From a0e19471073469a86e6b064cdf81436de21b8d12 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:05 +0200 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 66da0d707cb7bda482dd2335dfc2eff3c841201a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:07 +0200 Subject: [PATCH 02/15] Pin numpy to latest version 2.5.2 --- 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 86b912d9..8bcb5a47 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.3.0 -numpy +numpy==2.5.2 dask[array] From 48aa630cab842e610af0f7739d69e52ad5929229 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:08 +0200 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 8bcb5a47..bfc4f24a 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.3.0 numpy==2.5.2 -dask[array] +dask[array]==2026.8.0 From 7ac1f70f0d715bfc1cf05e73c4290197fd9119be Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:09 +0200 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 19826feebbb3d4aaf363c175fa7ab2e8d92c568f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:10 +0200 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.11.1 --- 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 4cff7209..c3de13ae 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.18.1 -matplotlib +matplotlib==3.11.1 seaborn pandas scikit-learn From 829bbd53ae0006404106e8482a90638d92c1a979 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:11 +0200 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 c3de13ae..945ef80c 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.18.1 matplotlib==3.11.1 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 65d2de8c3a146d9e1bc5eae1ba6fe032b9e56cdd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:12 +0200 Subject: [PATCH 07/15] Pin pandas to latest version 3.0.5 --- 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 945ef80c..adddb2be 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.18.1 matplotlib==3.11.1 seaborn==0.13.2 -pandas +pandas==3.0.5 scikit-learn h5py numexpr From 3d44b9d4ea00b67df9e73d09690c146525ab3b62 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:13 +0200 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 adddb2be..a7e0d3b6 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 986e11f7fc28255196484e967a3a0dc09b30ad35 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:15 +0200 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.9.0 --- 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 a7e0d3b6..97d5da2e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.18.1 matplotlib==3.11.1 seaborn==0.13.2 pandas==3.0.5 -scikit-learn +scikit-learn==1.9.0 h5py numexpr zarr From 72b0862cef295db326f8a1a1b8a03effead2c399 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:16 +0200 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 97d5da2e..90650e55 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.11.1 seaborn==0.13.2 pandas==3.0.5 scikit-learn==1.9.0 -h5py +h5py==3.16.0 numexpr zarr hmmlearn From 90184909921000e4eebeeb8c50b66d024ce5f594 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:17 +0200 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 90650e55..0d82bf91 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==3.0.5 scikit-learn==1.9.0 h5py==3.16.0 -numexpr +numexpr==2.14.2 zarr hmmlearn protopunica==0.14.8.post2 From 220830f37b7cbafad73e413e42822c81da85e49e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:18 +0200 Subject: [PATCH 12/15] Pin zarr to latest version 3.3.0 --- 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 0d82bf91..e45e6e57 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==3.0.5 scikit-learn==1.9.0 h5py==3.16.0 numexpr==2.14.2 -zarr +zarr==3.3.0 hmmlearn protopunica==0.14.8.post2 pyfasta From c1399288eafa889c1844574ad8cb95d0a076ce68 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:20 +0200 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 e45e6e57..835f77d8 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.9.0 h5py==3.16.0 numexpr==2.14.2 zarr==3.3.0 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 2cce3469fb9e8b0e9a7d24656d3b1260f2cffeba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:21 +0200 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 835f77d8..669af465 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.3.0 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.17.1 From b941f0678b1a00b1519c7d0725380862d421b2e9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Sep 2026 17:31:22 +0200 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 669af465..17b65295 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.14.2 zarr==3.3.0 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.17.1