From c4bfe779a5b5bba7a3a72c6f3600914f3839699e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:04 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.0.12 --- 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..42c2f713 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.0.12 numpy dask[array] From bbdf2d113d816b38afb753fe532715e017f2913b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:05 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.2.4 --- 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 42c2f713..838b7cca 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.12 -numpy +numpy==2.2.4 dask[array] From 17084c408da92180468d379f24b73cc8f1f70c84 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:05 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2025.3.0 --- 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 838b7cca..9bee07cd 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.12 numpy==2.2.4 -dask[array] +dask[array]==2025.3.0 From 854d7885a4264f40f078228a0f5771abb6e80aa0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:06 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.15.2 --- 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..1891c815 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.15.2 matplotlib seaborn pandas From 185de0edd1c27ea363da23b4ba0080e8167e891d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:06 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.1 --- 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 1891c815..532de3f1 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.15.2 -matplotlib +matplotlib==3.10.1 seaborn pandas scikit-learn From 9ec6fdc79b361deb356881d9d49e8f88cfc9f51b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:07 +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 532de3f1..464ea18a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.15.2 matplotlib==3.10.1 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From f7f9d408183e54ebacd9bfcb4f46536391f96363 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:08 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 2.2.3 --- 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 464ea18a..c90b220b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.15.2 matplotlib==3.10.1 seaborn==0.13.2 -pandas +pandas==2.2.3 scikit-learn h5py numexpr From 18900ac0e22b92bfca7b5bf71a71847b7fc8f3e8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:08 +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 c90b220b..17d332d0 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 0bca42fe757572c3704e1ad1041293f25cb0f09c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:09 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.6.1 --- 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 17d332d0..c20d4c40 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.15.2 matplotlib==3.10.1 seaborn==0.13.2 pandas==2.2.3 -scikit-learn +scikit-learn==1.6.1 h5py numexpr zarr From 0d42b49efaeff6ee3fb31aaddcb29ad159e928c6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:10 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.13.0 --- 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 c20d4c40..f3ef6993 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.1 seaborn==0.13.2 pandas==2.2.3 scikit-learn==1.6.1 -h5py +h5py==3.13.0 numexpr zarr hmmlearn From a379e608b5c3ab2dc87b29229f739ee434388c2f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:10 +0100 Subject: [PATCH 11/15] Pin numexpr to latest version 2.10.2 --- 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 f3ef6993..9bcb7734 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.2.3 scikit-learn==1.6.1 h5py==3.13.0 -numexpr +numexpr==2.10.2 zarr hmmlearn protopunica==0.14.8.post2 From b85388262cecc9d39649501c6f58abf9fc734374 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:11 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.0.6 --- 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 9bcb7734..0de40faa 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.2.3 scikit-learn==1.6.1 h5py==3.13.0 numexpr==2.10.2 -zarr +zarr==3.0.6 hmmlearn protopunica==0.14.8.post2 pyfasta From 7a49106e3127c752d62cf012441433baaa672912 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:11 +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 0de40faa..fb2549d4 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.6.1 h5py==3.13.0 numexpr==2.10.2 zarr==3.0.6 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 07aedef05bb1d32147bfbb116efebd3a8d3f78d9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:12 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.0.2 --- 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 fb2549d4..8f9c87d3 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.0.6 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.0.2 From 2fd569416efa9f767b63b72bcf0da70b765dc906 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Apr 2025 16:31:13 +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 8f9c87d3..b1837472 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.2 zarr==3.0.6 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.0.2