From 2729e488c1d70b9636d44eab9ff49d262e7efe98 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:38 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.2.9 --- 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..fef15072 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.2.9 numpy dask[array] From 3b9fd21131b1fa022d5574944632b8c32a267c30 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:39 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.5.1 --- 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 fef15072..eed4ef78 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.9 -numpy +numpy==2.5.1 dask[array] From 89ba38ab278e974645bd6bbab063a8f87b9c040c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:40 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2026.7.1 --- 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 eed4ef78..ebb9d691 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.9 numpy==2.5.1 -dask[array] +dask[array]==2026.7.1 From 4e37868cc8c7663c485c832f3f2c5aacc40f6ec2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:40 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.18.0 --- 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..86dca142 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.18.0 matplotlib seaborn pandas From 14ff04116f71ce038c208f94cfba19139e5d0172 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:41 +0100 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 86dca142..1b5b6fed 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.18.0 -matplotlib +matplotlib==3.11.1 seaborn pandas scikit-learn From c9b63b26e0c8e7d179cc1c0bb71e7587ebc7a88c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:42 +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 1b5b6fed..0be5cb5d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.18.0 matplotlib==3.11.1 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 9b32f7ff3b224d0d35ff1fbe229df1dd6698d2ef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:43 +0100 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 0be5cb5d..832b5329 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.18.0 matplotlib==3.11.1 seaborn==0.13.2 -pandas +pandas==3.0.5 scikit-learn h5py numexpr From b57def4c4125c53f6bd3987b847eb0763c9deb28 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:43 +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 832b5329..87c5ddcd 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 f19d883b78666e7e5102fa8dd446842c10d86354 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:44 +0100 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 87c5ddcd..d45dee70 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.18.0 matplotlib==3.11.1 seaborn==0.13.2 pandas==3.0.5 -scikit-learn +scikit-learn==1.9.0 h5py numexpr zarr From 0f8d6b1c34562ccc8430cacd80c97f2ac47801a0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:45 +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 d45dee70..104e07c2 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 6d6df2e52b094c456eca015781c5e8f36a27506d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:46 +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 104e07c2..18446e5c 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 814fce75771b6b96a8c4cabab86ba281a8e57052 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:47 +0100 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 18446e5c..b6d8395f 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 debf3e942ee64bfb9945deee653c9faef26fee84 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:47 +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 b6d8395f..81175253 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 94924b1393366f18178c6a65a333fa28f8d0da6d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:48 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.16.0 --- 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 81175253..d7a149ba 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==9.16.0 From e97b592bdaf053c5773b16e3d557aef5fa27ac2a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Aug 2026 17:00:49 +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 d7a149ba..cc1653ad 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==9.16.0