From c574a49c4ecd119d9d4e866cfae319507ee4e68e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:04 +0000 Subject: [PATCH 01/15] Pin cython to latest version 3.2.3 --- 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..c902809f 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.2.3 numpy dask[array] From 7f93ad969af7027cc29ff5c429e1516faf693428 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:04 +0000 Subject: [PATCH 02/15] Pin numpy to latest version 2.4.0 --- 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 c902809f..5baf0abc 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.3 -numpy +numpy==2.4.0 dask[array] From 28e32a2e8041bc441d6c215eca903a3aad19461c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:05 +0000 Subject: [PATCH 03/15] Pin dask to latest version 2025.12.0 --- 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 5baf0abc..d5863235 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.3 numpy==2.4.0 -dask[array] +dask[array]==2025.12.0 From 18a02f6da81b6996461b1638e6732824b32c4320 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:05 +0000 Subject: [PATCH 04/15] Pin scipy to latest version 1.16.3 --- 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 f72a5967..e69dd3db 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.16.3 matplotlib seaborn pandas From 01bc203dbcb87f50ec0fa377d1edd4510e20730f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:06 +0000 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.8 --- 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 e69dd3db..c0d2e954 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.16.3 -matplotlib +matplotlib==3.10.8 seaborn pandas scikit-learn From 842ac0683ffa15edd3b29b313677537b314a8fea Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:06 +0000 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 c0d2e954..fcea1fee 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.16.3 matplotlib==3.10.8 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 3063d900eaba7b007328218835e558e9607e9771 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:07 +0000 Subject: [PATCH 07/15] Pin pandas to latest version 2.3.3 --- 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 fcea1fee..ddfcb818 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.16.3 matplotlib==3.10.8 seaborn==0.13.2 -pandas +pandas==2.3.3 scikit-learn h5py numexpr From 452f08c8e6153b66ec5a2a533be1f1b15c0abf78 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:07 +0000 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 ddfcb818..2ef0f206 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 a53794d8f7402d4384dc7f121bab960ded359596 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:08 +0000 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 2ef0f206..c785dfd3 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.16.3 matplotlib==3.10.8 seaborn==0.13.2 pandas==2.3.3 -scikit-learn +scikit-learn==1.8.0 h5py numexpr zarr From 72f4d764fe5aae9c3e98a2db13c64dd0396b3458 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:09 +0000 Subject: [PATCH 10/15] Pin h5py to latest version 3.15.1 --- 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 c785dfd3..b62002f3 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.8 seaborn==0.13.2 pandas==2.3.3 scikit-learn==1.8.0 -h5py +h5py==3.15.1 numexpr zarr hmmlearn From f277963474116c02ab5b27bb37fd9918dde699ee Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:09 +0000 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 b62002f3..414f8528 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.3.3 scikit-learn==1.8.0 h5py==3.15.1 -numexpr +numexpr==2.14.1 zarr hmmlearn protopunica==0.14.8.post2 From b09c4fd4c121575500f20cc8d08474052a25d8ad Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:10 +0000 Subject: [PATCH 12/15] Pin zarr to latest version 3.1.5 --- 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 414f8528..b6997462 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.3.3 scikit-learn==1.8.0 h5py==3.15.1 numexpr==2.14.1 -zarr +zarr==3.1.5 hmmlearn protopunica==0.14.8.post2 pyfasta From 34fa07c18ecb41e3fe269ee00166c9346211a679 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:10 +0000 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 b6997462..0b448c7e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.8.0 h5py==3.15.1 numexpr==2.14.1 zarr==3.1.5 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From ebf865186100ff77492bc5df0a9e967cd3705aae Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:11 +0000 Subject: [PATCH 14/15] Pin ipython to latest version 9.8.0 --- 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 0b448c7e..e283ae0a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.1.5 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.8.0 From 9910d8d195ce4780a5e5c2e9f1f3d3aa14912b8b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Jan 2026 15:30:11 +0000 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 e283ae0a..f0779b45 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.14.1 zarr==3.1.5 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.8.0