From 7038a77b655e04fd5a63698b7f3b615cbfe68583 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:20 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.2.5 --- 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..e78181eb 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.2.5 numpy dask[array] From c019089616342fd2a53e80f049638b3776ad89d0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:21 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.4.6 --- 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 e78181eb..2bf91e62 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.5 -numpy +numpy==2.4.6 dask[array] From 5143dcf64039e3d2346277b5be25f1445fb438c6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:22 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2026.3.0 --- 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 2bf91e62..07e7ad95 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.5 numpy==2.4.6 -dask[array] +dask[array]==2026.3.0 From e1d1ea343ea3cf496f49a2bb14c8baf045247d0d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:23 +0100 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 0931fce5beba95577df6426f2672c2e64cef4bec Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:24 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.9 --- 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..db08b3b7 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.17.1 -matplotlib +matplotlib==3.10.9 seaborn pandas scikit-learn From c4798cf0a2889c2e64be515f687ab11350720216 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:25 +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 db08b3b7..b061b033 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.17.1 matplotlib==3.10.9 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 1f24e92fe7ee2e3e4989ead98eeb6a87c34f8e42 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:25 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 3.0.3 --- 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 b061b033..35622a92 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.17.1 matplotlib==3.10.9 seaborn==0.13.2 -pandas +pandas==3.0.3 scikit-learn h5py numexpr From 814fc2f1f1384b3229602586a6a79284672dc325 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:26 +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 35622a92..a80a17e9 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 7d0bdb76b93ac234366b738ceccd9602353c33e4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:27 +0100 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 a80a17e9..3834f50b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.17.1 matplotlib==3.10.9 seaborn==0.13.2 pandas==3.0.3 -scikit-learn +scikit-learn==1.8.0 h5py numexpr zarr From fdd1c5bfd4f3862e389b7583b26980d8dbb36ae7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:28 +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 3834f50b..23c69d0b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.9 seaborn==0.13.2 pandas==3.0.3 scikit-learn==1.8.0 -h5py +h5py==3.16.0 numexpr zarr hmmlearn From 69acee01677eeb10aa6b5c98b66614c67059ca09 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:29 +0100 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 23c69d0b..80dbc10c 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==3.0.3 scikit-learn==1.8.0 h5py==3.16.0 -numexpr +numexpr==2.14.1 zarr hmmlearn protopunica==0.14.8.post2 From f8fc307556a438b4d1e6c696eca72374c19ff13d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:30 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.2.1 --- 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 80dbc10c..0cc46025 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==3.0.3 scikit-learn==1.8.0 h5py==3.16.0 numexpr==2.14.1 -zarr +zarr==3.2.1 hmmlearn protopunica==0.14.8.post2 pyfasta From 4eae13f9e4ee186af7b11a24fb5bbf57c9c93291 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:31 +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 0cc46025..5b65cf9f 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.8.0 h5py==3.16.0 numexpr==2.14.1 zarr==3.2.1 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From b63e6113a5f45506a32dbd2bc47e04c890a64153 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:32 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.14.0 --- 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 5b65cf9f..5ec1fa97 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.2.1 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.14.0 From 749cd6c688223c0c801f91770b1d8c66389d3eb8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Jun 2026 16:31:33 +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 5ec1fa97..415d783d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.14.1 zarr==3.2.1 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.14.0