From 1c14ca3b7a161ed38ee0cac4f131e5da8280abb7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:05 +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 3f22d0be636986ebcd431085a1bf64d99a998317 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:06 +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 d35be628c7c8f5a7b782af60f2f0d70a15330296 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:07 +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 0efeacbd15e2f2d7dda8f9cfcf2db726363eebd7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:08 +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 1e85e289e9f3d269c7724372579b5de1d2fe8430 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:09 +0100 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 4c53c089..4a182f11 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.17.1 -matplotlib +matplotlib==3.10.8 seaborn pandas scikit-learn From d12606b3af37eeb1ef17def9960d825ba3c07ada Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:09 +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 4a182f11..6730ef12 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.17.1 matplotlib==3.10.8 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 9c12976cd8afe2d59d3df503eef806d510981e2f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:10 +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 6730ef12..9ea64820 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.17.1 matplotlib==3.10.8 seaborn==0.13.2 -pandas +pandas==3.0.2 scikit-learn h5py numexpr From 608ea390d8576c98b81e1566b9d379c5eadeb424 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:11 +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 9ea64820..b43d3ade 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 86309d7f89245cbf7cedfaab984ee6064e52dde0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:12 +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 b43d3ade..77074bd0 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.17.1 matplotlib==3.10.8 seaborn==0.13.2 pandas==3.0.2 -scikit-learn +scikit-learn==1.8.0 h5py numexpr zarr From 8573a3faf0ad31ab0c92e4c3d7cb94134fdcc7d2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:12 +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 77074bd0..e0539b07 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.8 seaborn==0.13.2 pandas==3.0.2 scikit-learn==1.8.0 -h5py +h5py==3.16.0 numexpr zarr hmmlearn From 1041177d44fa6c23a6a1ce23dd694010c55cc15a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:13 +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 e0539b07..14e360f7 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 a824a54314716a77761e3ece5efd2fed2f43b6fd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:14 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.1.6 --- 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 14e360f7..64438e4f 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==3.1.6 hmmlearn protopunica==0.14.8.post2 pyfasta From 279a0f6d58bf2530858bd753cc52ef91ec5b4e76 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:14 +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 64438e4f..3de26752 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==3.1.6 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 7af2861ceed55ca6af56115250cf8069da0b2d6f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:15 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.12.0 --- 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 3de26752..3f76919c 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.1.6 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.12.0 From 6ccf1e28b8160f8bac0a1efa27d165e72d30345a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Apr 2026 16:31:16 +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 3f76919c..abe14f41 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.14.1 zarr==3.1.6 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.12.0