From 66d3903e156b248c28213a7102c65c5bcd1adc23 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 2026 15:30:04 +0000 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 eaa2dba183c07ecc04ee43f2f38c4129dc0e2577 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 2026 15:30:04 +0000 Subject: [PATCH 02/15] Pin numpy to latest version 2.4.2 --- 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..58e87bd6 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.4 -numpy +numpy==2.4.2 dask[array] From d9ad4b4a05c9bb06418d2202b0bd5c913b3fa7a4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 2026 15:30:05 +0000 Subject: [PATCH 03/15] Pin dask to latest version 2026.1.2 --- 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 58e87bd6..557c6131 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.4 numpy==2.4.2 -dask[array] +dask[array]==2026.1.2 From 25a425a60672391362ce22bd2ee25b474ef6c9c7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 2026 15:30:05 +0000 Subject: [PATCH 04/15] Pin scipy to latest version 1.17.0 --- 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 f72a5967..8da4b94a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.17.0 matplotlib seaborn pandas From 63dbb3abb80bb665ffaff701dfa6d84271324845 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 8da4b94a..7d02b2a4 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.17.0 -matplotlib +matplotlib==3.10.8 seaborn pandas scikit-learn From 09a6d21d98e5e1e3bdbdd72720d0cd57b8cf64f9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 7d02b2a4..5d25266a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.17.0 matplotlib==3.10.8 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 98da8205a1df3d9ae9320ed62d1325aa8900a8d9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 2026 15:30:07 +0000 Subject: [PATCH 07/15] Pin pandas to latest version 3.0.0 --- 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 5d25266a..fa98e3cd 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.17.0 matplotlib==3.10.8 seaborn==0.13.2 -pandas +pandas==3.0.0 scikit-learn h5py numexpr From 7835dbbc099c1b7764dbfc1dd386280e76e04fc6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 fa98e3cd..c63e7fda 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 cbd5ff35e83b574addaecd9973234793bfce3dba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 c63e7fda..a0d74556 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.17.0 matplotlib==3.10.8 seaborn==0.13.2 pandas==3.0.0 -scikit-learn +scikit-learn==1.8.0 h5py numexpr zarr From dfc222020a7a4fb6bfbff7c5096d19a44b8ea5e2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 a0d74556..ca6461f6 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.8 seaborn==0.13.2 pandas==3.0.0 scikit-learn==1.8.0 -h5py +h5py==3.15.1 numexpr zarr hmmlearn From 0dfc6948bfaaa7fec26373bcb6697e29a68aaa51 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 ca6461f6..c742a035 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==3.0.0 scikit-learn==1.8.0 h5py==3.15.1 -numexpr +numexpr==2.14.1 zarr hmmlearn protopunica==0.14.8.post2 From 28a91538513b027656036287a542217f52aa71a5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 c742a035..acb36931 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==3.0.0 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 881e6c2e4c838cf0c7af6df0665734f4c4306414 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 acb36931..da945289 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 85ae8557eb2d097c80ae468720dacc5f1609060e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 2026 15:30:11 +0000 Subject: [PATCH 14/15] Pin ipython to latest version 9.9.0 --- 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 da945289..08dec509 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==9.9.0 From 156c5b65adba242fcf723130312640e433f82c46 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Feb 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 08dec509..235203eb 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==9.9.0