Code

Multi table#410

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melonora merged 209 commits intoscverse:multi_tablescverse/spatialdata:multi_tablefrom melonora:multi_tablemelonora/spatialdata:multi_tableCopy head branch name to clipboardJan 17, 2024

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Commits

Commits on Nov 21, 2023

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Commits on Nov 23, 2023

• initial tests multi_table design

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Commits on Nov 25, 2023

• add mock new table

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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• create test class and cleanup

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• additional cleanup

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• additional cleanup

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• additional cleanup

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Commits on Nov 26, 2023

• add pseudo methods

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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Commits on Nov 27, 2023

• Change table type in init

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• make tables plural and add to validation in __init__

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• revert to old public accessor

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• Validate each table in dictionary

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• iterate dict values

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• adjust table getter

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• Add tables getter

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• Fix missing parenthesis

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• change to warnings.warn DeprecationWarning

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• allow for backward compatibility in init

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Commits on Nov 28, 2023

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• fix dict subscriptable

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• fix string representation of sdata

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• Allow for tables not annotating elements

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Commits on Nov 29, 2023

• adjust io to multi_table

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• Alter io to give None as default value for spatialdata attrs keys

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Commits on Dec 2, 2023

• add tables setter

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• raise keyerror table getter

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• Give default table name

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• fix spatialdata without table

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Commits on Dec 6, 2023

• add int32 because of windows and add docstring

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• fix filtering by coordinate system

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• Change to Path to not be linux / mac specific

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• Change to Path to not be linux / mac specific

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• table should annotate existing element

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• return table with AnnData having 0 rows

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• Adjust for windows

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• fix change annotation target

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• add validation check

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• add table validation SpatialData.__init

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• fix ruff

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• only concatenate if annotating

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• adjust to tables

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Commits on Dec 8, 2023

• use tables parameter

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• some mypy fixes

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• fix another mypy

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• circumvent typing error on py3.9

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• down to 12 mypy errors

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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• down to 1mypy error

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• fixed mypy errors

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• refactor data loader (scverse#299)

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• add documentation

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• Merge branch 'main' into multi_table

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• minor adjustment docstring

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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• small fixes

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• added gen_elements docstrings

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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• add tables class

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• Merge branch 'multi_table' of https://github.com/melonora/spatialdata into multi_table

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• Added subset API; fix behavior with zero-len table (scverse#426)

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• [pre-commit.ci] pre-commit autoupdate (scverse#424)

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• remove docstring typehint

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• Warn user over overwrite in docstring

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• Fix query of 2D/3D data with 2D/3D bounding box (scverse#409)

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• [pre-commit.ci] pre-commit autoupdate (scverse#430)

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• updated changelog

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Commits on Jan 17, 2024

• Merge branch 'main' into multi_table

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• Merge branch 'multi_table' into multi_table

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• refactor subset

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• remove todo

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• Made _locate_spatial_element public, renamed to locate_element() (scverse#427)

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• fix test

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• Update test_and_deploy.yaml (scverse#434)

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• change docstring

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• Merge branch 'main' into multi_table

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• add todo

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• refactor filter_by_coordinate_system

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• test filter with keep table

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