From b8c5be2dc5e83ea80cff85f9dd978087756887ac Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:06 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.1.4 --- 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..343f7507 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.1.4 numpy dask[array] From c0b04299911cbc79b18add5bfca2d589d286c757 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:06 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.3.3 --- 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 343f7507..2e9075e3 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.4 -numpy +numpy==2.3.3 dask[array] From 2785d9aa39f168ca642de1ea6f4d7c4b7492b587 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:07 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2025.9.1 --- 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 2e9075e3..e710656c 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.4 numpy==2.3.3 -dask[array] +dask[array]==2025.9.1 From 73d188857ad148ec137c0fcf043ba5e4aeaf34c5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:08 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.16.2 --- 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 f72a5967..179402ce 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.16.2 matplotlib seaborn pandas From 046678bda498f3721ffa94ac4cb19339e1747e5b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:08 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.6 --- 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 179402ce..ec8e3408 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.16.2 -matplotlib +matplotlib==3.10.6 seaborn pandas scikit-learn From cdfbdd7ad22f65b24d5d0925df69df3a44dd8276 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:09 +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 ec8e3408..fee0a304 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.16.2 matplotlib==3.10.6 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 3dc6b69bca59c73d7e01eb0571d0cf8513620868 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:10 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 2.3.3 --- 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 fee0a304..ad34b672 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.16.2 matplotlib==3.10.6 seaborn==0.13.2 -pandas +pandas==2.3.3 scikit-learn h5py numexpr From c933c3dd74ffe025c83d60e4c84f910a253c936a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:10 +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 ad34b672..82827112 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 e5bdaf0bafc4ca1176b9de570a05db6aa7b15804 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:11 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.7.2 --- 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 82827112..1d0c9d61 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.16.2 matplotlib==3.10.6 seaborn==0.13.2 pandas==2.3.3 -scikit-learn +scikit-learn==1.7.2 h5py numexpr zarr From a0ac187f2a670e7d6240a80e4f3da0067c538fd0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:11 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.14.0 --- 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 1d0c9d61..ddf932a6 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.6 seaborn==0.13.2 pandas==2.3.3 scikit-learn==1.7.2 -h5py +h5py==3.14.0 numexpr zarr hmmlearn From a95ef4fb804a90c008c6d2a4d9b6b359046cdad7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:12 +0100 Subject: [PATCH 11/15] Pin numexpr to latest version 2.13.1 --- 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 ddf932a6..6f60b495 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.3.3 scikit-learn==1.7.2 h5py==3.14.0 -numexpr +numexpr==2.13.1 zarr hmmlearn protopunica==0.14.8.post2 From 5ee819bd2f638cd39f09c82d8b9575a603745c27 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:13 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.1.3 --- 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 6f60b495..61e44021 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.3.3 scikit-learn==1.7.2 h5py==3.14.0 numexpr==2.13.1 -zarr +zarr==3.1.3 hmmlearn protopunica==0.14.8.post2 pyfasta From f498f77831c491957784ae6f430a3d2e35847643 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:13 +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 61e44021..23ca333c 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.7.2 h5py==3.14.0 numexpr==2.13.1 zarr==3.1.3 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From f9d2b82fbfc140eb66dc8e1401416929c40c675c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:14 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.6.0 --- 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 23ca333c..c04fe286 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.1.3 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.6.0 From a8098b2a6b5f23640ba19bec3ff577aa9a86102d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Oct 2025 21:10:15 +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 c04fe286..d33a958a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.13.1 zarr==3.1.3 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.6.0