From f3cd18637d14d0ff23406e0dd8bc9371e0a4b8d4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:26 +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 be40280809fe73e24c186b788a9aa70c92b7ffce Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:26 +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 fdf0e032dcb50cca33ed24d16bf75027c3d8df18 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:27 +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 7471c4567d328cafdbc82f190b9434e1f81553ef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:27 +0000 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 128afd961a972825e891213f620c30691f9f8d35 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:28 +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 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 9dd3aaf777f32e9b196c3894a7f09e39a80bc58f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:28 +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 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 d32652f54119f76fe597426302b4a16d5e66389d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:29 +0000 Subject: [PATCH 07/15] Pin pandas to latest version 3.0.1 --- 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 6730ef12..62e8a64f 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==3.0.1 scikit-learn h5py numexpr From 16702f48725de90df7f07c362fd4eed48274ef2c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:29 +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 62e8a64f..c2593e81 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 edf5213920b931b50fddb65070d90891bf6cb71d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:30 +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 c2593e81..f4480efd 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==3.0.1 -scikit-learn +scikit-learn==1.8.0 h5py numexpr zarr From 4b3ae24e406b2c0604173932b6871d837d763b46 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:30 +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 f4480efd..4bb9c49e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.8 seaborn==0.13.2 pandas==3.0.1 scikit-learn==1.8.0 -h5py +h5py==3.15.1 numexpr zarr hmmlearn From 9e110a8fce388ed09a44bb5eb711024cabbb2653 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:31 +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 4bb9c49e..377ae010 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==3.0.1 scikit-learn==1.8.0 h5py==3.15.1 -numexpr +numexpr==2.14.1 zarr hmmlearn protopunica==0.14.8.post2 From a21c93d97398f9ae2b3e04b7ce65d530852a52df Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:31 +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 377ae010..5233b63f 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==3.0.1 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 51e15cc4734a3daadb42cb80ef3de17daace86d1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:32 +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 5233b63f..ad285b51 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 32b72fa9f05d898db9428c197d4bf7890c1b31fe Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:32 +0000 Subject: [PATCH 14/15] Pin ipython to latest version 9.10.0 --- 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 ad285b51..e26fde5f 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==9.10.0 From 876695203db3642a7bbbaf7c8ac92208406a3db4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Mar 2026 15:30:33 +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 e26fde5f..f4bd1e6d 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==9.10.0