What changed (17 files)

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.3.1] - 2026-10-09
+
+Patch release from the v1.3.0 review: faster Nx chunk and batch streams, a
+shuffle that leaves the caller's random state alone, livebooks that run, and
+docs that match measured behaviour. No public API was removed or renamed.
+
 ### Fixed
 - `ExZarr.Nx.stream_chunk_tensors/2` crops padded edge chunks with one
   contiguous copy per row instead of one copy per element. A 999x1000 float32
@@ -32,6 +38,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   environment carried forward, like Livebook, names the failing cell, and keeps
   the end of long output. `--local` runs notebooks against this checkout
   instead of the Hex release. CI runs `mix livebook.test --local`.
+- Livebooks, notebooks and guide install snippets use `{:ex_zarr, "~> 1.3"}`.
+- The Nx guide and `ExZarr.Nx` docs replace unbenchmarked speed claims
+  ("5-10x", "400-800 MB/s") with measured timings, and the chunk-reduction
+  example uses `include_missing: true` and `on_error: :halt` so its total is
+  correct.
+- The v1.3.0 entries in this changelog, the release notes, and the roadmap now
+  say that Explorer streaming was planned for 1.3 and dropped.
+
+### Tests
+- The streaming memory test measures the test process instead of the whole VM,
+  so other async tests no longer move the result; the limit is now 2 MB.
+- New tests cover `stream_chunk_tensors/2` options (`:include_missing`,
+  `:on_error`, `:backend`, unordered concurrency), 3D and 4D edge crops, seeded
+  shuffle orders matching 1.3.0, and cell-by-cell livebook evaluation.
 
 ## [1.3.0] - 2026-10-08
 
@@ -932,7 +952,8 @@ None - Full backward compatibility maintained with v2 arrays
 
 ---
 
-[Unreleased]: https://github.com/AnimaLogica/ExZarr/compare/v1.3.0...HEAD
+[Unreleased]: https://github.com/AnimaLogica/ExZarr/compare/v1.3.1...HEAD
+[1.3.1]: https://github.com/AnimaLogica/ExZarr/compare/v1.3.0...v1.3.1
 [1.3.0]: https://github.com/AnimaLogica/ExZarr/compare/v1.2.0...v1.3.0
 [1.2.0]: https://github.com/AnimaLogica/ExZarr/releases/tag/v1.2.0
 [1.1.0]: https://github.com/AnimaLogica/ExZarr/releases/tag/v1.1.0

README.md

@@ -874,6 +874,10 @@ Key modules:
 
 See [ROADMAP.md](docs/ROADMAP.md) for the full release plan.
 
+**v1.3.1 (released 2026-10-09)** - Patch release: faster Nx chunk crops and
+shuffled batches, livebooks checked in CI, measured performance figures. See
+[release notes](docs/release_notes_v1_3_1.md).
+
 **v1.3.0 (released 2026-10-08)** - Data science interop:
 `ExZarr.Nx.stream_chunk_tensors/2`, DataLoader batch recipes, livebook MVP
 (metadata, Nx conversion, minibatches, a small Axon train).

docs/ROADMAP.md

@@ -35,6 +35,12 @@ Released 2026-10-08.
 - [x] Livebook MVP: metadata, Zarr↔Nx, minibatches, Axon toy train
 - [ ] ~~Explorer direct streaming~~ Dropped from 1.3: columnar data and Explorer belong in [ex_arrow](https://hex.pm/packages/ex_arrow), and Binsparse in [ex_graphblas](https://hex.pm/packages/ex_graphblas)
 
+### v1.3.1
+
+Released 2026-10-09. Patch release: faster edge-chunk crops and shuffled
+batching, shuffling that leaves the caller's `:rand` state alone, runnable
+livebooks checked in CI, and measured performance figures in the Nx docs.
+
 ---
 
 ## v1.4.0 (Planned) - Performance & Packaging

docs/guides/installation.md

@@ -181,7 +181,7 @@ If tests pass, your installation is complete and working correctly.
 
 ```elixir
 iex> Application.spec(:ex_zarr, :vsn) |> to_string()
-"1.3.0"
+"1.3.1"
 ```
 
 ## Build Troubleshooting

docs/guides/migration_from_python.md

@@ -38,7 +38,7 @@ pip install zarr
 # In mix.exs
 def deps do
   [
-    {:ex_zarr, "~> 1.2"}
+    {:ex_zarr, "~> 1.3"}
   ]
 end
 ```

docs/guides/storage_providers.md

@@ -157,7 +157,7 @@ Add to `mix.exs`:
 ```elixir
 def deps do
   [
-    {:ex_zarr, "~> 1.2"},
+    {:ex_zarr, "~> 1.3"},
     {:ex_aws, "~> 2.5"},
     {:ex_aws_s3, "~> 2.5"},
     {:sweet_xml, "~> 0.7"}  # For XML response parsing
@@ -353,7 +353,7 @@ Add to `mix.exs`:
 ```elixir
 def deps do
   [
-    {:ex_zarr, "~> 1.2"},
+    {:ex_zarr, "~> 1.3"},
     {:goth, "~> 1.4"},      # Authentication
     {:req, "~> 0.6.1"}      # HTTP client
   ]
@@ -490,7 +490,7 @@ Add to `mix.exs`:
 ```elixir
 def deps do
   [
-    {:ex_zarr, "~> 1.2"},
+    {:ex_zarr, "~> 1.3"},
     {:azure_sdk, "~> 0.4.1"}
   ]
 end
@@ -641,7 +641,7 @@ Stores large chunks in MongoDB using GridFS.
 ```elixir
 def deps do
   [
-    {:ex_zarr, "~> 1.2"},
+    {:ex_zarr, "~> 1.3"},
     {:mongodb_driver, "~> 1.4"}
   ]
 end

docs/guides/troubleshooting.md

@@ -1244,7 +1244,7 @@ GitHub Issues: [https://github.com/AnimaLogica/ExZarr/issues](https://github.com
 
 ```markdown
 ## Environment
-- ExZarr version: 1.3.0
+- ExZarr version: 1.3.1
 - Elixir version: 1.19.5
 - Erlang/OTP version: 28.1
 - OS: macOS 15.2 (arm64)

docs/livebooks/06_cookbook/06_05_geospatial.livemd

@@ -2,7 +2,7 @@
 
 ```elixir
 Mix.install([
-  {:ex_zarr, "~> 1.2"}
+  {:ex_zarr, "~> 1.3"}
   # {:ex_zarr, path: Path.join(__DIR__, "../../..")},
 ])
 ```

docs/livebooks/PLAN.md

@@ -1,6 +1,6 @@
-## Status (v1.3.0)
+## Status (v1.3.1)
 
-Shipped for 1.3.0:
+Shipped in 1.3.0; in 1.3.1 every notebook below runs in CI against the current code:
 
 - `01_core_zarr/01_01` through `01_04`
 - `03_nx_ml/03_01_zarr_to_nx.livemd`
@@ -13,7 +13,7 @@ Shipped for 1.3.0:
 
 Deferred past 1.3.0: `02_concurrency`, `04_02`–`04_15`, `05_02`–`05_12`, `06_crypto` through `09_systems`, and the rest of the table below. Arrow and Explorer livebooks belong with ex_arrow. Binsparse livebooks belong with ex_graphblas.
 
-The livebooks directry should be a curated collection of **Elixir Livebooks** demonstrating how to use
+The livebooks directory should be a curated collection of **Elixir Livebooks** demonstrating how to use
 **ExZarr** — a Zarr v3–compatible array storage library — to build scalable data systems
 for **AI / GenAI, finance, crypto, and scientific workloads**.
 

docs/livebooks/scripts/00_01_welcome.exs

@@ -3,7 +3,7 @@
 # Title: Welcome to ExZarr
 
 # Mix.install([
-#   # {:ex_zarr, "~> 1.2"},
+#   # {:ex_zarr, "~> 1.3"},
 #   {:ex_zarr, path: "/Users/thanos/work/ExZarr"},
 #   {:nx, "~> 0.7"},
 #   {:kino, "~> 0.13"},

docs/livebooks/scripts/01_01_first_zarr_array.exs

@@ -3,7 +3,7 @@
 # Title: Your First Zarr Array
 
 Mix.install([
-  {:ex_zarr, "~> 1.2"},
+  {:ex_zarr, "~> 1.3"},
   {:kino, "~> 0.13"}
 ])
 

docs/livebooks/scripts/01_02_metadata_and_chunks.exs

@@ -3,7 +3,7 @@
 # Title: Metadata and Chunks: Inside a Zarr Array
 
 Mix.install([
-  {:ex_zarr, "~> 1.2"},
+  {:ex_zarr, "~> 1.3"},
   {:kino, "~> 0.13"},
   {:jason, "~> 1.4"}
 ])

docs/notebooks/earthmover_datacube.livemd

@@ -2,7 +2,7 @@
 
 ```elixir
 Mix.install([
-  {:ex_zarr, "~> 1.2"},
+  {:ex_zarr, "~> 1.3"},
   {:nx, "~> 0.7"},
   {:kino, "~> 0.13"},
   {:kino_vega_lite, "~> 0.1"}

docs/notebooks/xarray_zarr_intro.livemd

@@ -2,7 +2,7 @@
 
 ```elixir
 Mix.install([
-  {:ex_zarr, "~> 1.2"},
+  {:ex_zarr, "~> 1.3"},
   {:nx, "~> 0.7"},
   {:kino, "~> 0.13"}
 ])

docs/notebooks/zarr_fundamentals.livemd

@@ -2,7 +2,7 @@
 
 ```elixir
 Mix.install([
-  {:ex_zarr, "~> 1.2"},
+  {:ex_zarr, "~> 1.3"},
   {:nx, "~> 0.7"},
   {:kino, "~> 0.13"},
   {:kino_vega_lite, "~> 0.1"}

docs/release_notes_v1_3_1.md

@@ -0,0 +1,48 @@
+# v1.3.1 Release Notes
+
+ExZarr v1.3.1 is a patch release. It fixes performance and correctness issues
+found reviewing v1.3.0, and makes every shipped livebook run. Upgrading from
+1.3.0 needs no code changes.
+
+```elixir
+{:ex_zarr, "~> 1.3"}
+```
+
+## Nx
+
+- `ExZarr.Nx.stream_chunk_tensors/2` crops padded edge chunks one contiguous
+  row at a time. A 999x1000 float32 edge chunk took about 300 ms in 1.3.0 and
+  now takes under 1 ms.
+- An array whose dtype has no Nx type yields a single `{:error, reason}` from
+  `stream_chunk_tensors/2` instead of one error per chunk.
+- `ExZarr.Nx.DataLoader.shuffled_batch_stream/3` and
+  `paired_shuffled_batch_stream/4` group the shuffled indices in one pass. In
+  1.3.0 the index slicing alone grew with the square of the sample count.
+- Shuffling no longer changes the calling process's `:rand` state. The same
+  `:seed` still gives the same order as in 1.3.0.
+- `to_tensor_chunked/3` applies `:names`, as `to_tensor/2` does.
+
+## Livebooks
+
+- `01_04_codecs_and_pipelines` ran into `:gzip` with a Zarr v2 array and
+  `compressor: nil`; it now uses `:zlib` and `:none`. `:gzip` is a Zarr v3
+  codec.
+- `03_03_training_from_zarr` trains on an independent second feature from
+  zero-initialized weights with Adam, so it reliably reaches the line
+  (`weights` about `[2.0, 0.0]`, `bias` about `1.0`) and prints the same numbers
+  on every run. It uses Axon 0.8's `Axon.ModelState`.
+- `mix livebook.test` runs cells one at a time, as Livebook does, and
+  `--local` tests notebooks against the checkout. CI now runs every shipped
+  livebook.
+
+## Documentation
+
+- The guides no longer say `:gzip` always works; it applies to Zarr v3 arrays.
+- The Nx guide's speed figures are measured: for an 8 MB float64 array in
+  memory storage on an Apple M1 Max, `to_tensor/2` takes about 75 ms
+  uncompressed and 117 ms with the default zlib.
+- The v1.3.0 notes and roadmap record that Explorer streaming, planned for
+  1.3, was dropped. Columnar data and Explorer belong in
+  [ex_arrow](https://hex.pm/packages/ex_arrow).
+
+Full list: [CHANGELOG](https://github.com/AnimaLogica/ExZarr/blob/main/CHANGELOG.md).

mix.exs

@@ -1,7 +1,7 @@
 defmodule ExZarr.MixProject do
   use Mix.Project
 
-  @version "1.3.0"
+  @version "1.3.1"
   @source_url "https://github.com/AnimaLogica/ExZarr"
 
   def project do
@@ -200,6 +200,7 @@ defmodule ExZarr.MixProject do
         "docs/release_notes_v1_1_0.md",
         "docs/release_notes_v1_2_0.md",
         "docs/release_notes_v1_3_0.md",
+        "docs/release_notes_v1_3_1.md",
         "docs/ROADMAP.md",
         "docs/ZARR_V3_STATUS.md",
         "docs/INTEROPERABILITY.md",
@@ -290,6 +291,7 @@ defmodule ExZarr.MixProject do
           "docs/release_notes_v1_1_0.md",
           "docs/release_notes_v1_2_0.md",
           "docs/release_notes_v1_3_0.md",
+          "docs/release_notes_v1_3_1.md",
           "docs/migration_guide_v1_1_0.md"
         ],
         Reference: [