Unpin numpy and bump ICF metadata version

jeromekelleher · jeromekelleher · commit 0b872afc9242 · 2024-10-23T12:29:30.000+01:00
Closes #258
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,10 @@
+# 0.1.2 2024-XX-XX
+
+Breaking changes
+
+- ICF metadata format version bumped to ensure long-term compatility between numpy 1.26.x
+  and numpy >= 2. Existing ICFs will need to be recreated.
+
 # 0.1.1 2024-06-19
 
 Maintenance release:
diff --git a/bio2zarr/vcf2zarr/icf.py b/bio2zarr/vcf2zarr/icf.py
@@ -110,7 +110,7 @@ class VcfPartition:
     num_records: int = -1
 
 
-ICF_METADATA_FORMAT_VERSION = "0.3"
+ICF_METADATA_FORMAT_VERSION = "0.4"
 ICF_DEFAULT_COMPRESSOR = numcodecs.Blosc(
     cname="zstd", clevel=7, shuffle=numcodecs.Blosc.NOSHUFFLE
 )
diff --git a/pyproject.toml b/pyproject.toml
@@ -11,7 +11,9 @@ authors = [
   {name = "sgkit Developers", email = "project@sgkit.dev"},
 ]
 dependencies = [
-  "numpy < 2",
+  # Pin numpy to >= 1.26 because this enables ICF files to be supported
+  # across numpy 1 and 2 (due to pickle format)
+  "numpy >= 1.26",
   "zarr >= 2.17,< 3",
   "click",
   "tabulate",

Original file line number	Diff line number	Diff line change
`@@ -110,7 +110,7 @@ class VcfPartition:`
`110`	`110`	`num_records: int = -1`
`111`	`111`
`112`	`112`
`113`		`-ICF_METADATA_FORMAT_VERSION = "0.3"`
	`113`	`+ICF_METADATA_FORMAT_VERSION = "0.4"`
`114`	`114`	`ICF_DEFAULT_COMPRESSOR = numcodecs.Blosc(`
`115`	`115`	`cname="zstd", clevel=7, shuffle=numcodecs.Blosc.NOSHUFFLE`
`116`	`116`	`)`