From 0a1cf92efae4291a5d3a0134de7a70c32ec6c4a7 Mon Sep 17 00:00:00 2001
From: Kai Zhang <kai@kzhang.org>
Date: Fri, 27 Oct 2023 22:42:28 -0700
Subject: [PATCH] fix #179: AnnDataSet to AnnData conversion error when `.X` is
 empty.

---
 docs/changelog.md           | 3 ++-
 snapatac2-core/Cargo.toml   | 2 +-
 snapatac2-python/Cargo.lock | 6 +++---
 snapatac2-python/Cargo.toml | 6 +++---
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index bff001250..32c609857 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -11,7 +11,8 @@
 - Fix a bug in `pp.add_tile_matrix` that causes the function to fail when the genome
   contains a large number (>1000) of chromosomes.
 - Fix #177: counter overflow in `pp.make_fragment_file` when duplicate reads are more than 2^16.
-- Fix #178: issue a warning instead of an error when no cells pass the filter in `pp.import_data`
+- Fix #178: issue a warning instead of an error when no cells pass the filter in `pp.import_data`.
+- Fix #179: AnnDataSet to AnnData conversion error when `.X` is empty.
 - Fix #182: compression type detection problem.
 
 ## Release 2.5.1 (released Oct 23, 2023)
diff --git a/snapatac2-core/Cargo.toml b/snapatac2-core/Cargo.toml
index 1d8d80fad..c8039b5a1 100644
--- a/snapatac2-core/Cargo.toml
+++ b/snapatac2-core/Cargo.toml
@@ -11,7 +11,7 @@ homepage = "https://github.com/"
 keywords = ["single-cell", "biology"]
 
 [dependencies]
-anndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c39ee5428dfe0d1c8274a12d56241806feae0516" }
+anndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c90e5fa1cfbc9fec0736eb475ebcc85f77125d44" }
 anyhow = "1.0"
 bigtools = { version = "0.2", features = ["read", "write"] }
 bincode = "1.3"
diff --git a/snapatac2-python/Cargo.lock b/snapatac2-python/Cargo.lock
index 5f70f0a29..4c5a0714f 100644
--- a/snapatac2-python/Cargo.lock
+++ b/snapatac2-python/Cargo.lock
@@ -63,7 +63,7 @@ dependencies = [
 [[package]]
 name = "anndata"
 version = "0.2.1"
-source = "git+https://github.com/kaizhang/anndata-rs.git?rev=c39ee5428dfe0d1c8274a12d56241806feae0516#c39ee5428dfe0d1c8274a12d56241806feae0516"
+source = "git+https://github.com/kaizhang/anndata-rs.git?rev=c90e5fa1cfbc9fec0736eb475ebcc85f77125d44#c90e5fa1cfbc9fec0736eb475ebcc85f77125d44"
 dependencies = [
  "anyhow",
  "flate2",
@@ -84,7 +84,7 @@ dependencies = [
 [[package]]
 name = "anndata-hdf5"
 version = "0.1.0"
-source = "git+https://github.com/kaizhang/anndata-rs.git?rev=c39ee5428dfe0d1c8274a12d56241806feae0516#c39ee5428dfe0d1c8274a12d56241806feae0516"
+source = "git+https://github.com/kaizhang/anndata-rs.git?rev=c90e5fa1cfbc9fec0736eb475ebcc85f77125d44#c90e5fa1cfbc9fec0736eb475ebcc85f77125d44"
 dependencies = [
  "anndata",
  "anyhow",
@@ -2597,7 +2597,7 @@ dependencies = [
 [[package]]
 name = "pyanndata"
 version = "0.2.1"
-source = "git+https://github.com/kaizhang/anndata-rs.git?rev=c39ee5428dfe0d1c8274a12d56241806feae0516#c39ee5428dfe0d1c8274a12d56241806feae0516"
+source = "git+https://github.com/kaizhang/anndata-rs.git?rev=c90e5fa1cfbc9fec0736eb475ebcc85f77125d44#c90e5fa1cfbc9fec0736eb475ebcc85f77125d44"
 dependencies = [
  "anndata",
  "anndata-hdf5",
diff --git a/snapatac2-python/Cargo.toml b/snapatac2-python/Cargo.toml
index 143fc5a14..f23e9373f 100644
--- a/snapatac2-python/Cargo.toml
+++ b/snapatac2-python/Cargo.toml
@@ -13,9 +13,9 @@ keywords = ["single-cell", "biology"]
 [dependencies]
 snapatac2-core = { path = "../snapatac2-core" }
 #snapatac2-core = { git = "https://github.com/kaizhang/SnapATAC2.git", rev = "b526e4907a01c46821716545622394518348a2ac" }
-anndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c39ee5428dfe0d1c8274a12d56241806feae0516" }
-anndata-hdf5 = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c39ee5428dfe0d1c8274a12d56241806feae0516" }
-pyanndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c39ee5428dfe0d1c8274a12d56241806feae0516" }
+anndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c90e5fa1cfbc9fec0736eb475ebcc85f77125d44" }
+anndata-hdf5 = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c90e5fa1cfbc9fec0736eb475ebcc85f77125d44" }
+pyanndata = { git = "https://github.com/kaizhang/anndata-rs.git", rev = "c90e5fa1cfbc9fec0736eb475ebcc85f77125d44" }
 extsort = "0.4"
 anyhow = "1.0"
 bed-utils = { git = "https://github.com/kaizhang/bed-utils.git", rev = "d06f2b4ff189c64bc0d3f7054f4ee8d0797368ca" }