From d27c4e805f2a4778944ad4ebe72205857e07911b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:49 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.3.0 --- 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 c955fe5d..86b912d9 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.3.0 numpy dask[array] From cf3fd96e355b1957e0e4ade1ce296cd4da046bac Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:50 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.5.3 --- 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 86b912d9..70a5093d 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.3.0 -numpy +numpy==2.5.3 dask[array] From bbd03afb0bf1e0c1b5ca642b30b7df0077314cbb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:52 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2026.8.0 --- 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 70a5093d..a09d5247 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.3.0 numpy==2.5.3 -dask[array] +dask[array]==2026.8.0 From 9647ea967029650f2d5da5874037d554b03c9b4e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:53 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.18.1 --- 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..4cff7209 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.18.1 matplotlib seaborn pandas From 732bfeb3207bd4773a600480260fd6f9dce10381 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:54 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.11.2 --- 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 4cff7209..033d9663 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.18.1 -matplotlib +matplotlib==3.11.2 seaborn pandas scikit-learn From 85c089063c052681ee21885776f849ad96bd041e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:56 +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 033d9663..b16bfaaa 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.18.1 matplotlib==3.11.2 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 5e467f3c67ea86a93eb2c13905b2145af0eb2f87 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:57 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 3.0.6 --- 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 b16bfaaa..36d7aed5 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.18.1 matplotlib==3.11.2 seaborn==0.13.2 -pandas +pandas==3.0.6 scikit-learn h5py numexpr From 2ef7808f3b5bf9edec84af37a56d23353c620594 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:00:58 +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 36d7aed5..29c7e8fa 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 ae044c6f924e22c30b700b930a77d2f1109632b7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:01:00 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.9.1 --- 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 29c7e8fa..eeaa412a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.18.1 matplotlib==3.11.2 seaborn==0.13.2 pandas==3.0.6 -scikit-learn +scikit-learn==1.9.1 h5py numexpr zarr From 4128b02797e27bec99870ea829a414b334238fd9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:01:01 +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 eeaa412a..e7808de2 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.11.2 seaborn==0.13.2 pandas==3.0.6 scikit-learn==1.9.1 -h5py +h5py==3.16.0 numexpr zarr hmmlearn From 296999534766092f20c598733395211d3a68d4a6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:01:02 +0100 Subject: [PATCH 11/15] Pin numexpr to latest version 2.14.2 --- 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 e7808de2..96855cf7 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==3.0.6 scikit-learn==1.9.1 h5py==3.16.0 -numexpr +numexpr==2.14.2 zarr hmmlearn protopunica==0.14.8.post2 From 0185ea6ca542428bd8b602fd8308209da81f926d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:01:04 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.4.0 --- 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 96855cf7..081b8b81 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==3.0.6 scikit-learn==1.9.1 h5py==3.16.0 numexpr==2.14.2 -zarr +zarr==3.4.0 hmmlearn protopunica==0.14.8.post2 pyfasta From 56188dcf84acdaaff5983a39f691885fe82d0709 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:01:05 +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 081b8b81..d451a1eb 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.9.1 h5py==3.16.0 numexpr==2.14.2 zarr==3.4.0 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 4ca42b07809f5ed08e47d589735f2c0c9c496c8a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:01:06 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.17.1 --- 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 d451a1eb..b677de91 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.4.0 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.17.1 From d2d808e348648ad96287597d80bda20b22cc34d7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Oct 2026 17:01:07 +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 b677de91..5557dd69 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.14.2 zarr==3.4.0 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.17.1