From d478db8cfa15da028b283dfffeeed222795fe918 Mon Sep 17 00:00:00 2001
From: nick-youngblut <nyoungb2@gmail.com>
Date: Wed, 23 Sep 2026 21:31:53 -0700
Subject: [PATCH] chore: bump workspace version to 0.20.0
MIME-Version: 1.0
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All 16 versioned workspace members, `pyscx/pyproject.toml` and
`rscx/DESCRIPTION`; `tests/scx-integration-tests` stays at `0.0.0`. README's
`scx-cli` download snippet follows. (ROADMAP.md no longer exists, so there is
no date stamp to move.)

0.20.0 collects the merged PRs since 0.19.0 (#544-#561):

- CSC sidecar series: one-pass bucketed CSC builder (#555); `build-csc` as an
  in-place, rollback-able append (#556); same-pass CSC build on ingest and
  carry-through on rewrite ops (#557); parallel CSC build and `csc="auto"` as
  the ingest default (#558); CSC dispatch for row-indexed transforms and
  row-filtered / gene-subset handles (#553, #554); CSC route coverage and the
  exact-nnz Wilcoxon kernel as the 1-vs-rest CSC default (#559)
- Correctness: Leiden parallel local moving keeps decliners eligible (#544);
  five CPU-accelerator parity / convergence fixes (#548); GPU cuVS stream sync,
  reduction determinism, decoder bounds and VRAM accounting (#549); CLI
  destination-overwrite safety and MTX multimodal / streaming / integer
  integrity (#550); unscoped whole-matrix reads of a multimodal file refused
  (#551); dictionary (categorical) output from append / merge / merge
  --sort-by (#546) and `scx sort`'s obs spill path (#547)
- Benchmarks and docs: four community analytical benchmarks (#552), laptop-test
  recapture (#560), README refresh (#545), docs split into per-topic
  directories (#561)

Behaviour changes worth calling out in the release notes:

- **`csc="auto"` is the ingest default** on every entry point and preset
  (`from_mudata` keeps `off`): files with `n_obs >= 50000` and
  `n_vars >= 5000` now get a CSC sidecar, costing ingest wall time and
  +42-71 % on disk. `--csc off` / `csc="off"` opts out (#558).
- **Rewrite ops carry the CSC sidecar by default** (`compact`, `merge`,
  `optimize`, `sort`, `subset`), rebuilt from the output's own shards;
  `--csc carry|always|off`. `--rebuild-csc` / `rebuild_csc=True` are
  deprecated aliases for `always` (#557).
- **`scx build-csc` appends in place** rather than rewriting the file, and
  `scx rollback` removes the sidecar (#556).
- **Ten CLI subcommands no longer silently overwrite an existing destination**;
  `--force` is required (convert, merge, subset, query --output, upgrade,
  cloud-optimize, explode, pack, pull; compact / optimize / sort migrated onto
  the same guard) and is refused where nothing is written (#550).
- **MTX**: a declared-`integer` MTX with a value past 2^24, a non-integral
  value or `nan`/`inf` is refused on ingest (`--allow-lossy` restores the old
  behaviour); multimodal MTX export requires a modality (`pyscx.to_mtx` gains
  `modality=`); export streams one shard at a time (#550).
- **An unscoped whole-matrix read of a multimodal file raises**
  `MultimodalRequiresModality` instead of folding every modality into one
  `n_obs x n_modalities`-row answer — `to_anndata()`, `to_memory()`,
  `read_all_csr_shards*`, `scx pull --filter` (#551).
- **Numerical changes**: UMAP init scale and `random_init` now match
  umap-learn, the kNN sigma search, and NB-GLM dispersion shrinkage (the
  `above_min_disp` residual filter always runs; new `disp_outlier_sd=2.0`
  carve-out, `None` disables only the carve-out) (#548); parallel Leiden
  labels change (#544).
- **Wilcoxon on the CPU CSC route** defaults to the exact-nnz kernel (route id
  `cpu_csc_nnz`); `SCX_ACCEL_WILCOXON_NNZ=0` restores densify (`cpu_csc`), and
  `reference=` / `rankby_abs=True` still use densify (#559).
- **Categorical obs columns** keep their declared categories, unused levels and
  `ordered` bit through append / merge / sort (#546, #547).

No benchmark recapture for this release.

Pre-release gate on this tree: `cargo fmt --check`; `cargo clippy --workspace
--exclude rscx --all-targets -D warnings`; `cargo test --workspace --exclude
rscx` (4,220 passed, 0 failed); `cargo test -p scx-convert --features hdf5`
(474 passed); `cargo test -p scx-cli --features hdf5 -- --test-threads=1` (253
passed); `maturin develop --release` + `pytest tests/` (3,247 passed, 140
skipped, 2 xfailed; `pyscx.__version__ == "0.20.0"`). Not run: rscx tests,
`--features cloud`, GPU pytest, fuzzing, benchmarks.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01RwRKstgr4TNkXhLhkQwmjA
---
 Cargo.lock               | 32 ++++++++++++++++----------------
 README.md                |  2 +-
 pyscx/Cargo.toml         |  2 +-
 pyscx/pyproject.toml     |  2 +-
 rscx/Cargo.toml          |  2 +-
 rscx/DESCRIPTION         |  2 +-
 scx-accel/Cargo.toml     |  2 +-
 scx-cli/Cargo.toml       |  2 +-
 scx-cloud/Cargo.toml     |  2 +-
 scx-codec/Cargo.toml     |  2 +-
 scx-convert/Cargo.toml   |  2 +-
 scx-engine/Cargo.toml    |  2 +-
 scx-format-io/Cargo.toml |  2 +-
 scx-format/Cargo.toml    |  2 +-
 scx-gpu/Cargo.toml       |  2 +-
 scx-loader/Cargo.toml    |  2 +-
 scx-mtx/Cargo.toml       |  2 +-
 scx-ops/Cargo.toml       |  2 +-
 scx-sparse/Cargo.toml    |  2 +-
 scx-testkit/Cargo.toml   |  2 +-
 20 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 9a56ac2a..d86a2736 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2902,7 +2902,7 @@ dependencies = [
 
 [[package]]
 name = "pyscx"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "base64",
@@ -3273,7 +3273,7 @@ dependencies = [
 
 [[package]]
 name = "rscx"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "extendr-api",
@@ -3441,7 +3441,7 @@ checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
 
 [[package]]
 name = "scx-accel"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "criterion",
@@ -3468,7 +3468,7 @@ dependencies = [
 
 [[package]]
 name = "scx-cli"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "byteorder",
@@ -3500,7 +3500,7 @@ dependencies = [
 
 [[package]]
 name = "scx-cloud"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "async-trait",
@@ -3523,7 +3523,7 @@ dependencies = [
 
 [[package]]
 name = "scx-codec"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "bitpacking",
  "bytemuck",
@@ -3540,7 +3540,7 @@ dependencies = [
 
 [[package]]
 name = "scx-convert"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "base64",
@@ -3571,7 +3571,7 @@ dependencies = [
 
 [[package]]
 name = "scx-engine"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "blake3",
@@ -3591,7 +3591,7 @@ dependencies = [
 
 [[package]]
 name = "scx-format"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "blake3",
@@ -3609,7 +3609,7 @@ dependencies = [
 
 [[package]]
 name = "scx-format-io"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "blake3",
@@ -3635,7 +3635,7 @@ dependencies = [
 
 [[package]]
 name = "scx-gpu"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "byteorder",
  "crossbeam-channel",
@@ -3679,7 +3679,7 @@ dependencies = [
 
 [[package]]
 name = "scx-loader"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "blake3",
@@ -3709,7 +3709,7 @@ dependencies = [
 
 [[package]]
 name = "scx-mtx"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "flate2",
@@ -3723,7 +3723,7 @@ dependencies = [
 
 [[package]]
 name = "scx-ops"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "blake3",
@@ -3750,7 +3750,7 @@ dependencies = [
 
 [[package]]
 name = "scx-sparse"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "criterion",
  "half",
@@ -3765,7 +3765,7 @@ dependencies = [
 
 [[package]]
 name = "scx-testkit"
-version = "0.19.0"
+version = "0.20.0"
 dependencies = [
  "arrow",
  "blake3",
diff --git a/README.md b/README.md
index 5bef4363..62a1dfc9 100644
--- a/README.md
+++ b/README.md
@@ -667,7 +667,7 @@ GitHub-Release-wheel-vs-source guidance aimed at agents, see
 ```bash
 # Last published release — see https://github.com/ArcInstitute/scx/releases
 # for whether a newer one ever shipped
-VERSION=0.19.0
+VERSION=0.20.0
 # Pick the matching target for your platform:
 #   linux x86_64 → x86_64-unknown-linux-gnu
 #   linux arm64  → aarch64-unknown-linux-gnu
diff --git a/pyscx/Cargo.toml b/pyscx/Cargo.toml
index 2e475528..84278b5a 100644
--- a/pyscx/Cargo.toml
+++ b/pyscx/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "pyscx"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Python bindings for SCX via PyO3"
 license.workspace = true
diff --git a/pyscx/pyproject.toml b/pyscx/pyproject.toml
index c04d3e3a..be32939d 100644
--- a/pyscx/pyproject.toml
+++ b/pyscx/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "pyscx"
-version = "0.19.0"
+version = "0.20.0"
 description = "Python bindings for SCX (Sparse Cell eXpression System)"
 license = {text = "MIT"}
 authors = [
diff --git a/rscx/Cargo.toml b/rscx/Cargo.toml
index f188a361..b2c1e2ac 100644
--- a/rscx/Cargo.toml
+++ b/rscx/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "rscx"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "R bindings for SCX via extendr"
 license.workspace = true
diff --git a/rscx/DESCRIPTION b/rscx/DESCRIPTION
index 0a80f84e..6399c31d 100644
--- a/rscx/DESCRIPTION
+++ b/rscx/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rscx
 Title: SCX File Format for Single-Cell RNA-seq
-Version: 0.19.0
+Version: 0.20.0
 Authors@R:
     person("Arc Institute", role = c("aut", "cre"),
            email = "scx@arcinstitute.org")
diff --git a/scx-accel/Cargo.toml b/scx-accel/Cargo.toml
index 237aeda7..4a37cb6c 100644
--- a/scx-accel/Cargo.toml
+++ b/scx-accel/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-accel"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Rust-native analysis accelerators for SCX (PCA, kNN, etc.)"
 license.workspace = true
diff --git a/scx-cli/Cargo.toml b/scx-cli/Cargo.toml
index d1df572c..712a0380 100644
--- a/scx-cli/Cargo.toml
+++ b/scx-cli/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-cli"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "CLI tool for SCX: convert, info, validate"
 license.workspace = true
diff --git a/scx-cloud/Cargo.toml b/scx-cloud/Cargo.toml
index 70ddf233..43f54bcd 100644
--- a/scx-cloud/Cargo.toml
+++ b/scx-cloud/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-cloud"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Cloud operations for SCX: pull, push, explode, pack, cloud-optimize"
 license.workspace = true
diff --git a/scx-codec/Cargo.toml b/scx-codec/Cargo.toml
index dfe6bb90..1179a7f6 100644
--- a/scx-codec/Cargo.toml
+++ b/scx-codec/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-codec"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Compression codecs for SCX (Rice, FOR-BP, Delta-Golomb)"
 license.workspace = true
diff --git a/scx-convert/Cargo.toml b/scx-convert/Cargo.toml
index 309e83ea..d326c708 100644
--- a/scx-convert/Cargo.toml
+++ b/scx-convert/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-convert"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "External format <-> SCX conversion (h5ad, h5mu, MTX, 10x)"
 license.workspace = true
diff --git a/scx-engine/Cargo.toml b/scx-engine/Cargo.toml
index 31c9eb1c..a7deb42f 100644
--- a/scx-engine/Cargo.toml
+++ b/scx-engine/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-engine"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Lazy query engine for SCX files"
 license.workspace = true
diff --git a/scx-format-io/Cargo.toml b/scx-format-io/Cargo.toml
index 8d862e6b..95cdc311 100644
--- a/scx-format-io/Cargo.toml
+++ b/scx-format-io/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-format-io"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Runtime reader/writer, backed/streaming access, and shard codec dispatch for the SCX format"
 license.workspace = true
diff --git a/scx-format/Cargo.toml b/scx-format/Cargo.toml
index 52ac7a76..1f62bcac 100644
--- a/scx-format/Cargo.toml
+++ b/scx-format/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-format"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "On-disk layout/spec for the SCX format: header, catalog, shard structs, modality, codec selection (pure, no I/O)"
 license.workspace = true
diff --git a/scx-gpu/Cargo.toml b/scx-gpu/Cargo.toml
index ad64f3e2..13328348 100644
--- a/scx-gpu/Cargo.toml
+++ b/scx-gpu/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-gpu"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "GPU-accelerated codec decoding, cuSPARSE interop, and GPUDirect Storage for SCX"
 license.workspace = true
diff --git a/scx-loader/Cargo.toml b/scx-loader/Cargo.toml
index 85b89969..da4cb032 100644
--- a/scx-loader/Cargo.toml
+++ b/scx-loader/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-loader"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "ML training data loader for SCX files"
 license.workspace = true
diff --git a/scx-mtx/Cargo.toml b/scx-mtx/Cargo.toml
index 60d9eb00..e5856e8b 100644
--- a/scx-mtx/Cargo.toml
+++ b/scx-mtx/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-mtx"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Matrix Market (MTX) I/O for SCX: read/write Cell Ranger MTX directories"
 license.workspace = true
diff --git a/scx-ops/Cargo.toml b/scx-ops/Cargo.toml
index c92e314c..62da341b 100644
--- a/scx-ops/Cargo.toml
+++ b/scx-ops/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-ops"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "File lifecycle operations (append, delete, compact, rollback, merge) for SCX files"
 license.workspace = true
diff --git a/scx-sparse/Cargo.toml b/scx-sparse/Cargo.toml
index 2838fa96..070e7fa8 100644
--- a/scx-sparse/Cargo.toml
+++ b/scx-sparse/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-sparse"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "CSR sparse matrix operations for SCX"
 license.workspace = true
diff --git a/scx-testkit/Cargo.toml b/scx-testkit/Cargo.toml
index 3a3e2b36..fb16e900 100644
--- a/scx-testkit/Cargo.toml
+++ b/scx-testkit/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "scx-testkit"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 description = "Test-only harness for asserting SCX output identity across refactors"
 license.workspace = true