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Zarr support #190

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Zarr support #190

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19698c3
WIP
keller-mark May 6, 2024
5100a40
More tests passing
keller-mark May 6, 2024
4c9d01f
Fix df read bug
keller-mark May 6, 2024
eb8b69c
More tests passing after fixing zero-dimensional get bug in pizzarr
keller-mark May 7, 2024
58f5ce4
WIP: writing
keller-mark May 7, 2024
a15513a
Fix more tests
keller-mark May 7, 2024
1ef1be6
Zarr df writing
keller-mark May 7, 2024
77a7ee2
WIP: ZarrAnnData class
keller-mark May 7, 2024
27ce6c1
Tests passing
keller-mark May 7, 2024
8790715
Tests that compare h5ad to zarr
keller-mark May 8, 2024
bb0c6c7
Use Rarr to read full numeric arrays
keller-mark May 17, 2024
0456ecd
Fix bugs. Add test for from_SingleCellExperiment with Zarr
keller-mark Jun 18, 2024
acac772
Add a to_dense param to ZarrAnnData constructor. Add overwrite params…
keller-mark Jun 20, 2024
30316ed
Update
keller-mark Jun 20, 2024
c6b4d89
Backwards dense/sparse
keller-mark Jun 20, 2024
9cadc26
Merge branch 'keller-mark/zarr' of https://github.com/keller-mark/ann…
Artur-man Nov 1, 2024
a40a618
Merge branch 'keller-mark/zarr' into zarr
Artur-man Nov 1, 2024
1afd6eb
Simplify how obs and var names handled in ZarrAnnData (similar to #171)
Artur-man Nov 1, 2024
7f53049
update extdata and documentation
Artur-man Nov 1, 2024
3800f38
fix set/get zarr _index, update text example.zarr and update tests si…
Artur-man Nov 2, 2024
4a7d4c2
Merge pull request #5 from Artur-man/zarr
keller-mark Nov 5, 2024
c881bb9
Merge
keller-mark Nov 5, 2024
4a1bbde
Fix test
keller-mark Nov 5, 2024
15dfbde
Revert unnecessary changes
keller-mark Nov 5, 2024
438809a
Formatting
keller-mark Nov 5, 2024
2215402
Merge pull request #6 from keller-mark/keller-mark/zarr-2
keller-mark Nov 5, 2024
087ffb7
Add comments
keller-mark Nov 5, 2024
37d1ae5
Merge pull request #7 from keller-mark/keller-mark/comments
keller-mark Nov 5, 2024
357a8d7
remove unnecessary example zarr store
Artur-man Nov 6, 2024
d192e68
lintr and R check for zarr related utilities and functions, updated s…
Artur-man Nov 6, 2024
1e0e868
add pizzarr to Suggests and README
Artur-man Nov 6, 2024
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4 changes: 4 additions & 0 deletions .gitignore
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Expand Up @@ -52,3 +52,7 @@ po/*~

# RStudio Connect folder
rsconnect/

.DS_Store
.ipynb_checkpoints/
*.ipynb
1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -69,6 +69,7 @@ Suggests:
knitr,
reticulate (>= 1.36.1),
hdf5r (>= 1.3.11),
pizzarr,
rmarkdown,
S4Vectors,
SeuratObject,
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -5,7 +5,9 @@ export(from_Seurat)
export(from_SingleCellExperiment)
export(generate_dataset)
export(read_h5ad)
export(read_zarr)
export(write_h5ad)
export(write_zarr)
importFrom(Matrix,as.matrix)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
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2 changes: 1 addition & 1 deletion R/Seurat.R
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Expand Up @@ -121,7 +121,7 @@ to_Seurat <- function(obj) { # nolint
from_Seurat <- function(
# nolint end: object_name_linter
seurat_obj,
output_class = c("InMemoryAnnData", "HDF5AnnData"),
output_class = c("InMemoryAnnData", "HDF5AnnData", "ZarrAnnData"),
assay = NULL,
X = "counts",
...) {
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2 changes: 1 addition & 1 deletion R/SingleCellExperiment.R
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Expand Up @@ -117,7 +117,7 @@ to_SingleCellExperiment <- function(object) { # nolint
from_SingleCellExperiment <- function(
# nolint end: object_name_linter
sce,
output_class = c("InMemory", "HDF5AnnData"),
output_class = c("InMemory", "HDF5AnnData", "ZarrAnnData"),
...) {
stopifnot(
inherits(sce, "SingleCellExperiment")
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