request - State: closed - Opened by benjijamorris about 2 years ago - 3 comments

#173 - make dtype specification truly optional

Pull Request - State: closed - Opened by colobas about 2 years ago

#172 - remove old docs

Pull Request - State: closed - Opened by colobas about 2 years ago

#171 - fix artifact folder location inference

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#170 - Bugfix/failing GitHub actions

Pull Request - State: closed - Opened by colobas about 2 years ago

#169 - Address failing `MLFlowLogger` test

Issue - State: closed - Opened by colobas about 2 years ago
Labels: bug, v1

#168 - Bugfix/failing GitHub actions

Pull Request - State: closed - Opened by colobas about 2 years ago

#167 - Bugfix/linting

Pull Request - State: closed - Opened by colobas about 2 years ago

#166 - use correct python version to match precommit's (python3.8)

Pull Request - State: closed - Opened by colobas about 2 years ago

#165 - remove erroneous class docstring

Pull Request - State: closed - Opened by colobas about 2 years ago

#164 - Improv/move to pdm

Pull Request - State: closed - Opened by colobas about 2 years ago

#163 - Dev

Pull Request - State: closed - Opened by colobas about 2 years ago

#162 - add ability to cast read cols and refactor class

Pull Request - State: closed - Opened by colobas about 2 years ago

#161 - Improv/dataframe transforms

Pull Request - State: closed - Opened by colobas about 2 years ago

#160 - Upkeep/move to pdm

Pull Request - State: closed - Opened by colobas about 2 years ago

#159 - Bugfix/dataframe io

Pull Request - State: closed - Opened by colobas about 2 years ago

#158 - fix column filtering transform

Pull Request - State: closed - Opened by colobas about 2 years ago

#157 - add monai as dependency

Pull Request - State: closed - Opened by colobas about 2 years ago

#156 - Upkeep/old deps and tests

Pull Request - State: closed - Opened by colobas about 2 years ago

#155 - fix sptial dim check

Pull Request - State: closed - Opened by benjijamorris about 2 years ago - 1 comment

#154 - fix cropping with patch size = image size

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#153 - fix subsampling when not specified in config

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#152 - Feature/mixed 3d and 2d cropping

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#151 - Bugfix/add cachedir

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#150 - set seed appropriately in datamodule

Pull Request - State: closed - Opened by colobas about 2 years ago

#149 - update docs and README to reflect new philosophy

Issue - State: closed - Opened by colobas about 2 years ago - 2 comments
Labels: documentation, help wanted, v1

#148 - set tracking uri in logger init

Pull Request - State: closed - Opened by colobas about 2 years ago

#147 - logger does not have access to trainer. pass instead

Pull Request - State: closed - Opened by colobas about 2 years ago

#146 - Add tests for `DataframeDatamodule` class

Issue - State: open - Opened by colobas about 2 years ago
Labels: enhancement, v1

#145 - add optimizer idx

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#144 - Bugfix/datamodule part 2

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#143 - Bugfix/datamodule

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#142 - add mlflow logger with checkpointing ability

Pull Request - State: closed - Opened by colobas about 2 years ago - 2 comments

#141 - add transforms from im2im

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#140 - V1

Pull Request - State: closed - Opened by colobas about 2 years ago - 2 comments
Labels: v1

#139 - refactored dataframe datamodule, using monai

Pull Request - State: closed - Opened by colobas about 2 years ago

#138 - improve include_cols / required_cols

Pull Request - State: closed - Opened by colobas about 2 years ago

#137 - Bugfix/minor base vae fixes

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#136 - account for dicts and omegaconf configs when determining depth

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#135 - add flag to model loading

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#134 - add default dimensionality to prior abstract class

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#133 - Model checkpointing

Issue - State: closed - Opened by benjijamorris about 2 years ago
Labels: enhancement, v1

#132 - make sure we log only scalars

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#131 - add new mlflow autolog param

Pull Request - State: closed - Opened by colobas about 2 years ago

#130 - Add integration tests for VAE family of models

Issue - State: closed - Opened by colobas about 2 years ago
Labels: enhancement, help wanted

#129 - fix search for -cd in argv

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment
Labels: bug

#128 - feature/split_df_seed

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#127 - Bump version and fix PyPI publishing

Pull Request - State: closed - Opened by colobas about 2 years ago

#126 - bugfix/lightning-bolts-version

Pull Request - State: closed - Opened by colobas about 2 years ago - 1 comment

#125 - fix hydra multirun link

Pull Request - State: closed - Opened by benjijamorris about 2 years ago

#124 - Idea: Callback to run parameterizable jupyter notebooks against trained models

Issue - State: closed - Opened by colobas over 2 years ago
Labels: discussion, proposal

#123 - Feature/eq vae

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago - 4 comments

#122 - Proposal: Do IO in monai?

Issue - State: closed - Opened by benjijamorris over 2 years ago - 4 comments
Labels: discussion, proposal

#121 - Having `lightning-bolts` pinned to a commit hash is breaking publishing to PyPI

Issue - State: closed - Opened by colobas over 2 years ago - 1 comment
Labels: bug, good first issue, help wanted

#120 - add forward kwargs to basic model

Pull Request - State: closed - Opened by colobas over 2 years ago

#119 - force hydra's omegaconf resolvers to be registered

Pull Request - State: closed - Opened by colobas over 2 years ago

#118 - Fix/security fix jupyter core

Pull Request - State: closed - Opened by colobas over 2 years ago - 1 comment

#117 - ignore bumpversion.cfg in pre commit hook

Pull Request - State: closed - Opened by colobas over 2 years ago

#116 - Improv/guidelines deps and tests

Pull Request - State: closed - Opened by colobas over 2 years ago - 1 comment

#115 - lint triggering files

Pull Request - State: closed - Opened by colobas over 2 years ago

#114 - update guidelines and dev dependencies

Pull Request - State: closed - Opened by colobas over 2 years ago

#113 - Modin instead of pandas

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago - 1 comment

#112 - Modin instead of pandas

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago

#111 - Suppress aicsimageio warnings

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago - 1 comment

#110 - Suppress aicsimageio warnings

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago

#109 - remove detach cpu calls to make distributed training work

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago

#108 - default to not chdiring and creating subdirectories

Pull Request - State: closed - Opened by colobas over 2 years ago

#107 - Feature/more logging flexibility

Pull Request - State: closed - Opened by colobas over 2 years ago

#106 - specify error to suppress

Pull Request - State: closed - Opened by colobas over 2 years ago

#105 - Improve debugging for IDEs

Issue - State: closed - Opened by oeway over 2 years ago - 1 comment
Labels: enhancement, discussion, proposal

#104 - Support seed for the split_dataframe

Issue - State: closed - Opened by oeway over 2 years ago
Labels: enhancement, good first issue, proposal

#103 - Fix/mlflow deprecated methos

Pull Request - State: closed - Opened by colobas over 2 years ago

#102 - Improv/console logging

Pull Request - State: closed - Opened by colobas over 2 years ago

#101 - apply refurb suggestions

Pull Request - State: closed - Opened by colobas over 2 years ago

#100 - fix dependency vulnerabilities and bump version

Pull Request - State: closed - Opened by colobas over 2 years ago

#99 - Bump joblib from 1.1.0 to 1.2.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#98 - Bump serotiny version

Pull Request - State: closed - Opened by colobas over 2 years ago

#97 - Feature/scale mlp

Pull Request - State: closed - Opened by colobas over 2 years ago - 1 comment

#96 - add image vae code

Pull Request - State: closed - Opened by colobas over 2 years ago - 1 comment

#94 - feature/cytodata_image_vae

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago - 1 comment

#91 - add cpa latent loss vae

Pull Request - State: closed - Opened by colobas over 2 years ago

#87 - make diagonal gaussian prior interface consistent with isotropic gaus…

Pull Request - State: closed - Opened by ritvikvasan over 2 years ago - 1 comment

#80 - Cross validation splits

Issue - State: open - Opened by ritvikvasan over 2 years ago
Labels: enhancement, discussion, proposal

#68 - Specify package version numbers for torch and lightning

Issue - State: closed - Opened by ritvikvasan over 3 years ago

#53 - add more flexible conditioning to the MLP VAE

Issue - State: closed - Opened by ritvikvasan almost 4 years ago

#52 - embeddings zoo

Issue - State: closed - Opened by ritvikvasan almost 4 years ago

#48 - To use VAE, interpolate dimensions to the nearest multiple of (2 ** n_convs)

Issue - State: closed - Opened by colobas almost 4 years ago

#37 - Comments on numbers appearing in functions

Issue - State: closed - Opened by prismofeverything almost 4 years ago

#16 - Boxplot for 2d+3d mitotic classifier

Issue - State: closed - Opened by tknijnen about 4 years ago

#15 - Save actual and predicted class labels of trained model for confusion matrices and f1 bar plots

Issue - State: closed - Opened by tknijnen about 4 years ago

GitHub / AllenCell/serotiny issues and pull requests