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Out of core concatenation support #955

Merged
merged 141 commits into from
Jul 21, 2023
Merged

Out of core concatenation support #955

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6245a6f
start with unit tests
selmanozleyen Mar 17, 2023
41f6369
signature clarification
selmanozleyen Mar 17, 2023
c7103a8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 17, 2023
d008f6c
Merge branch 'main' into concat-on-disk
selmanozleyen Mar 21, 2023
fbdbca5
restricted concat on zarr
selmanozleyen Mar 26, 2023
f2200b3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 26, 2023
7009d49
works for layers
selmanozleyen Mar 26, 2023
275052b
Merge branch 'concat-on-disk' of https://github.com/syelman/anndata i…
selmanozleyen Mar 26, 2023
ebc88b5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 26, 2023
5543952
added test
selmanozleyen Mar 26, 2023
4b35de0
obs and var annotations concatenation
selmanozleyen Mar 26, 2023
4c01055
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 26, 2023
722958b
Merge branch 'main' into concat-on-disk
selmanozleyen Mar 30, 2023
43ff24c
init
selmanozleyen Mar 31, 2023
120d21b
getting ready for merge
selmanozleyen Apr 2, 2023
cfd9bd4
fixing index names remaining
selmanozleyen Apr 2, 2023
80b14e2
obsm varm now works
selmanozleyen Apr 2, 2023
8a67f29
formatting
selmanozleyen Apr 2, 2023
381d102
Revert "signature clarification"
selmanozleyen Apr 2, 2023
6c27dcf
fix imports
selmanozleyen Apr 2, 2023
75c8328
refactor
selmanozleyen Apr 2, 2023
865c1d6
Merge branch 'scverse:main' into restricted-ooc-concat
selmanozleyen Apr 4, 2023
403bc36
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 4, 2023
5bfbc76
Merge branch 'main' into concat-on-disk
selmanozleyen Apr 4, 2023
9ad06ae
added unit test
selmanozleyen Apr 4, 2023
7136947
Merge branch 'restricted-ooc-concat' of https://github.com/syelman/an…
selmanozleyen Apr 4, 2023
e240bbe
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 4, 2023
c7b5333
merged conflicts
selmanozleyen Apr 4, 2023
aa8c6d3
Merge branch 'restricted-ooc-concat' of https://github.com/syelman/an…
selmanozleyen Apr 4, 2023
fbf77fd
inner still works
selmanozleyen Apr 10, 2023
8a9c5f4
is it worth supporting h5ad
selmanozleyen Apr 11, 2023
8c6c0a7
inner with reindexing passes
selmanozleyen Apr 13, 2023
0e401eb
outer also seems to be working
selmanozleyen Apr 13, 2023
540941a
resolve
selmanozleyen Apr 13, 2023
cad3dcd
Merge branch 'concat-on-disk' of https://github.com/syelman/anndata i…
selmanozleyen Apr 13, 2023
e746274
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 13, 2023
9666e7d
Merge branch 'concat-on-disk' of https://github.com/syelman/anndata i…
selmanozleyen Apr 13, 2023
a016300
Revert "outer also seems to be working"
selmanozleyen Apr 13, 2023
480d73d
formatting
selmanozleyen Apr 13, 2023
b94840b
Merge branch 'concat-on-disk' into reindexing-ooc-concat
selmanozleyen Apr 13, 2023
f8958ac
Merge pull request #1 from syelman/reindexing-ooc-concat
selmanozleyen Apr 13, 2023
f5f04eb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 13, 2023
7766176
Merge branch 'main' into concat-on-disk
selmanozleyen Apr 13, 2023
e3e47dc
revert registry
selmanozleyen Apr 13, 2023
2432fb0
Merge branch 'concat-on-disk' of https://github.com/syelman/anndata i…
selmanozleyen Apr 13, 2023
b16e2c3
revert methods
selmanozleyen Apr 13, 2023
f4c66fb
revert merge core
selmanozleyen Apr 13, 2023
ee6016b
change to old list typing
selmanozleyen Apr 13, 2023
ede26b8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 13, 2023
61fe35e
refactoring
selmanozleyen Apr 13, 2023
befb086
fixed wrong import
selmanozleyen Apr 13, 2023
6229940
refactor
selmanozleyen Apr 13, 2023
fe70d5e
refactor
selmanozleyen Apr 13, 2023
80d6876
fix
selmanozleyen Apr 13, 2023
b86a572
Merge branch 'main' into dask-index-fix
selmanozleyen Apr 13, 2023
4e1e4dc
maybe this is why it fails
selmanozleyen Apr 13, 2023
891d06f
import refactor
selmanozleyen Apr 13, 2023
b803c74
refactor
selmanozleyen Apr 13, 2023
36dad98
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 13, 2023
39b5839
fix attempt
selmanozleyen Apr 13, 2023
9c3d033
add exact to check_column
selmanozleyen Apr 14, 2023
dcca03c
write not implemented errors
selmanozleyen Apr 14, 2023
5f00860
fix tests
selmanozleyen Apr 14, 2023
18ae5bb
to show dask indexing bug
selmanozleyen Apr 21, 2023
3f34dc1
Merge branch 'dask-index-fix' into concat-on-disk
selmanozleyen Apr 21, 2023
f51784c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 21, 2023
e798a5a
undo dask reindexing
selmanozleyen Apr 21, 2023
912fc03
Merge branch 'main' into concat-on-disk
selmanozleyen May 5, 2023
3469db4
first show it fails
selmanozleyen May 5, 2023
ec22d14
then fix
selmanozleyen May 5, 2023
fb6a322
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 5, 2023
6abf51c
Merge pull request #3 from syelman/concat-nullable
selmanozleyen May 6, 2023
be1c04f
remove invalid outer test
selmanozleyen May 6, 2023
64e29d4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 6, 2023
82d09b8
change zarr append and benchmark gitignore
selmanozleyen May 8, 2023
af973b4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 8, 2023
6752707
add axis param
selmanozleyen May 8, 2023
3927ac3
fix
selmanozleyen May 8, 2023
947f18e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 8, 2023
83543d6
Refactor so categoricals and boolean use same code path
ivirshup May 12, 2023
d5106c9
Merge branch 'main' into concat-nullable
selmanozleyen May 12, 2023
983b6fc
Merge branch 'scverse:main' into concat-on-disk
selmanozleyen May 16, 2023
78e76b4
gitignore update
selmanozleyen May 16, 2023
3132288
Merge branch 'concat-nullable' into concat-on-disk
selmanozleyen May 16, 2023
dba088c
new unify method
selmanozleyen May 16, 2023
1deb4ef
update name of func
selmanozleyen May 16, 2023
510eba8
will need to add more tests for this
selmanozleyen May 16, 2023
de2ea30
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 16, 2023
202da0c
added new test cases and implemented slice by slice writing on sparse
selmanozleyen Jun 5, 2023
90b918e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 5, 2023
b3c0114
refactoring now dense arrays are also written in slices
selmanozleyen Jun 5, 2023
9c878fd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 5, 2023
a58a7c3
refactor
selmanozleyen Jun 5, 2023
1486481
Merge branch 'concat-on-disk' of https://github.com/syelman/anndata i…
selmanozleyen Jun 5, 2023
562e1af
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 5, 2023
677acf5
refactoring
selmanozleyen Jun 6, 2023
f9e2c8d
Merge branch 'concat-on-disk' of https://github.com/syelman/anndata i…
selmanozleyen Jun 6, 2023
3a4df07
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 6, 2023
f85bd29
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 12, 2023
a587840
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 16, 2023
a99bf26
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 16, 2023
eb4380e
refactor method decorator
selmanozleyen Jun 18, 2023
9e54da3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2023
4fe3040
read_as_backed update
selmanozleyen Jun 18, 2023
feec888
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2023
5e94c5e
Update anndata/_io/merge.py
selmanozleyen Jun 18, 2023
1e0967b
move to experimental
selmanozleyen Jun 18, 2023
90f79de
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2023
069ad24
remove duplicate codes
selmanozleyen Jun 18, 2023
9f3fe9d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2023
34fb29b
remove duplicate code
selmanozleyen Jun 20, 2023
dd3aaf6
organizing
selmanozleyen Jun 20, 2023
fe46844
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 20, 2023
190e694
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 21, 2023
3fe8d6b
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 22, 2023
f357d1c
sparse global variable removed and docs updated
selmanozleyen Jun 27, 2023
7c9b8d7
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 27, 2023
21005b3
remove the global variable
selmanozleyen Jun 27, 2023
cd209ec
Merge branch 'main' into concat-on-disk
selmanozleyen Jun 30, 2023
8e14c1b
added test case
selmanozleyen Jun 30, 2023
e0906d7
Update anndata/experimental/merge.py
selmanozleyen Jul 3, 2023
e86471a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 3, 2023
12a599e
write_concat revision
selmanozleyen Jul 3, 2023
fe88652
Merge branch 'concat-on-disk' of https://github.com/syelman/anndata i…
selmanozleyen Jul 3, 2023
16e980a
import in init
selmanozleyen Jul 3, 2023
b8996e5
back to old init
selmanozleyen Jul 3, 2023
e5c7e31
annot update
selmanozleyen Jul 3, 2023
13a99a9
refactor test functions
selmanozleyen Jul 3, 2023
67abf3f
Merge branch 'main' into concat-on-disk
selmanozleyen Jul 10, 2023
6e2459e
fix init file
selmanozleyen Jul 10, 2023
31c7b24
no branches for concat
selmanozleyen Jul 10, 2023
7caa5c9
Merge branch 'main' into concat-on-disk
selmanozleyen Jul 12, 2023
75152b7
Merge branch 'main' into concat-on-disk
selmanozleyen Jul 18, 2023
eadcd81
Merge branch 'main' into concat-on-disk
ivirshup Jul 18, 2023
9fa5772
group register decorators
flying-sheep Jul 20, 2023
0c25ed6
Merge branch 'main' into concat-on-disk
flying-sheep Jul 20, 2023
205e6f4
Update anndata/experimental/merge.py
selmanozleyen Jul 20, 2023
145b438
Update anndata/experimental/merge.py
selmanozleyen Jul 20, 2023
0d7c277
Update anndata/experimental/merge.py
selmanozleyen Jul 20, 2023
bfebddc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 20, 2023
c0408bb
rewrite api
selmanozleyen Jul 20, 2023
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