From 4ad1a8d5994d9e84834d38efed5d02715591184e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:11:03 +0000 Subject: [PATCH 1/4] Update cython from 0.29.23 to 3.2.3 --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index 6380aca..668610a 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,4 +1,4 @@ -Cython==0.29.23 +Cython==3.2.3 numpy==1.21.0 pysam==0.16.0.1 nose==1.3.7 From fb1a23ebae3c547760d46f73af926cffe1eb9be7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:11:04 +0000 Subject: [PATCH 2/4] Update numpy from 1.21.0 to 2.4.0 --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index 668610a..b8cbdf6 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,5 +1,5 @@ Cython==3.2.3 -numpy==1.21.0 +numpy==2.4.0 pysam==0.16.0.1 nose==1.3.7 tables==3.6.1 From a0e7a419eee633877bca63dced9cb96324c7eb77 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:11:04 +0000 Subject: [PATCH 3/4] Update pysam from 0.16.0.1 to 0.23.3 --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index b8cbdf6..dc0b3e7 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,5 +1,5 @@ Cython==3.2.3 numpy==2.4.0 -pysam==0.16.0.1 +pysam==0.23.3 nose==1.3.7 tables==3.6.1 From ee087f27d76773695073c44e22c7bfcf5572b6cf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:11:05 +0000 Subject: [PATCH 4/4] Update tables from 3.6.1 to 3.10.2 --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index dc0b3e7..01c5306 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -2,4 +2,4 @@ Cython==3.2.3 numpy==2.4.0 pysam==0.23.3 nose==1.3.7 -tables==3.6.1 +tables==3.10.2