BLD Version 1.6.0

luispedro · luispedro · commit 8a8e5ce8fe8c · 2025-11-24T17:01:34.000+10:00
Big change is switching to ONNX for model storage to avoid depending on very particular versions of scikit-learn - Fix float counts in Paladin mapping (BigDataBiology#74) - Fix some issues in MacOS
diff --git a/ChangeLog b/ChangeLog
@@ -1,5 +1,7 @@
-Unreleased
+Version 1.6.0 2025-11-24
 	* Switch to ONNX for model storage
+	* Fix float counts in Paladin mapping (#74)
+	* Fix some issues in MacOS
 
 Version 1.5.0 2024-09-20
 	* Add support for local searching
diff --git a/docs/whatsnew.md b/docs/whatsnew.md
@@ -1,5 +1,13 @@
 # What's new? (History)
 
+## Version 1.6.0
+
+*Released 24 November 2025*
+
+- Switch to ONNX for model storage. This makes the models more portable between versions
+- Fix float counts in Paladin mapping ([#74](https://github.com/BigDataBiology/macrel/issues/74))
+- Fix some issues in MacOS
+
 ## Version 1.5.0
 
 *Released 20 September 2024*
diff --git a/macrel/macrel_version.py b/macrel/macrel_version.py
@@ -1 +1 @@
-__version__ = '1.6.0.dev0'
+__version__ = '1.6.0'
diff --git a/tests/contigs.cluster/expected.prediction b/tests/contigs.cluster/expected.prediction
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 Access	Sequence	AMP_family	AMP_probability	Hemolytic	Hemolytic_probability
 smORF_0	KVIKKVVAALMVLGALAALTVGVVLKPGRKGDET	CLP	0.554	Hemo	0.772
 smORF_2	RFLIKMVKVNLMNGKLIRKISLM	CLP	0.733	Hemo	0.921
diff --git a/tests/contigs.nosmorfs/expected.percontigs b/tests/contigs.nosmorfs/expected.percontigs
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 # Macrel calculated for the sample a density of 0.000 AMPs / Mbp.
 contig	length	ORFs	smORFs	AMPs
 scaffold2530_2_MH0058	1324	1	0	0
diff --git a/tests/contigs.nosmorfs/expected.prediction b/tests/contigs.nosmorfs/expected.prediction
@@ -1,2 +1,2 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 Access	Sequence	AMP_family	AMP_probability	Hemolytic	Hemolytic_probability
diff --git a/tests/contigs/expected.percontigs b/tests/contigs/expected.percontigs
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 # Macrel calculated for the sample a density of 90.125 AMPs / Mbp.
 contig	length	ORFs	smORFs	AMPs
 C4060843_1_MH0058	518	1	1	0
diff --git a/tests/contigs/expected.prediction b/tests/contigs/expected.prediction
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 Access	Sequence	AMP_family	AMP_probability	Hemolytic	Hemolytic_probability
 scaffold2530_2_MH0058_1	KVIKKVVAALMVLGALAALTVGVVLKPGRKGDET	CLP	0.554	Hemo	0.772
 scaffold75334_1_MH0058_1	RFLIKMVKVNLMNGKLIRKISLM	CLP	0.733	Hemo	0.921
diff --git a/tests/peptides/expected.prediction b/tests/peptides/expected.prediction
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 Access	Sequence	AMP_family	AMP_probability	Hemolytic	Hemolytic_probability
 AP00002|AMP	YVPLPNVPQPGRRPFPTFPGQGPFNPKIKWPQGY	CLP	0.792	Hemo	0.574
 AP00007|AMP	GNNRPVYIPQPRPPHPRL	CLP	0.980	Hemo	0.554
diff --git a/tests/reads.se/expected.percontigs b/tests/reads.se/expected.percontigs
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 # Macrel calculated for the sample a density of 89.614 AMPs / Mbp.
 contig	length	ORFs	smORFs	AMPs
 k47_0	3379	4	2	0
diff --git a/tests/reads.se/expected.prediction b/tests/reads.se/expected.prediction
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 Access	Sequence	AMP_family	AMP_probability	Hemolytic	Hemolytic_probability
 k47_1_3	TIVVKKVPKCLRGIVKLLFGIKEKWYEKRGYSYSLYFLFVYLL	CDP	0.505	Hemo	0.871
 k47_10_1	RFLIKMVKVNLMNGKLIRKISLM	CLP	0.733	Hemo	0.921
diff --git a/tests/reads/expected.percontigs b/tests/reads/expected.percontigs
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 # Macrel calculated for the sample a density of 86.440 AMPs / Mbp.
 contig	length	ORFs	smORFs	AMPs
 k77_11	1303	2	1	0
diff --git a/tests/reads/expected.prediction b/tests/reads/expected.prediction
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.6.0.dev0
+# Prediction from macrel v1.6.0
 Access	Sequence	AMP_family	AMP_probability	Hemolytic	Hemolytic_probability
 k77_7_7	TIVVKKVPKCLRGIVKLLFGIKEKWYEKRGYSYSLYFLFVYLL	CDP	0.505	Hemo	0.871
 k77_12_1	RFLIKMVKVNLMNGKLIRKISLM	CLP	0.733	Hemo	0.921

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__version__ = '1.6.0.dev0'`
	`1`	`+__version__ = '1.6.0'`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# Prediction from macrel v1.6.0.dev0`
	`1`	`+# Prediction from macrel v1.6.0`
`2`	`2`	`Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability`
`3`	`3`	`smORF_0 KVIKKVVAALMVLGALAALTVGVVLKPGRKGDET CLP 0.554 Hemo 0.772`
`4`	`4`	`smORF_2 RFLIKMVKVNLMNGKLIRKISLM CLP 0.733 Hemo 0.921`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`		`-# Prediction from macrel v1.6.0.dev0`
	`1`	`+# Prediction from macrel v1.6.0`
`2`	`2`	`Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability`