Fix bug and add tests and anndataR fixtures

.gitignore

@@ -10,4 +10,6 @@ data/
 check/
 vignettes/data/
 *.Rproj
-tests/testthat/test_data
+tests/testthat/test_data
+.ipynb_checkpoints/
+*.ipynb

R/zarr-array.R

@@ -830,7 +830,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
         private$load_metadata()
       }
       # Handle zero-dimensional arrays
-      if(is.null(private$shape)) {
+      if(is.null(private$shape) || length(private$shape) == 0) {
         return(private$get_basic_selection_zd(selection, out = out, fields = fields))
       }
       return(private$get_basic_selection_nd(selection, out = out, fields = fields))
@@ -852,7 +852,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
     },
     set_basic_selection = function(selection, value, fields = NA) {
       # Handle zero-dimensional arrays
-      if(is.null(private$shape)) {
+      if(is.null(private$shape) || length(private$shape) == 0) {
         return(private$set_basic_selection_zd(selection, value = value, fields = fields))
       }
       return(private$set_basic_selection_nd(selection, value = value, fields = fields))

inst/extdata/fixtures/v2/example.zarr/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "anndata",
+    "encoding-version": "0.1.0"
+}

inst/extdata/fixtures/v2/example.zarr/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/X/.zattrs

@@ -0,0 +1,8 @@
+{
+    "encoding-type": "csr_matrix",
+    "encoding-version": "0.1.0",
+    "shape": [
+        50,
+        100
+    ]
+}

inst/extdata/fixtures/v2/example.zarr/X/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/X/indices/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        4317
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i4",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        4317
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/X/indptr/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        51
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i4",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        51
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "dict",
+    "encoding-version": "0.1.0"
+}

inst/extdata/fixtures/v2/example.zarr/layers/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/counts/.zattrs

@@ -0,0 +1,8 @@
+{
+    "encoding-type": "csr_matrix",
+    "encoding-version": "0.1.0",
+    "shape": [
+        50,
+        100
+    ]
+}

inst/extdata/fixtures/v2/example.zarr/layers/counts/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/counts/indices/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        4317
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i4",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        4317
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/counts/indptr/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        51
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i4",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        51
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/csc_counts/.zattrs

@@ -0,0 +1,8 @@
+{
+    "encoding-type": "csc_matrix",
+    "encoding-version": "0.1.0",
+    "shape": [
+        50,
+        100
+    ]
+}

inst/extdata/fixtures/v2/example.zarr/layers/csc_counts/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/csc_counts/indices/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        4317
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i4",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        4317
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/csc_counts/indptr/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        101
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i4",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        101
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/dense_X/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        50,
+        100
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<f4",
+    "fill_value": 0.0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        50,
+        100
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/dense_X/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "array",
+    "encoding-version": "0.2.0"
+}

inst/extdata/fixtures/v2/example.zarr/layers/dense_counts/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        50,
+        100
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        50,
+        100
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/layers/dense_counts/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "array",
+    "encoding-version": "0.2.0"
+}

inst/extdata/fixtures/v2/example.zarr/obs/.zattrs

@@ -0,0 +1,18 @@
+{
+    "_index": "_index",
+    "column-order": [
+        "Float",
+        "FloatNA",
+        "Int",
+        "IntNA",
+        "Bool",
+        "BoolNA",
+        "n_genes_by_counts",
+        "log1p_n_genes_by_counts",
+        "total_counts",
+        "log1p_total_counts",
+        "leiden"
+    ],
+    "encoding-type": "dataframe",
+    "encoding-version": "0.2.0"
+}

inst/extdata/fixtures/v2/example.zarr/obs/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/obs/Bool/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "nullable-boolean",
+    "encoding-version": "0.1.0"
+}

inst/extdata/fixtures/v2/example.zarr/obs/Bool/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/obs/Bool/mask/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        50
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|b1",
+    "fill_value": false,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        50
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/obs/Bool/mask/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "array",
+    "encoding-version": "0.2.0"
+}

inst/extdata/fixtures/v2/example.zarr/obs/Bool/values/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        50
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|b1",
+    "fill_value": false,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        50
+    ],
+    "zarr_format": 2
+}

inst/extdata/fixtures/v2/example.zarr/obs/Bool/values/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "array",
+    "encoding-version": "0.2.0"
+}

inst/extdata/fixtures/v2/example.zarr/obs/BoolNA/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "nullable-boolean",
+    "encoding-version": "0.1.0"
+}

inst/extdata/fixtures/v2/example.zarr/obs/BoolNA/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}