From b9c1468a0361349ae869c74fccaeacda0e56e52b Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Jul 2026 10:31:11 +0200
Subject: [PATCH 01/13] Add consolidated metadata when writing zarr anndata

---
 DESCRIPTION     | 2 +-
 R/ZarrAnnData.R | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6249a500..f4966762 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,7 +56,7 @@ Suggests:
     knitr,
     processx,
     rhdf5 (>= 2.52.1),
-    Rarr (>= 2.1.13),
+    Rarr (>= 2.1.28),
     rmarkdown,
     S4Vectors,
     Seurat,
diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index dcf515b2..805e42c6 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -493,6 +493,7 @@ ZarrAnnData <- R6::R6Class(
             self[[slot]] <- value
           }
         }
+        Rarr::zarr_consolidate_metadata(file)
       }
 
       self

From 56278683495cdc74a2a5a59aa204b49e1153800a Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Jul 2026 11:40:42 +0200
Subject: [PATCH 02/13] Leverage consolidated metadata to get encoding info in
 a single file read

---
 R/ZarrAnnData.R | 84 ++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 73 insertions(+), 11 deletions(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index 805e42c6..ae3108d9 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -21,6 +21,7 @@ ZarrAnnData <- R6::R6Class(
   private = list(
     .zarrobj = NULL,
     .zarrformat = NULL,
+    .consolidated_metadata = NULL,
     .compression = NULL,
     .readonly = NULL,
 
@@ -48,7 +49,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_X, status=done
-        read_zarr_element(private$.zarrobj, "X") |>
+        read_zarr_element(
+          private$.zarrobj, 
+          "X", 
+          private$.consolidated_metadata[["X"]][["encoding-type"]],
+          private$.consolidated_metadata[["X"]][["encoding-version"]]
+        ) |>
           private$.add_matrix_dimnames("X")
       } else {
         private$.check_writeable()
@@ -74,7 +80,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_layers, status=done
-        read_zarr_element(private$.zarrobj, "layers") |>
+        read_zarr_element(
+          private$.zarrobj, 
+          "layers",
+          private$.consolidated_metadata[["layers"]][["encoding-type"]],
+          private$.consolidated_metadata[["layers"]][["encoding-version"]]
+        ) |>
           private$.add_mapping_dimnames("layers")
       } else {
         private$.check_writeable()
@@ -100,7 +111,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obsm, status=done
-        read_zarr_element(private$.zarrobj, "obsm") |>
+        read_zarr_element(
+          private$.zarrobj, 
+          "obsm",
+          private$.consolidated_metadata[["obsm"]][["encoding-type"]],
+          private$.consolidated_metadata[["obsm"]][["encoding-version"]]
+        ) |>
           private$.add_mapping_dimnames("obsm")
       } else {
         private$.check_writeable()
@@ -128,7 +144,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_varm, status=done
-        read_zarr_element(private$.zarrobj, "varm") |>
+        read_zarr_element(
+          private$.zarrobj, 
+          "varm",
+          private$.consolidated_metadata[["varm"]][["encoding-type"]],
+          private$.consolidated_metadata[["varm"]][["encoding-version"]]
+        ) |>
           private$.add_mapping_dimnames("varm")
       } else {
         private$.check_writeable()
@@ -156,7 +177,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obsp, status=done
-        read_zarr_element(private$.zarrobj, "obsp") |>
+        read_zarr_element(
+          private$.zarrobj, 
+          "obsp",
+          private$.consolidated_metadata[["obsp"]][["encoding-type"]],
+          private$.consolidated_metadata[["obsp"]][["encoding-version"]]
+        ) |>
           private$.add_mapping_dimnames("obsp")
       } else {
         private$.check_writeable()
@@ -182,7 +208,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_varp, status=done
-        read_zarr_element(private$.zarrobj, "varp") |>
+        read_zarr_element(
+          private$.zarrobj, 
+          "varp",
+          private$.consolidated_metadata[["varp"]][["encoding-type"]],
+          private$.consolidated_metadata[["varp"]][["encoding-version"]]
+        ) |>
           private$.add_mapping_dimnames("varp")
       } else {
         private$.check_writeable()
@@ -208,7 +239,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obs, status=done
-        read_zarr_element(private$.zarrobj, "obs")
+        read_zarr_element(
+          private$.zarrobj, 
+          "obs",
+          private$.consolidated_metadata[["obs"]][["encoding-type"]],
+          private$.consolidated_metadata[["obs"]][["encoding-version"]]
+        )
       } else {
         private$.check_writeable()
         # trackstatus: class=ZarrAnnData, feature=set_obs, status=done
@@ -227,7 +263,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_var, status=done
-        read_zarr_element(private$.zarrobj, "var")
+        read_zarr_element(
+          private$.zarrobj, 
+          "var",
+          private$.consolidated_metadata[["var"]][["encoding-type"]],
+          private$.consolidated_metadata[["var"]][["encoding-version"]]
+        )
       } else {
         private$.check_writeable()
         # trackstatus: class=ZarrAnnData, feature=set_var, status=done
@@ -246,7 +287,13 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obs_names, status=done
-        read_zarr_element_keys(private$.zarrobj, "obs", dim = "rows")
+        read_zarr_element_keys(
+          private$.zarrobj, 
+          "obs",
+          private$.consolidated_metadata[["obs"]][["encoding-type"]],
+          private$.consolidated_metadata[["obs"]][["encoding-version"]],
+          dim = "rows"
+        )
       } else {
         private$.check_writeable()
         # trackstatus: class=ZarrAnnData, feature=set_obs_names, status=done
@@ -259,7 +306,13 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_var_names, status=done
-        read_zarr_element_keys(private$.zarrobj, "var", dim = "rows")
+        read_zarr_element_keys(
+          private$.zarrobj, 
+          "var",
+          private$.consolidated_metadata[["var"]][["encoding-type"]],
+          private$.consolidated_metadata[["var"]][["encoding-version"]],
+          dim = "rows"
+        )
       } else {
         private$.check_writeable()
         # trackstatus: class=ZarrAnnData, feature=set_var_names, status=done
@@ -272,7 +325,12 @@ ZarrAnnData <- R6::R6Class(
 
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_uns, status=done
-        read_zarr_element(private$.zarrobj, "uns")
+        read_zarr_element(
+          private$.zarrobj, 
+          "uns",
+          private$.consolidated_metadata[["uns"]][["encoding-type"]],
+          private$.consolidated_metadata[["uns"]][["encoding-version"]]
+        )
       } else {
         private$.check_writeable()
         # trackstatus: class=ZarrAnnData, feature=set_uns, status=done
@@ -496,6 +554,10 @@ ZarrAnnData <- R6::R6Class(
         Rarr::zarr_consolidate_metadata(file)
       }
 
+      # Create consolidated metadata on the fly, in memory, if it doesn't exist on disk
+      private$.consolidated_metadata <- Rarr:::.read_consolidated_metadata(file)$metadata %||%
+        Rarr::zarr_consolidate_metadata(file, action = "return")
+
       self
     },
 

From 05841029a5b45b28005f41f056f3a16b4af95b65 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Wed, 29 Jul 2026 10:30:18 +0200
Subject: [PATCH 03/13] Use hashed env for consolidated metadata

---
 R/ZarrAnnData.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index ae3108d9..ad2393c2 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -555,8 +555,9 @@ ZarrAnnData <- R6::R6Class(
       }
 
       # Create consolidated metadata on the fly, in memory, if it doesn't exist on disk
-      private$.consolidated_metadata <- Rarr:::.read_consolidated_metadata(file)$metadata %||%
+      consolidated <- Rarr:::.read_consolidated_metadata(file)$metadata %||%
         Rarr::zarr_consolidate_metadata(file, action = "return")
+      private$.consolidated_metadata <- list2env(consolidated, hash = TRUE, parent = emptyenv())
 
       self
     },

From f7c8d941f7ff6359c62b074a22c51fd0540ef7b8 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Wed, 29 Jul 2026 10:51:56 +0200
Subject: [PATCH 04/13] Define helper function to get attrs from consolidated

---
 R/ZarrAnnData.R | 52 ++++++++++++++++++++++++++++---------------------
 1 file changed, 30 insertions(+), 22 deletions(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index ad2393c2..142d0a3e 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -40,6 +40,14 @@ ZarrAnnData <- R6::R6Class(
           call = rlang::caller_env()
         )
       }
+    },
+
+    .get_attrs_from_consolidated = function(slot, attr) {
+      if (private$.zarrformat == 3L) {
+        private$.consolidated_metadata[[slot]]$attributes[[attr]]
+      } else {
+        private$.consolidated_metadata[[file.path(slot, ".zattrs")]][[attr]]
+      }
     }
   ),
   active = list(
@@ -52,8 +60,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "X", 
-          private$.consolidated_metadata[["X"]][["encoding-type"]],
-          private$.consolidated_metadata[["X"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("X", "encoding-type"),
+          private$.get_attrs_from_consolidated("X", "encoding-version")
         ) |>
           private$.add_matrix_dimnames("X")
       } else {
@@ -83,8 +91,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "layers",
-          private$.consolidated_metadata[["layers"]][["encoding-type"]],
-          private$.consolidated_metadata[["layers"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("layers", "encoding-type"),
+          private$.get_attrs_from_consolidated("layers", "encoding-version")
         ) |>
           private$.add_mapping_dimnames("layers")
       } else {
@@ -114,8 +122,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "obsm",
-          private$.consolidated_metadata[["obsm"]][["encoding-type"]],
-          private$.consolidated_metadata[["obsm"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("obsm", "encoding-type"),
+          private$.get_attrs_from_consolidated("obsm", "encoding-version")
         ) |>
           private$.add_mapping_dimnames("obsm")
       } else {
@@ -147,8 +155,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "varm",
-          private$.consolidated_metadata[["varm"]][["encoding-type"]],
-          private$.consolidated_metadata[["varm"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("varm", "encoding-type"),
+          private$.get_attrs_from_consolidated("varm", "encoding-version")
         ) |>
           private$.add_mapping_dimnames("varm")
       } else {
@@ -180,8 +188,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "obsp",
-          private$.consolidated_metadata[["obsp"]][["encoding-type"]],
-          private$.consolidated_metadata[["obsp"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("obsp", "encoding-type"),
+          private$.get_attrs_from_consolidated("obsp", "encoding-version")
         ) |>
           private$.add_mapping_dimnames("obsp")
       } else {
@@ -211,8 +219,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "varp",
-          private$.consolidated_metadata[["varp"]][["encoding-type"]],
-          private$.consolidated_metadata[["varp"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("varp", "encoding-type"),
+          private$.get_attrs_from_consolidated("varp", "encoding-version")
         ) |>
           private$.add_mapping_dimnames("varp")
       } else {
@@ -242,8 +250,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "obs",
-          private$.consolidated_metadata[["obs"]][["encoding-type"]],
-          private$.consolidated_metadata[["obs"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("obs", "encoding-type"),
+          private$.get_attrs_from_consolidated("obs", "encoding-version")
         )
       } else {
         private$.check_writeable()
@@ -266,8 +274,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "var",
-          private$.consolidated_metadata[["var"]][["encoding-type"]],
-          private$.consolidated_metadata[["var"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("var", "encoding-type"),
+          private$.get_attrs_from_consolidated("var", "encoding-version")
         )
       } else {
         private$.check_writeable()
@@ -290,8 +298,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element_keys(
           private$.zarrobj, 
           "obs",
-          private$.consolidated_metadata[["obs"]][["encoding-type"]],
-          private$.consolidated_metadata[["obs"]][["encoding-version"]],
+          private$.get_attrs_from_consolidated("obs", "encoding-type"),
+          private$.get_attrs_from_consolidated("obs", "encoding-version"),
           dim = "rows"
         )
       } else {
@@ -309,8 +317,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element_keys(
           private$.zarrobj, 
           "var",
-          private$.consolidated_metadata[["var"]][["encoding-type"]],
-          private$.consolidated_metadata[["var"]][["encoding-version"]],
+          private$.get_attrs_from_consolidated("var", "encoding-type"),
+          private$.get_attrs_from_consolidated("var", "encoding-version"),
           dim = "rows"
         )
       } else {
@@ -328,8 +336,8 @@ ZarrAnnData <- R6::R6Class(
         read_zarr_element(
           private$.zarrobj, 
           "uns",
-          private$.consolidated_metadata[["uns"]][["encoding-type"]],
-          private$.consolidated_metadata[["uns"]][["encoding-version"]]
+          private$.get_attrs_from_consolidated("uns", "encoding-type"),
+          private$.get_attrs_from_consolidated("uns", "encoding-version")
         )
       } else {
         private$.check_writeable()

From 325cfad32733491875d0538b293d4d54fa5a0e38 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Wed, 29 Jul 2026 11:12:37 +0200
Subject: [PATCH 05/13] Add missing trailing slash to root path

---
 R/ZarrAnnData.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index 142d0a3e..059525cc 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -563,7 +563,7 @@ ZarrAnnData <- R6::R6Class(
       }
 
       # Create consolidated metadata on the fly, in memory, if it doesn't exist on disk
-      consolidated <- Rarr:::.read_consolidated_metadata(file)$metadata %||%
+      consolidated <- Rarr:::.read_consolidated_metadata(paste0(file, "/"))$metadata %||%
         Rarr::zarr_consolidate_metadata(file, action = "return")
       private$.consolidated_metadata <- list2env(consolidated, hash = TRUE, parent = emptyenv())
 

From 0c6712f53163748b60c651d7dc8bbc5726848522 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Wed, 29 Jul 2026 11:17:02 +0200
Subject: [PATCH 06/13] Support both v2 and v3 when creating consolidated on
 the fly

---
 R/ZarrAnnData.R | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index 059525cc..7ca768dc 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -563,9 +563,14 @@ ZarrAnnData <- R6::R6Class(
       }
 
       # Create consolidated metadata on the fly, in memory, if it doesn't exist on disk
-      consolidated <- Rarr:::.read_consolidated_metadata(paste0(file, "/"))$metadata %||%
-        Rarr::zarr_consolidate_metadata(file, action = "return")
-      private$.consolidated_metadata <- list2env(consolidated, hash = TRUE, parent = emptyenv())
+      consolidated <- Rarr:::.read_consolidated_metadata(paste0(file, "/"))
+      if (is.null(consolidated)) {
+        raw_consolidated <- Rarr::zarr_consolidate_metadata(file, action = "return")
+        if (private$.zarrformat == 3L) {
+          consolidated <- raw_consolidated$consolidated_metadata
+        }
+      }
+      private$.consolidated_metadata <- list2env(consolidated$metadata, hash = TRUE, parent = emptyenv())
 
       self
     },

From a46c40497dd19778d9826a15a3a9fc07610f0bda Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 30 Jul 2026 11:56:21 +0200
Subject: [PATCH 07/13] Use new read_consolidate_metadata(consolidate = ) arg

---
 R/ZarrAnnData.R | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index 7ca768dc..187a1414 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -562,15 +562,13 @@ ZarrAnnData <- R6::R6Class(
         Rarr::zarr_consolidate_metadata(file)
       }
 
-      # Create consolidated metadata on the fly, in memory, if it doesn't exist on disk
-      consolidated <- Rarr:::.read_consolidated_metadata(paste0(file, "/"))
-      if (is.null(consolidated)) {
-        raw_consolidated <- Rarr::zarr_consolidate_metadata(file, action = "return")
-        if (private$.zarrformat == 3L) {
-          consolidated <- raw_consolidated$consolidated_metadata
-        }
-      }
-      private$.consolidated_metadata <- list2env(consolidated$metadata, hash = TRUE, parent = emptyenv())
+      # Create consolidated metadata on the fly, in memory, 
+      # if it doesn't exist on disk.
+      private$.consolidated_metadata <- Rarr:::.read_consolidated_metadata(
+        file,
+        consolidate = "missing"
+      ) |>
+        list2env(hash = TRUE, parent = emptyenv())
 
       self
     },

From 8d8dc283e78ff876a3db0727bb95b79bc6b49e41 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 30 Jul 2026 15:49:04 +0200
Subject: [PATCH 08/13] Simplify .get_attrs_from_consolidated()

Since consolidated metadata is now always returned under v3 format
---
 R/ZarrAnnData.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index 187a1414..519a79e4 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -43,11 +43,7 @@ ZarrAnnData <- R6::R6Class(
     },
 
     .get_attrs_from_consolidated = function(slot, attr) {
-      if (private$.zarrformat == 3L) {
         private$.consolidated_metadata[[slot]]$attributes[[attr]]
-      } else {
-        private$.consolidated_metadata[[file.path(slot, ".zattrs")]][[attr]]
-      }
     }
   ),
   active = list(

From 4ef8184d9ccee6569b6f3e25680ba271eb78cb24 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 30 Jul 2026 15:49:40 +0200
Subject: [PATCH 09/13] Require more recent Rarr version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f4966762..d40aab41 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,7 +56,7 @@ Suggests:
     knitr,
     processx,
     rhdf5 (>= 2.52.1),
-    Rarr (>= 2.1.28),
+    Rarr (>= 2.1.31),
     rmarkdown,
     S4Vectors,
     Seurat,

From a5a705167fc718f938a02c243e99956d51e51bda Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 30 Jul 2026 15:50:35 +0200
Subject: [PATCH 10/13] Use new read_zarr_consolidated_metadata() name

---
 R/ZarrAnnData.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index 519a79e4..b257cdc9 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -559,8 +559,8 @@ ZarrAnnData <- R6::R6Class(
       }
 
       # Create consolidated metadata on the fly, in memory, 
-      # if it doesn't exist on disk.
-      private$.consolidated_metadata <- Rarr:::.read_consolidated_metadata(
+      # if it doesn't exist on disk (only happens for readonly stores).
+      private$.consolidated_metadata <- Rarr::read_zarr_consolidated_metadata(
         file,
         consolidate = "missing"
       ) |>

From c36a7125ed14c34da30468e9b3c235151e9f3cb9 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Fri, 31 Jul 2026 18:32:08 +0200
Subject: [PATCH 11/13] Add NEWS bullet

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index a824fb38..a246359d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# anndataR 1.3.2
+
+- Write consolidated metadata on non-readonly anndata stores. Consolidated metadata is used to read encoding type and version of elements one level deep into the store (PR #492).
+
 # anndataR 1.3.1
 
 - Add support for reading backed objects using `DelayedArray` matrices, including a `backed` argument for `HDF5AnnData` and `InMemoryAnnData`, and conversion of backed `AnnData` objects to `SingleCellExperiment`/`Seurat` (PR #387).

From f84626c4df476aee350cc7961aa8717df5374dd9 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Mon, 3 Aug 2026 11:00:38 +0200
Subject: [PATCH 12/13] Run air

---
 R/ZarrAnnData.R | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/R/ZarrAnnData.R b/R/ZarrAnnData.R
index b257cdc9..2b0b5bfb 100644
--- a/R/ZarrAnnData.R
+++ b/R/ZarrAnnData.R
@@ -43,7 +43,7 @@ ZarrAnnData <- R6::R6Class(
     },
 
     .get_attrs_from_consolidated = function(slot, attr) {
-        private$.consolidated_metadata[[slot]]$attributes[[attr]]
+      private$.consolidated_metadata[[slot]]$attributes[[attr]]
     }
   ),
   active = list(
@@ -54,8 +54,8 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_X, status=done
         read_zarr_element(
-          private$.zarrobj, 
-          "X", 
+          private$.zarrobj,
+          "X",
           private$.get_attrs_from_consolidated("X", "encoding-type"),
           private$.get_attrs_from_consolidated("X", "encoding-version")
         ) |>
@@ -85,7 +85,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_layers, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "layers",
           private$.get_attrs_from_consolidated("layers", "encoding-type"),
           private$.get_attrs_from_consolidated("layers", "encoding-version")
@@ -116,7 +116,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obsm, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "obsm",
           private$.get_attrs_from_consolidated("obsm", "encoding-type"),
           private$.get_attrs_from_consolidated("obsm", "encoding-version")
@@ -149,7 +149,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_varm, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "varm",
           private$.get_attrs_from_consolidated("varm", "encoding-type"),
           private$.get_attrs_from_consolidated("varm", "encoding-version")
@@ -182,7 +182,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obsp, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "obsp",
           private$.get_attrs_from_consolidated("obsp", "encoding-type"),
           private$.get_attrs_from_consolidated("obsp", "encoding-version")
@@ -213,7 +213,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_varp, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "varp",
           private$.get_attrs_from_consolidated("varp", "encoding-type"),
           private$.get_attrs_from_consolidated("varp", "encoding-version")
@@ -244,7 +244,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obs, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "obs",
           private$.get_attrs_from_consolidated("obs", "encoding-type"),
           private$.get_attrs_from_consolidated("obs", "encoding-version")
@@ -268,7 +268,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_var, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "var",
           private$.get_attrs_from_consolidated("var", "encoding-type"),
           private$.get_attrs_from_consolidated("var", "encoding-version")
@@ -292,7 +292,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_obs_names, status=done
         read_zarr_element_keys(
-          private$.zarrobj, 
+          private$.zarrobj,
           "obs",
           private$.get_attrs_from_consolidated("obs", "encoding-type"),
           private$.get_attrs_from_consolidated("obs", "encoding-version"),
@@ -311,7 +311,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_var_names, status=done
         read_zarr_element_keys(
-          private$.zarrobj, 
+          private$.zarrobj,
           "var",
           private$.get_attrs_from_consolidated("var", "encoding-type"),
           private$.get_attrs_from_consolidated("var", "encoding-version"),
@@ -330,7 +330,7 @@ ZarrAnnData <- R6::R6Class(
       if (missing(value)) {
         # trackstatus: class=ZarrAnnData, feature=get_uns, status=done
         read_zarr_element(
-          private$.zarrobj, 
+          private$.zarrobj,
           "uns",
           private$.get_attrs_from_consolidated("uns", "encoding-type"),
           private$.get_attrs_from_consolidated("uns", "encoding-version")
@@ -558,7 +558,7 @@ ZarrAnnData <- R6::R6Class(
         Rarr::zarr_consolidate_metadata(file)
       }
 
-      # Create consolidated metadata on the fly, in memory, 
+      # Create consolidated metadata on the fly, in memory,
       # if it doesn't exist on disk (only happens for readonly stores).
       private$.consolidated_metadata <- Rarr::read_zarr_consolidated_metadata(
         file,

From c32da76c84e8a17313278583896931f61be2b6b6 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Mon, 3 Aug 2026 11:00:43 +0200
Subject: [PATCH 13/13] Bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d40aab41..d51816e0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: anndataR
 Title: AnnData interoperability in R
-Version: 1.3.1
+Version: 1.3.2
 Authors@R: c(
     person("Robrecht", "Cannoodt", , "rcannood@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),