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Multi table #410

Merged
merged 209 commits into from
Jan 17, 2024
Merged

Multi table #410

merged 209 commits into from
Jan 17, 2024

Commits on Nov 21, 2023

  1. [pre-commit.ci] pre-commit autoupdate (scverse#394) 

    * [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.10.1 → 23.11.0](psf/black@23.10.1...23.11.0)
- [github.com/pre-commit/mirrors-prettier: v3.0.3 → v3.1.0](pre-commit/mirrors-prettier@v3.0.3...v3.1.0)
- [github.com/pre-commit/mirrors-mypy: v1.6.1 → v1.7.0](pre-commit/mirrors-mypy@v1.6.1...v1.7.0)
- [github.com/astral-sh/ruff-pre-commit: v0.1.3 → v0.1.6](astral-sh/ruff-pre-commit@v0.1.3...v0.1.6)

* ficx pre-precommit

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: giovp <[email protected]>
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    pre-commit-ci[bot] and giovp authored Nov 21, 2023
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Commits on Nov 23, 2023

  1. initial tests multi_table design

    @melonora
    melonora committed Nov 23, 2023
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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Commits on Nov 25, 2023

  1. add mock new table

    @melonora
    melonora committed Nov 25, 2023
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  2. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
    @melonora
    melonora committed Nov 25, 2023
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  3. create test class and cleanup

    @melonora
    melonora committed Nov 25, 2023
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  4. additional cleanup

    @melonora
    melonora committed Nov 25, 2023
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  5. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  6. additional cleanup

    @melonora
    melonora committed Nov 25, 2023
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  7. additional cleanup

    @melonora
    melonora committed Nov 25, 2023
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  8. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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Commits on Nov 26, 2023

  1. add pseudo methods

    @melonora
    melonora committed Nov 26, 2023
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  2. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
    @melonora
    melonora committed Nov 26, 2023
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Commits on Nov 27, 2023

  1. Change table type in init

    @melonora
    melonora committed Nov 27, 2023
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  2. make tables plural and add to validation in __init__

    @melonora
    melonora committed Nov 27, 2023
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  3. revert to old public accessor

    @melonora
    melonora committed Nov 27, 2023
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  4. Validate each table in dictionary

    @melonora
    melonora committed Nov 27, 2023
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  5. iterate dict values

    @melonora
    melonora committed Nov 27, 2023
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  6. add comment

    @melonora
    melonora committed Nov 27, 2023
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  7. adjust table getter

    @melonora
    melonora committed Nov 27, 2023
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  8. Add tables getter

    @melonora
    melonora committed Nov 27, 2023
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  9. Fix missing parenthesis

    @melonora
    melonora committed Nov 27, 2023
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  10. change to warnings.warn DeprecationWarning

    @melonora
    melonora committed Nov 27, 2023
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  11. allow for backward compatibility in init

    @melonora
    melonora committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. [pre-commit.ci] pre-commit autoupdate (scverse#408) 

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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  2. fix dict subscriptable

    @melonora
    melonora committed Nov 28, 2023
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  3. fix string representation of sdata

    @melonora
    melonora committed Nov 28, 2023
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  4. add deprecation decorator for future

    @melonora
    melonora committed Nov 28, 2023
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  5. Allow for tables not annotating elements

    @melonora
    melonora committed Nov 28, 2023
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  6. switch to using tables with deprecation

    @melonora
    melonora committed Nov 28, 2023
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  7. fix string representation

    @melonora
    melonora committed Nov 28, 2023
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  8. write tables element group

    @melonora
    melonora committed Nov 28, 2023
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Commits on Nov 29, 2023

  1. adjust io to multi_table

    @melonora
    melonora committed Nov 29, 2023
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  2. Alter io to give None as default value for spatialdata attrs keys

    @melonora
    melonora committed Nov 29, 2023
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Commits on Dec 2, 2023

  1. add tables setter

    @melonora
    melonora committed Dec 2, 2023
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  2. raise keyerror table getter

    @melonora
    melonora committed Dec 2, 2023
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  3. remove commented tables setter

    @melonora
    melonora committed Dec 2, 2023
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  4. raise keyerror in table deleter

    @melonora
    melonora committed Dec 2, 2023
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  5. add deprecation warning

    @melonora
    melonora committed Dec 2, 2023
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  6. fix tests

    @melonora
    melonora committed Dec 2, 2023
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  7. add DeprecationWarning

    @melonora
    melonora committed Dec 2, 2023
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  8. comment test

    @melonora
    melonora committed Dec 2, 2023
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  9. change setter into method

    @melonora
    melonora committed Dec 2, 2023
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  10. circumvent mappingproxy set issue

    @melonora
    melonora committed Dec 2, 2023
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  11. adjust set get test

    @melonora
    melonora committed Dec 2, 2023
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  12. add get table keys

    @melonora
    melonora committed Dec 2, 2023
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Commits on Dec 3, 2023

  1. add column getters

    @melonora
    melonora committed Dec 3, 2023
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Commits on Dec 4, 2023

  1. add change set target table

    @melonora
    melonora committed Dec 4, 2023
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Commits on Dec 5, 2023

  1. Give default table name

    @melonora
    melonora committed Dec 5, 2023
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  2. fix spatialdata without table

    @melonora
    melonora committed Dec 5, 2023
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Commits on Dec 6, 2023

  1. add int32 because of windows and add docstring

    @melonora
    melonora committed Dec 6, 2023
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  2. fix filtering by coordinate system

    @melonora
    melonora committed Dec 6, 2023
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  3. Change to Path to not be linux / mac specific

    @melonora
    melonora committed Dec 6, 2023
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  4. Change to Path to not be linux / mac specific

    @melonora
    melonora committed Dec 6, 2023
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  5. table should annotate existing element

    @melonora
    melonora committed Dec 6, 2023
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  6. return table with AnnData having 0 rows

    @melonora
    melonora committed Dec 6, 2023
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  7. Adjust for windows

    @melonora
    melonora committed Dec 6, 2023
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  8. adjust for accessing table elements

    @melonora
    melonora committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. fix change annotation target

    @melonora
    melonora committed Dec 7, 2023
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  2. fix set annotation target

    @melonora
    melonora committed Dec 7, 2023
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  3. fix/add tests

    @melonora
    melonora committed Dec 7, 2023
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  4. fix init from elements

    @melonora
    melonora committed Dec 7, 2023
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  5. fix init from elements tests

    @melonora
    melonora committed Dec 7, 2023
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  6. add validation check

    @melonora
    melonora committed Dec 7, 2023
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  7. add table validation SpatialData.__init

    @melonora
    melonora committed Dec 7, 2023
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  8. fix ruff

    @melonora
    melonora committed Dec 7, 2023
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  9. only concatenate if annotating

    @melonora
    melonora committed Dec 7, 2023
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  10. change into warning because of filtering

    @melonora
    melonora committed Dec 7, 2023
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  11. fix last tests

    @melonora
    melonora committed Dec 7, 2023
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  12. adjust to tables

    @melonora
    melonora committed Dec 7, 2023
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Commits on Dec 8, 2023

  1. use tables parameter

    @melonora
    melonora committed Dec 8, 2023
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  2. fix some mypy

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    melonora committed Dec 8, 2023
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Commits on Dec 9, 2023

  1. some mypy fixes

    @melonora
    melonora committed Dec 9, 2023
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  2. some more mypy

    @melonora
    melonora committed Dec 9, 2023
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  3. fix another mypy

    @melonora
    melonora committed Dec 9, 2023
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Commits on Dec 11, 2023

  1. circumvent typing error on py3.9

    @melonora
    melonora committed Dec 11, 2023
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  2. mypy yet again

    @melonora
    melonora committed Dec 11, 2023
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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    pre-commit-ci[bot] committed Dec 11, 2023
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  4. fix pre_commit

    @melonora
    melonora committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. down to 12 mypy errors

    @melonora
    melonora committed Dec 12, 2023
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  2. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
    @melonora
    melonora committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. down to 1mypy error

    @melonora
    melonora committed Dec 13, 2023
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  2. fixed mypy errors

    @melonora
    melonora committed Dec 13, 2023
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  3. fix set_table_annotation

    @melonora
    melonora committed Dec 13, 2023
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Commits on Dec 14, 2023

  1. added docstring

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    melonora committed Dec 14, 2023
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  2. refactor data loader (scverse#299) 

    Co-authored-by: LucaMarconato <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Commits on Dec 15, 2023

  1. add documentation

    @melonora
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  2. add documentation

    @melonora
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  3. Merge branch 'main' into multi_table

    @melonora
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  4. minor adjustment docstring

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  5. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
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  6. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  7. Added / adjusted docstrings

    @melonora
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  8. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
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  9. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  10. fix mypy after merge

    @melonora
    melonora committed Dec 15, 2023
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  11. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
    @melonora
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  12. refactor function name 

    This is to avoid confusion. Many not easily resolved errors are created if we let this function generate table values. This makes it clear that
only spatial element values are generated and not tables. This in opposite to gen_elements which does return tables as well.
    @melonora
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Commits on Dec 17, 2023

  1. [pre-commit.ci] pre-commit autoupdate (scverse#411) 

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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  2. small fixes

    @LucaMarconato
    LucaMarconato authored Dec 17, 2023
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Commits on Dec 18, 2023

  1. added gen_elements docstrings

    @melonora
    melonora committed Dec 18, 2023
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  2. tiny comments

    @LucaMarconato
    LucaMarconato authored Dec 18, 2023
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  3. fix ruff pre-commit

    @melonora
    melonora committed Dec 18, 2023
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  4. removed types from docstring

    @LucaMarconato
    LucaMarconato authored Dec 18, 2023
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  5. refactor of set_table_annotation_target

    @melonora
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  6. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

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  7. add quotes

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  8. fix (?)

    @LucaMarconato
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Commits on Dec 19, 2023

  1. refactor error messages

    @melonora
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  2. fix incremental update (scverse#329) 

    Co-authored-by: Wouter-Michiel Vierdag <[email protected]>
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  3. add concatenate argument

    @melonora
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  4. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

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  5. Merge branch 'main' into multi_table

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  7. add util functions to init

    @melonora
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  9. add util functions to init

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  10. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

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  11. add tables class

    @melonora
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Commits on Dec 21, 2023

  1. add table class

    @melonora
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  2. add deprecation back

    @melonora
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  3. rename function in tests

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  4. rename function in tests

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  6. fix precommit

    @giovp
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  7. update precommit and remove add_table, store_table and general fixes

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  8. adjust tables init to incremental update pr

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  9. adjust tables init to incremental update pr

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Commits on Dec 22, 2023

  1. fix deletion of deprecated table

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  2. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
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  3. revert filter change

    @melonora
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  4. add public generators

    @melonora
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  5. adjust to public generators

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  6. Find element uses public generator

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  7. add validation in sdata for tables

    @melonora
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  8. add deprecation version number

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  9. fix mypy errors

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  10. Fix backing when deleting table

    @melonora
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  11. Fix mypy

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  12. cleanup

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  13. chance target_element_name to region

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  14. refactor test

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Commits on Dec 23, 2023

  1. adjust concatenate regarding not concatenating tables

    @melonora
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  2. add utility function

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  3. concatenate if in multiple sdata objects

    @melonora
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  4. minor docstring refactor

    @melonora
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  5. fix import

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  6. concatenate with tables

    @melonora
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  7. cleanup

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  8. fix test

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Commits on Jan 4, 2024

  1. [pre-commit.ci] pre-commit autoupdate (scverse#415) 

    updates:
- [github.com/psf/black: 23.11.0 → 23.12.1](psf/black@23.11.0...23.12.1)
- [github.com/pre-commit/mirrors-prettier: v4.0.0-alpha.4 → v4.0.0-alpha.8](pre-commit/mirrors-prettier@v4.0.0-alpha.4...v4.0.0-alpha.8)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](pre-commit/mirrors-mypy@v1.7.1...v1.8.0)
- [github.com/astral-sh/ruff-pre-commit: v0.1.7 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.7...v0.1.9)

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  2. Merge branch 'main' into multi_table

    @LucaMarconato
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  3. fixed typings; made pytest raises explicit

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Commits on Jan 5, 2024

  1. minor fixes human readable strings

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  2. fixed tests

    @LucaMarconato
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  3. fix

    @LucaMarconato
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  4. Add changes to changelog

    @melonora
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  5. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

    …into multi_table
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  6. make private

    @melonora
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  7. Remove commented code

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  8. add cache to ignore

    @melonora
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  9. updated changelog with giovp old pr

    @LucaMarconato
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  10. refactor into private function

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  11. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

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  12. Fix docstring

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  13. Fix import

    @melonora
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  14. specify key reuse in docstring

    @melonora
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  15. add orphan_table argument

    @melonora
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  16. Change docstring

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  17. remove todo

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  18. add example

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  19. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

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  20. change concatenate logic

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Commits on Jan 6, 2024

  1. updated changelog

    @LucaMarconato
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  2. Allow force-overwriting existing files (non-backing) (scverse#344) 

    * Add test for writing unbacked data over existing files

* Protect overwriting existing file only if it is backing file

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

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* Simplify assertion, remove try/except

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Commits on Jan 7, 2024

  1. Added error message for removed add_elements functions (scverse#420) 

    * added error message for removed add_elements functions

* moved _error_message_add_element() to _utils
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Commits on Jan 8, 2024

  1. added validate and set region key

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  2. fix docstring

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  3. Merge branch 'main' into multi_table

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  5. Added public functions Spatialdata

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  6. Merge branch 'multi_table' of https://github.com/melonora/spatialdata … 

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  7. fix tests

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  8. add docstrings

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Commits on Jan 9, 2024

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

    * added subset API, returning None instead of empty table for APIs with  filter_table=True

* fix 3.9
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  2. [pre-commit.ci] pre-commit autoupdate (scverse#424) 

    updates:
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Commits on Jan 10, 2024

  1. remove docstring typehint

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  2. Warn user over overwrite in docstring

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Commits on Jan 16, 2024

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

    * wip

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

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* wip

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

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* fix 2d/3d bb for raster data

* support for 2d/3d bb for 2d/3d points

* better tests

* applied suggestions from giovp

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

    updates:
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  3. updated changelog

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Commits on Jan 17, 2024

  1. Merge branch 'main' into multi_table

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

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  3. Merge branch 'multi_table' into multi_table

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

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  5. refactor subset

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  6. remove todo

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  7. Made _locate_spatial_element public, renamed to locate_element() (scv… 

    …erse#427)

* made _locate_spatial_element public, renamed to locate_element()

* returning path instead of tuple in locate_element()

* updated changelog

* locate_elements() now returns a list
    @LucaMarconato
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  8. fix test

    @melonora
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  9. Update test_and_deploy.yaml (scverse#434) 

    Triggering the tests for pull requests to any branch.
    @LucaMarconato
    LucaMarconato authored Jan 17, 2024
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  10. change docstring

    @melonora
    melonora committed Jan 17, 2024
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  11. Merge branch 'main' into multi_table

    @melonora
    melonora committed Jan 17, 2024
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  12. fix query test

    @melonora
    melonora committed Jan 17, 2024
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  13. add todo

    @melonora
    melonora committed Jan 17, 2024
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  14. refactor filter_by_coordinate_system

    @melonora
    melonora committed Jan 17, 2024
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  15. test filter with keep table

    @melonora
    melonora committed Jan 17, 2024
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  16. adjust docstring

    @melonora
    melonora committed Jan 17, 2024
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  17. adjust docstring

    @melonora
    melonora committed Jan 17, 2024
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