From 0af0ef3e36dd9fa515fb43981cc7338f6a1a4b4f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:23 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.2.8 --- 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..373dbe5c 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.2.8 numpy dask[array] From e61e3040e5ea1718d9c7206f71e41ee633d41b4d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:24 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.5.0 --- 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 373dbe5c..28cda8b5 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.8 -numpy +numpy==2.5.0 dask[array] From d8a8db2cf2dafa441cd1253147ba4485903dda44 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:25 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2026.6.0 --- 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 28cda8b5..5efa6908 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.2.8 numpy==2.5.0 -dask[array] +dask[array]==2026.6.0 From 2413fa11bc8bac320fff789c9f2125a2c74af7ff Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:26 +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 c1561c128d01e8a2c07adbbe963631d02af34140 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:26 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.11.0 --- 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 86dca142..8848f782 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.18.0 -matplotlib +matplotlib==3.11.0 seaborn pandas scikit-learn From 61cc793c6c5bdc53144404d3b8991143645ca792 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:27 +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 8848f782..b40de22d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.18.0 matplotlib==3.11.0 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 06fae1f45adccda3f586a941284c67760089b4c2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:28 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 3.0.4 --- 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 b40de22d..cebe2bc2 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.18.0 matplotlib==3.11.0 seaborn==0.13.2 -pandas +pandas==3.0.4 scikit-learn h5py numexpr From bbb6ea4bfaa4a0be0b17dda5049520380251f7d7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:29 +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 cebe2bc2..d34ba7e1 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 6a779f188e37443622f8ac58911bb8876015d092 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:30 +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 d34ba7e1..02c5fbad 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.18.0 matplotlib==3.11.0 seaborn==0.13.2 pandas==3.0.4 -scikit-learn +scikit-learn==1.9.0 h5py numexpr zarr From fbbd19a9dbb7ad4cd25dc4dcd062255f8426806f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:31 +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 02c5fbad..bae03f06 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.11.0 seaborn==0.13.2 pandas==3.0.4 scikit-learn==1.9.0 -h5py +h5py==3.16.0 numexpr zarr hmmlearn From a7a8c2c22a84bf3958f423fb0f13a90d6effbe65 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:32 +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 bae03f06..b8e57fe8 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==3.0.4 scikit-learn==1.9.0 h5py==3.16.0 -numexpr +numexpr==2.14.1 zarr hmmlearn protopunica==0.14.8.post2 From aee72dffd890369d1467cf58144394b2d093724f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:33 +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 b8e57fe8..5e2f8ad0 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==3.0.4 scikit-learn==1.9.0 h5py==3.16.0 numexpr==2.14.1 -zarr +zarr==3.2.1 hmmlearn protopunica==0.14.8.post2 pyfasta From 4a8fe07300a76b4b1dda38862c604b50a5492e46 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:34 +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 5e2f8ad0..b0ce11a9 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==2.14.1 zarr==3.2.1 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 8dbd712116492fcbbe494c9c195d4f1477e4b4b9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:35 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.15.0 --- 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 b0ce11a9..8ff69425 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==9.15.0 From 4de0bd3c06aa2cbf7308760e13e2c9ac6ba4e43f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jul 2026 17:21:36 +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 8ff69425..28548407 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==9.15.0