Code

Master merge into dev#26

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davidsebfischer merged 66 commits intodevtheislab/sfaira:devfrom master_merge_into_devtheislab/sfaira:master_merge_into_devCopy head branch name to clipboardDec 10, 2020

+2,327-1,486

Commits

Commits on Nov 6, 2020

• add plot_npc and plot_active_latent_units (#9)

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Commits on Nov 9, 2020

• added data loader for interactive workflows with unprocessed data

  davidsebfischer

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• made cell type loading optional in dataset .load()

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• enabled usage of type estimator on data without labels in prediction mode

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Commits on Nov 10, 2020

• recursively search custom model repo for weights files

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• sort model lookuptable alphabetically before writing it

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• make sure mode_path is set correctly in model_lookuptable when recursive weights loading is used

  le-ander

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• fix os.path.join usage in dataloaders

  le-ander

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• replace path handling through string concatenations with os.paths.join and f-strings

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Commits on Nov 11, 2020

• fix bug in lookup table writing

  le-ander

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• add mdoel file path to lookup table

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• reset index in model lookuptable before saving

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• add method to user interface for pushing local model weights to zenodo

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• fix bug in user interface

  le-ander

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• fix bux in summaries.py

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• use absolute model paths when model_lookuptable is used

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• fix bug in pretrained weights loading

  le-ander

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• fix bug in pretrained weights loading

  le-ander

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• automatically create an InteractiveDataset when loading data through the UI

  le-ander

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• fix bug inUI data loading

  le-ander

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Commits on Nov 20, 2020

• Explicitly cast indices and indptr of final backed file to int64. (#17)

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Commits on Nov 26, 2020

• update human lung dataset doi

  le-ander

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Commits on Dec 1, 2020

• align mouse organ names with human organ names

  le-ander

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• fix typo in trachea organ naming in mouse

  le-ander

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• rename mouse ovary organ to femalegonad

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• rename mouse ovary organ to femalegonad

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Commits on Dec 2, 2020

• sort by model type in classwise f1 heatmap plot

  le-ander

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• another hacky solution to ensure a summary tab can be created when both vae and other models are loaded at once

  le-ander

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Commits on Dec 3, 2020

• allow custom metadata in zenodo submission

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• do not return doi but deposit url after depositing to zenodo sandbox as dois don't wrk on sandbox

  le-ander

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• updated model zoo description

  davidsebfischer

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• recognise all .h5 and .data-0000... files as sfaira weights when constructing lookuptable

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Commits on Dec 4, 2020

• Update README.rst

  davidsebfischer

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• Add selu activation and lecun_normal weight_init scheme for human VAEVAMP. (#19)

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Commits on Dec 5, 2020

• update sfaira erpo url and handle .h5 extension in model lookuptable id

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Commits on Dec 7, 2020

• add meta_data download information to all human dataloaders

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• updated docs

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• updated reference to README in docs

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• updated index

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• included reference to svensson et al data base in docs

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• fixed typo in docs

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• fixed typos in docs

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Commits on Dec 8, 2020

• restructured docs

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• fixed bug in reference roadmap in docs

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• updated data and model zoo description

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• added summary picture into index of docs

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• fixed typo in docs

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• updated summary panel

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• add badges to readme and docs index

  le-ander

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• Merge branch 'master' of https://github.com/theislab/sfaira

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• updated summary panel (#20)

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• Merge branch 'master' of https://github.com/theislab/sfaira

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• Doc updates (#21)

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• Doc updates (#22)

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Commits on Dec 9, 2020

• move from import sfaira.api as sfaira to import sfaira

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• add custom genomes to sfaira_extension

  le-ander

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• fix loading of custom topology versions from sfaira_extension

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• fix circular imports between sfaira_extension and sfaira

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• fix dataloader

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• fix celltype versioning through sfaira_extension

  le-ander

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• fix celltype versioning through sfaira_extension

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• formatting

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Commits on Dec 10, 2020

• Merge branch 'master' of https://github.com/theislab/sfaira

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• Doc updates (#25)

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• Merge branch 'master' of https://github.com/theislab/sfaira

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• Merge branch 'master' into dev

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