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general fixes to adapt table model - #417

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general fixes to adapt table model#417
giovp wants to merge 126 commits into
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giov/multitable

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@giovp

@giovpgiovp commented Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.

pre-commit-ciBotand others added 30 commits November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
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* [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
@melonora
revert to old public accessor
3031950
@melonora
Validate each table in dictionary
c149c71
@melonora
iterate dict values
cb826e0
@melonora
add comment
da4cc86
@melonora
adjust table getter
d6589a0
@melonora
Add tables getter
1ad33b0
@melonora
Fix missing parenthesis
1d1907b
@melonora
change to warnings.warn DeprecationWarning
bec136f
@melonora
allow for backward compatibility in init
22e2bef
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#408)
ef0a2dc
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
fix dict subscriptable
c75c684
@melonora
fix string representation of sdata
9819a09
@melonora
add deprecation decorator for future
59b5d21
@melonora
Allow for tables not annotating elements
3cdc492
@melonora
switch to using tables with deprecation
2c51b69
melonoraand others added 22 commits December 18, 2023 18:04
@melonora
refactor of set_table_annotation_target
a708594
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
c1d83f3
…into multi_table
@melonora
add quotes
b957906
@LucaMarconato
fix (?)
31fca71
@melonora
refactor error messages
e780d6f
@giovp@melonora@pre-commit-ci
fix incremental update (#329)
4eed839
Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
add concatenate argument
f7cebb5
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
aca8965
…into multi_table
@melonora
Merge branch 'main' into multi_table
aff28c2
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c2c062f
for more information, see https://pre-commit.ci
@melonora
add util functions to init
c3690b7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
415022c
for more information, see https://pre-commit.ci
@melonora
add util functions to init
207b411
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
@melonora
add deprecation back
31dc81d
@melonora
rename function in tests
d3eef8e
@melonora
rename function in tests
f16b357
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3c80380
for more information, see https://pre-commit.ci
@giovp
fix precommit
3a713a8
@giovp
update precommit and remove add_table, store_table and general fixes
798a978
@melonora

melonora commented Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.

Agreed, was doing that but keep losing connection in the car:)

@melonora

melonora commented Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.
We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?

@giovpgiovp mentioned this pull request Jan 4, 2024
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@LucaMarconato

LucaMarconato commented Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?

melonora
melonora reviewed Jan 17, 2024
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Comment threadsrc/spatialdata/_core/spatialdata.py
# filtering with tables having potentially different keys.
if filter_tables:
tables = {}
tables: Tables = Tables(shared_keys=self._shared_keys)

@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?

@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!

@melonoramelonoraJan 17, 2024

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After offline conversation with Giovanni, we agreed it is not required.

@melonora

melonora commented Jan 17, 2024

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I will close this PR as all the changes have already been implemented in #410

@LucaMarconato
LucaMarconato deleted the giov/multitable branch February 9, 2024 10:29
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@giovp@melonora@LucaMarconato
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general fixes to adapt table model by giovp · Pull Request #417 · scverse/spatialdata · GitHub
Skip to content
general fixes to adapt table model - #417
Closed
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Closed
general fixes to adapt table model#417
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Conversation
@giovp
@giovpgiovp
commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
pre-commit-ciBotand others
added 30 commits
November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
5848756
* [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
@melonora
revert to old public accessor
3031950
@melonora
Validate each table in dictionary
c149c71
@melonora
iterate dict values
cb826e0
@melonora
add comment
da4cc86
@melonora
adjust table getter
d6589a0
@melonora
Add tables getter
1ad33b0
@melonora
Fix missing parenthesis
1d1907b
@melonora
change to warnings.warn DeprecationWarning
bec136f
@melonora
allow for backward compatibility in init
22e2bef
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#408)
ef0a2dc
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
fix dict subscriptable
c75c684
@melonora
fix string representation of sdata
9819a09
@melonora
add deprecation decorator for future
59b5d21
@melonora
Allow for tables not annotating elements
3cdc492
@melonora
switch to using tables with deprecation
2c51b69
melonoraand others
added 22 commits
December 18, 2023 18:04
@melonora
refactor of set_table_annotation_target
a708594
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
c1d83f3
…into multi_table
@melonora
add quotes
b957906
@LucaMarconato
fix (?)
31fca71
@melonora
refactor error messages
e780d6f
@giovp@melonora@pre-commit-ci
fix incremental update (#329)
4eed839
Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
add concatenate argument
f7cebb5
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
aca8965
…into multi_table
@melonora
Merge branch 'main' into multi_table
aff28c2
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c2c062f
for more information, see https://pre-commit.ci
@melonora
add util functions to init
c3690b7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
415022c
for more information, see https://pre-commit.ci
@melonora
add util functions to init
207b411
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
@melonora
add deprecation back
31dc81d
@melonora
rename function in tests
d3eef8e
@melonora
rename function in tests
f16b357
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3c80380
for more information, see https://pre-commit.ci
@giovp
fix precommit
3a713a8
@giovp
update precommit and remove add_table, store_table and general fixes
798a978
@melonora
melonora
commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
Agreed, was doing that but keep losing connection in the car:)
@melonora
melonora
commented
Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.

We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?
@giovpgiovp
mentioned this pull request
Jan 4, 2024
 Merged

@LucaMarconato
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commented
Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?
melonora
melonora
reviewed
Jan 17, 2024
View reviewed changes
Comment threadsrc/spatialdata/_core/spatialdata.py
 # filtering with tables having potentially different keys.
 if filter_tables:
 tables = {}
 tables: Tables = Tables(shared_keys=self._shared_keys)
@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?
@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!
@melonoramelonoraJan 17, 2024

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After offline conversation with Giovanni, we agreed it is not required.
@melonora
melonora
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Jan 17, 2024

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I will close this PR as all the changes have already been implemented in #410
@LucaMarconato
LucaMarconato
deleted the

giov/multitable

branch
February 9, 2024 10:29
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general fixes to adapt table model by giovp · Pull Request #417 · scverse/spatialdata · GitHub
Skip to content
general fixes to adapt table model - #417
Closed
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Closed
general fixes to adapt table model#417
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Conversation
@giovp
@giovpgiovp
commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
pre-commit-ciBotand others
added 30 commits
November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
5848756
* [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
@melonora
revert to old public accessor
3031950
@melonora
Validate each table in dictionary
c149c71
@melonora
iterate dict values
cb826e0
@melonora
add comment
da4cc86
@melonora
adjust table getter
d6589a0
@melonora
Add tables getter
1ad33b0
@melonora
Fix missing parenthesis
1d1907b
@melonora
change to warnings.warn DeprecationWarning
bec136f
@melonora
allow for backward compatibility in init
22e2bef
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#408)
ef0a2dc
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
fix dict subscriptable
c75c684
@melonora
fix string representation of sdata
9819a09
@melonora
add deprecation decorator for future
59b5d21
@melonora
Allow for tables not annotating elements
3cdc492
@melonora
switch to using tables with deprecation
2c51b69
melonoraand others
added 22 commits
December 18, 2023 18:04
@melonora
refactor of set_table_annotation_target
a708594
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
c1d83f3
…into multi_table
@melonora
add quotes
b957906
@LucaMarconato
fix (?)
31fca71
@melonora
refactor error messages
e780d6f
@giovp@melonora@pre-commit-ci
fix incremental update (#329)
4eed839
Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
add concatenate argument
f7cebb5
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
aca8965
…into multi_table
@melonora
Merge branch 'main' into multi_table
aff28c2
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c2c062f
for more information, see https://pre-commit.ci
@melonora
add util functions to init
c3690b7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
415022c
for more information, see https://pre-commit.ci
@melonora
add util functions to init
207b411
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
@melonora
add deprecation back
31dc81d
@melonora
rename function in tests
d3eef8e
@melonora
rename function in tests
f16b357
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3c80380
for more information, see https://pre-commit.ci
@giovp
fix precommit
3a713a8
@giovp
update precommit and remove add_table, store_table and general fixes
798a978
@melonora
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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
Agreed, was doing that but keep losing connection in the car:)
@melonora
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Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.

We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?
@giovpgiovp
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Jan 4, 2024
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@LucaMarconato
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Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?
melonora
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Jan 17, 2024
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Comment threadsrc/spatialdata/_core/spatialdata.py
 # filtering with tables having potentially different keys.
 if filter_tables:
 tables = {}
 tables: Tables = Tables(shared_keys=self._shared_keys)
@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?
@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!
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After offline conversation with Giovanni, we agreed it is not required.
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I will close this PR as all the changes have already been implemented in #410
@LucaMarconato
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general fixes to adapt table model by giovp · Pull Request #417 · scverse/spatialdata · GitHub
Skip to content
general fixes to adapt table model - #417
Closed
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Closed
general fixes to adapt table model#417
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Conversation
@giovp
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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
pre-commit-ciBotand others
added 30 commits
November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
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* [pre-commit.ci] pre-commit autoupdate
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- [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
@melonora
revert to old public accessor
3031950
@melonora
Validate each table in dictionary
c149c71
@melonora
iterate dict values
cb826e0
@melonora
add comment
da4cc86
@melonora
adjust table getter
d6589a0
@melonora
Add tables getter
1ad33b0
@melonora
Fix missing parenthesis
1d1907b
@melonora
change to warnings.warn DeprecationWarning
bec136f
@melonora
allow for backward compatibility in init
22e2bef
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#408)
ef0a2dc
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
fix dict subscriptable
c75c684
@melonora
fix string representation of sdata
9819a09
@melonora
add deprecation decorator for future
59b5d21
@melonora
Allow for tables not annotating elements
3cdc492
@melonora
switch to using tables with deprecation
2c51b69
melonoraand others
added 22 commits
December 18, 2023 18:04
@melonora
refactor of set_table_annotation_target
a708594
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
c1d83f3
…into multi_table
@melonora
add quotes
b957906
@LucaMarconato
fix (?)
31fca71
@melonora
refactor error messages
e780d6f
@giovp@melonora@pre-commit-ci
fix incremental update (#329)
4eed839
Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
add concatenate argument
f7cebb5
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
aca8965
…into multi_table
@melonora
Merge branch 'main' into multi_table
aff28c2
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c2c062f
for more information, see https://pre-commit.ci
@melonora
add util functions to init
c3690b7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
415022c
for more information, see https://pre-commit.ci
@melonora
add util functions to init
207b411
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
@melonora
add deprecation back
31dc81d
@melonora
rename function in tests
d3eef8e
@melonora
rename function in tests
f16b357
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3c80380
for more information, see https://pre-commit.ci
@giovp
fix precommit
3a713a8
@giovp
update precommit and remove add_table, store_table and general fixes
798a978
@melonora
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Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
Agreed, was doing that but keep losing connection in the car:)
@melonora
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commented
Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.

We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?
@giovpgiovp
mentioned this pull request
Jan 4, 2024
 Merged

@LucaMarconato
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Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?
melonora
melonora
reviewed
Jan 17, 2024
View reviewed changes
Comment threadsrc/spatialdata/_core/spatialdata.py
 # filtering with tables having potentially different keys.
 if filter_tables:
 tables = {}
 tables: Tables = Tables(shared_keys=self._shared_keys)
@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?
@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!
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After offline conversation with Giovanni, we agreed it is not required.
@melonora
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I will close this PR as all the changes have already been implemented in #410
@LucaMarconato
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branch
February 9, 2024 10:29
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general fixes to adapt table model by giovp · Pull Request #417 · scverse/spatialdata · GitHub
Skip to content
general fixes to adapt table model - #417
Closed
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Closed
general fixes to adapt table model#417
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Conversation
@giovp
@giovpgiovp
commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
pre-commit-ciBotand others
added 30 commits
November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
5848756
* [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
@melonora
revert to old public accessor
3031950
@melonora
Validate each table in dictionary
c149c71
@melonora
iterate dict values
cb826e0
@melonora
add comment
da4cc86
@melonora
adjust table getter
d6589a0
@melonora
Add tables getter
1ad33b0
@melonora
Fix missing parenthesis
1d1907b
@melonora
change to warnings.warn DeprecationWarning
bec136f
@melonora
allow for backward compatibility in init
22e2bef
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#408)
ef0a2dc
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
fix dict subscriptable
c75c684
@melonora
fix string representation of sdata
9819a09
@melonora
add deprecation decorator for future
59b5d21
@melonora
Allow for tables not annotating elements
3cdc492
@melonora
switch to using tables with deprecation
2c51b69
melonoraand others
added 22 commits
December 18, 2023 18:04
@melonora
refactor of set_table_annotation_target
a708594
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
c1d83f3
…into multi_table
@melonora
add quotes
b957906
@LucaMarconato
fix (?)
31fca71
@melonora
refactor error messages
e780d6f
@giovp@melonora@pre-commit-ci
fix incremental update (#329)
4eed839
Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
add concatenate argument
f7cebb5
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
aca8965
…into multi_table
@melonora
Merge branch 'main' into multi_table
aff28c2
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c2c062f
for more information, see https://pre-commit.ci
@melonora
add util functions to init
c3690b7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
415022c
for more information, see https://pre-commit.ci
@melonora
add util functions to init
207b411
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
@melonora
add deprecation back
31dc81d
@melonora
rename function in tests
d3eef8e
@melonora
rename function in tests
f16b357
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3c80380
for more information, see https://pre-commit.ci
@giovp
fix precommit
3a713a8
@giovp
update precommit and remove add_table, store_table and general fixes
798a978
@melonora
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commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
Agreed, was doing that but keep losing connection in the car:)
@melonora
melonora
commented
Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.

We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?
@giovpgiovp
mentioned this pull request
Jan 4, 2024
 Merged

@LucaMarconato
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Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?
melonora
melonora
reviewed
Jan 17, 2024
View reviewed changes
Comment threadsrc/spatialdata/_core/spatialdata.py
 # filtering with tables having potentially different keys.
 if filter_tables:
 tables = {}
 tables: Tables = Tables(shared_keys=self._shared_keys)
@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?
@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!
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After offline conversation with Giovanni, we agreed it is not required.
@melonora
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Jan 17, 2024

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I will close this PR as all the changes have already been implemented in #410
@LucaMarconato
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February 9, 2024 10:29
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general fixes to adapt table model by giovp · Pull Request #417 · scverse/spatialdata · GitHub
Skip to content
general fixes to adapt table model - #417
Closed
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Closed
general fixes to adapt table model#417
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Conversation
@giovp
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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
pre-commit-ciBotand others
added 30 commits
November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
5848756
* [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
@melonora
revert to old public accessor
3031950
@melonora
Validate each table in dictionary
c149c71
@melonora
iterate dict values
cb826e0
@melonora
add comment
da4cc86
@melonora
adjust table getter
d6589a0
@melonora
Add tables getter
1ad33b0
@melonora
Fix missing parenthesis
1d1907b
@melonora
change to warnings.warn DeprecationWarning
bec136f
@melonora
allow for backward compatibility in init
22e2bef
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#408)
ef0a2dc
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
fix dict subscriptable
c75c684
@melonora
fix string representation of sdata
9819a09
@melonora
add deprecation decorator for future
59b5d21
@melonora
Allow for tables not annotating elements
3cdc492
@melonora
switch to using tables with deprecation
2c51b69
melonoraand others
added 22 commits
December 18, 2023 18:04
@melonora
refactor of set_table_annotation_target
a708594
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
c1d83f3
…into multi_table
@melonora
add quotes
b957906
@LucaMarconato
fix (?)
31fca71
@melonora
refactor error messages
e780d6f
@giovp@melonora@pre-commit-ci
fix incremental update (#329)
4eed839
Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
add concatenate argument
f7cebb5
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
aca8965
…into multi_table
@melonora
Merge branch 'main' into multi_table
aff28c2
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c2c062f
for more information, see https://pre-commit.ci
@melonora
add util functions to init
c3690b7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
415022c
for more information, see https://pre-commit.ci
@melonora
add util functions to init
207b411
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
@melonora
add deprecation back
31dc81d
@melonora
rename function in tests
d3eef8e
@melonora
rename function in tests
f16b357
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3c80380
for more information, see https://pre-commit.ci
@giovp
fix precommit
3a713a8
@giovp
update precommit and remove add_table, store_table and general fixes
798a978
@melonora
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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
Agreed, was doing that but keep losing connection in the car:)
@melonora
melonora
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Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.

We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?
@giovpgiovp
mentioned this pull request
Jan 4, 2024
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@LucaMarconato
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Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?
melonora
melonora
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Jan 17, 2024
View reviewed changes
Comment threadsrc/spatialdata/_core/spatialdata.py
 # filtering with tables having potentially different keys.
 if filter_tables:
 tables = {}
 tables: Tables = Tables(shared_keys=self._shared_keys)
@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?
@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!
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After offline conversation with Giovanni, we agreed it is not required.
@melonora
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I will close this PR as all the changes have already been implemented in #410
@LucaMarconato
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general fixes to adapt table model by giovp · Pull Request #417 · scverse/spatialdata · GitHub
Skip to content
general fixes to adapt table model - #417
Closed
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Closed
general fixes to adapt table model#417
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Conversation
@giovp
@giovpgiovp
commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
pre-commit-ciBotand others
added 30 commits
November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
5848756
* [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
@melonora
revert to old public accessor
3031950
@melonora
Validate each table in dictionary
c149c71
@melonora
iterate dict values
cb826e0
@melonora
add comment
da4cc86
@melonora
adjust table getter
d6589a0
@melonora
Add tables getter
1ad33b0
@melonora
Fix missing parenthesis
1d1907b
@melonora
change to warnings.warn DeprecationWarning
bec136f
@melonora
allow for backward compatibility in init
22e2bef
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#408)
ef0a2dc
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
fix dict subscriptable
c75c684
@melonora
fix string representation of sdata
9819a09
@melonora
add deprecation decorator for future
59b5d21
@melonora
Allow for tables not annotating elements
3cdc492
@melonora
switch to using tables with deprecation
2c51b69
melonoraand others
added 22 commits
December 18, 2023 18:04
@melonora
refactor of set_table_annotation_target
a708594
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
c1d83f3
…into multi_table
@melonora
add quotes
b957906
@LucaMarconato
fix (?)
31fca71
@melonora
refactor error messages
e780d6f
@giovp@melonora@pre-commit-ci
fix incremental update (#329)
4eed839
Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@melonora
add concatenate argument
f7cebb5
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
aca8965
…into multi_table
@melonora
Merge branch 'main' into multi_table
aff28c2
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c2c062f
for more information, see https://pre-commit.ci
@melonora
add util functions to init
c3690b7
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
415022c
for more information, see https://pre-commit.ci
@melonora
add util functions to init
207b411
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
@melonora
add deprecation back
31dc81d
@melonora
rename function in tests
d3eef8e
@melonora
rename function in tests
f16b357
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3c80380
for more information, see https://pre-commit.ci
@giovp
fix precommit
3a713a8
@giovp
update precommit and remove add_table, store_table and general fixes
798a978
@melonora
melonora
commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
Agreed, was doing that but keep losing connection in the car:)
@melonora
melonora
commented
Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.

We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?
@giovpgiovp
mentioned this pull request
Jan 4, 2024
 Merged

@LucaMarconato
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commented
Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?
melonora
melonora
reviewed
Jan 17, 2024
View reviewed changes
Comment threadsrc/spatialdata/_core/spatialdata.py
 # filtering with tables having potentially different keys.
 if filter_tables:
 tables = {}
 tables: Tables = Tables(shared_keys=self._shared_keys)
@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?
@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!
@melonoramelonoraJan 17, 2024

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After offline conversation with Giovanni, we agreed it is not required.
@melonora
melonora
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Jan 17, 2024

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I will close this PR as all the changes have already been implemented in #410
@LucaMarconato
LucaMarconato
deleted the

giov/multitable

branch
February 9, 2024 10:29
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general fixes to adapt table model by giovp · Pull Request #417 · scverse/spatialdata · GitHub
Skip to content
general fixes to adapt table model - #417
Closed
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Closed
general fixes to adapt table model#417
giovp wants to merge 126 commits into
multi_tablefrom 
giov/multitable
Conversation
@giovp
@giovpgiovp
commented
Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
pre-commit-ciBotand others
added 30 commits
November 21, 2023 13:43
@pre-commit-ci@giovp
[pre-commit.ci] pre-commit autoupdate (#394)
5848756
* [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 <giov.pll@gmail.com>
@melonora
initial tests multi_table design
9d68766
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d5e3ee3
for more information, see https://pre-commit.ci
@melonora
add mock new table
a47c0cf
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e1c71aa
…into multi_table
@melonora
create test class and cleanup
f857d4e
@melonora
additional cleanup
3c32b27
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
3f47c3b
for more information, see https://pre-commit.ci
@melonora
additional cleanup
bfb4c7c
@melonora
additional cleanup
8cc1acf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4de59c
for more information, see https://pre-commit.ci
@melonora
add pseudo methods
c6d0976
@melonora
Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
e8eeda8
…into multi_table
@melonora
Change table type in init
cd3def6
@melonora
make tables plural and add to validation in __init__
b815980
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revert to old public accessor
3031950
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Validate each table in dictionary
c149c71
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iterate dict values
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add comment
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adjust table getter
d6589a0
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Add tables getter
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Fix missing parenthesis
1d1907b
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change to warnings.warn DeprecationWarning
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allow for backward compatibility in init
22e2bef
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[pre-commit.ci] pre-commit autoupdate (#408)
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@melonora
fix dict subscriptable
c75c684
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fix string representation of sdata
9819a09
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add deprecation decorator for future
59b5d21
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Allow for tables not annotating elements
3cdc492
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switch to using tables with deprecation
2c51b69
melonoraand others
added 22 commits
December 18, 2023 18:04
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refactor of set_table_annotation_target
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Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
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add quotes
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@LucaMarconato
fix (?)
31fca71
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refactor error messages
e780d6f
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fix incremental update (#329)
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@melonora
add concatenate argument
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Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
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…into multi_table
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Merge branch 'main' into multi_table
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add util functions to init
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add util functions to init
207b411
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Merge branch 'multi_table' ofhttps://github.com/melonora/spatialdata…
29f8ecf
…into multi_table
@melonora
add tables class
a5d4d5d
@melonora
add table class
de74482
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add deprecation back
31dc81d
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rename function in tests
d3eef8e
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rename function in tests
f16b357
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fix precommit
3a713a8
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update precommit and remove add_table, store_table and general fixes
798a978
@melonora
melonora
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Dec 21, 2023

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@melonora these are some additional fixes, I think we need to remove the add_table/store_table etc. due to the merge of #329 and keep the Tables element as close as possible to the rest.
Agreed, was doing that but keep losing connection in the car:)
@melonora
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Dec 22, 2023

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In the other PR there is currently 1 remaining errors which relates to removing the store_tables.

We used to immediately create a zarr group if not there and store the table upon adding so removing this is a backward incompatible change. If we want to keep it this way for this PR, we need to have a check per element whether it is backed or not. What do you think?
@giovpgiovp
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Jan 4, 2024
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@LucaMarconato
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Jan 16, 2024

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@melonora can you please check if this branch can merged/removed?
melonora
melonora
reviewed
Jan 17, 2024
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Comment threadsrc/spatialdata/_core/spatialdata.py
 # filtering with tables having potentially different keys.
 if filter_tables:
 tables = {}
 tables: Tables = Tables(shared_keys=self._shared_keys)
@melonoramelonoraJan 17, 2024

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comparing this to #410 there is a difference here. However, I am not certain that shared_keys needs to be passed here since we are returning a new SpatialData object. What do you think @giovp@LucaMarconato ?
@giovpgiovpJan 17, 2024

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yeah I agree, the shared keys should be instantiated in the return line 680. I think this can be closed!
@melonoramelonoraJan 17, 2024

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After offline conversation with Giovanni, we agreed it is not required.
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Jan 17, 2024

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I will close this PR as all the changes have already been implemented in #410
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February 9, 2024 10:29
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