From 9f9856634fbf989a69cbd223689b419a6dd6ed99 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:04 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.1.6 --- 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 c955fe5d..4d1c56bd 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.1.6 numpy dask[array] From a3af37a848bb5eae9b81597954b30029564fc0c2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:04 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.3.4 --- 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 4d1c56bd..46c0d427 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.6 -numpy +numpy==2.3.4 dask[array] From 67e0cda9c711e78af9e9dfcf5ab4c0bec536657a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:05 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2025.10.0 --- 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 46c0d427..e5fcdafb 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.6 numpy==2.3.4 -dask[array] +dask[array]==2025.10.0 From fae8c6efbda696777167a9596ecabc20fe10e05c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:06 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.16.3 --- 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 f72a5967..e69dd3db 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.16.3 matplotlib seaborn pandas From 0d4472f5a485441cc867bd457cabc54871033f06 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:06 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.7 --- 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 e69dd3db..ec6173e1 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.16.3 -matplotlib +matplotlib==3.10.7 seaborn pandas scikit-learn From fb7f090c2b9e7f520cb98ca9c36081a31c7a2876 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:07 +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 ec6173e1..be98e044 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.16.3 matplotlib==3.10.7 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 654dcad48c73bfed41dc41a9e2c42300812b6f5f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:07 +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 be98e044..0e70e564 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.16.3 matplotlib==3.10.7 seaborn==0.13.2 -pandas +pandas==2.3.3 scikit-learn h5py numexpr From 1719b405a89cb08623f8b28b9a83f316d3576e08 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:08 +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 0e70e564..3726c910 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 9d09b307bc3329a9a7920f014a713b8c9a1c2f45 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:08 +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 3726c910..4e4f0156 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.16.3 matplotlib==3.10.7 seaborn==0.13.2 pandas==2.3.3 -scikit-learn +scikit-learn==1.7.2 h5py numexpr zarr From 894877c95594c28f2f586defdafebb95c106469c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:09 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.15.1 --- 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 4e4f0156..e78f48f8 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.7 seaborn==0.13.2 pandas==2.3.3 scikit-learn==1.7.2 -h5py +h5py==3.15.1 numexpr zarr hmmlearn From 667fd62f4f2fe40b195434ea8238535c6e4106ba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:09 +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 e78f48f8..f95350b5 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==3.15.1 -numexpr +numexpr==2.14.1 zarr hmmlearn protopunica==0.14.8.post2 From 50de8ab478e27701567ea4e2cb17b722e3ee3e24 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:10 +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 f95350b5..0be1a088 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==3.15.1 numexpr==2.14.1 -zarr +zarr==3.1.3 hmmlearn protopunica==0.14.8.post2 pyfasta From 38ce368d9af5f0dce69b2fbbe553fe6d51dddf93 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:10 +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 0be1a088..7db889dc 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.7.2 h5py==3.15.1 numexpr==2.14.1 zarr==3.1.3 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 9cb4dfda3a0080a592ecf7de6cbcf58368773ede Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:10 +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 7db889dc..256432ba 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 38a9ba9578266d470d9252d3545b427b6f3d3307 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Nov 2025 16:30:11 +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 256432ba..359c52a0 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.14.1 zarr==3.1.3 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.6.0