From 3e86168d3f78800423f45c8619040188af278c09 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:23 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.2.4 --- requirements_dev_base.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_base.txt b/requirements_dev_base.txt index c955fe5d..f0877abd 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.2.4 numpy dask[array] From 14887f890c62a65253d4dc845b341405401d1e36 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:24 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.4.4 --- requirements_dev_base.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_base.txt b/requirements_dev_base.txt index f0877abd..670a72f8 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.4 -numpy +numpy==2.4.4 dask[array] From 6f2f0c84a8528502617973953b0fb2c2b6d6375a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:25 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2026.3.0 --- requirements_dev_base.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_base.txt b/requirements_dev_base.txt index 670a72f8..ff338e23 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.4 numpy==2.4.4 -dask[array] +dask[array]==2026.3.0 From 174ada2f59a05e82a3b8d3e63f5f5123e31c5bc1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:25 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.17.1 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index f72a5967..4c53c089 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.17.1 matplotlib seaborn pandas From 7b2be7e267e082467cd7668f44f67843453c28d6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:26 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.9 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index 4c53c089..db08b3b7 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.17.1 -matplotlib +matplotlib==3.10.9 seaborn pandas scikit-learn From a5c1ad2288d2870630d2b6bbaa1835df71e4f2ad Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:27 +0100 Subject: [PATCH 06/15] Pin seaborn to latest version 0.13.2 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index db08b3b7..b061b033 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.17.1 matplotlib==3.10.9 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From c8c513dd50ef1289c98777affddc1af1e5559d41 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:28 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 3.0.2 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index b061b033..020f501f 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.17.1 matplotlib==3.10.9 seaborn==0.13.2 -pandas +pandas==3.0.2 scikit-learn h5py numexpr From 5ab454a72dc897c64547700a927ee77b80658072 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:29 +0100 Subject: [PATCH 08/15] Pin protopunica to latest version 0.14.8.post2 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index 020f501f..5a16eb1a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -8,6 +8,6 @@ h5py numexpr zarr hmmlearn -protopunica +protopunica==0.14.8.post2 pyfasta ipython From 65f4706998c40b9769802759c578c79b5059e905 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:29 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.8.0 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index 5a16eb1a..3583bd7e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.17.1 matplotlib==3.10.9 seaborn==0.13.2 pandas==3.0.2 -scikit-learn +scikit-learn==1.8.0 h5py numexpr zarr From c765e1e052dfa3b4ee37e0af74052a3b253c01ad Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:30 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.16.0 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index 3583bd7e..4f9af54b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.9 seaborn==0.13.2 pandas==3.0.2 scikit-learn==1.8.0 -h5py +h5py==3.16.0 numexpr zarr hmmlearn From 02af176f9432e8bfb818bc5de9a90062db3d4047 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:31 +0100 Subject: [PATCH 11/15] Pin numexpr to latest version 2.14.1 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index 4f9af54b..e745248f 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==3.0.2 scikit-learn==1.8.0 h5py==3.16.0 -numexpr +numexpr==2.14.1 zarr hmmlearn protopunica==0.14.8.post2 From 45e4aaa16ebb9bf0b826ab2820d28d9990549b66 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:32 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.2.0 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index e745248f..a9f3dbad 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==3.0.2 scikit-learn==1.8.0 h5py==3.16.0 numexpr==2.14.1 -zarr +zarr==3.2.0 hmmlearn protopunica==0.14.8.post2 pyfasta From e631acd5975d08913f5cc8014a32cc37af5b0312 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:33 +0100 Subject: [PATCH 13/15] Pin hmmlearn to latest version 0.3.3 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index a9f3dbad..74559910 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.8.0 h5py==3.16.0 numexpr==2.14.1 zarr==3.2.0 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 1f748d0379109759eba5e2610940aa9e7f730a39 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:34 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.13.0 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index 74559910..e9ed6693 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.2.0 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.13.0 From 93baf54b33e80a107f90779e4094d31f14f72f95 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 May 2026 16:31:35 +0100 Subject: [PATCH 15/15] Pin pyfasta to latest version 0.5.2 --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index e9ed6693..d6b98bc9 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.14.1 zarr==3.2.0 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.13.0