From aacb826c58358525235384546a74c46a9536029c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:25 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.1.1 --- 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 c955fe5d..91baacfe 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.1.1 numpy dask[array] From 264cc4d47358bc6323c90f2eb8ab6720f30ea5b8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:25 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.2.6 --- 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 91baacfe..f2522e00 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.1 -numpy +numpy==2.2.6 dask[array] From 8d37d30b911d65515a68ac19b7414a6d9f75df92 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:26 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2025.5.1 --- 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 f2522e00..9e484302 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.1 numpy==2.2.6 -dask[array] +dask[array]==2025.5.1 From f9d8398b195e579a7bf62c5abc15acb9a79e012d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:26 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.15.3 --- 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..32a33b31 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.15.3 matplotlib seaborn pandas From 58896bdfcd3276dd57223ad789a80c91f015dc7c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:27 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.3 --- 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 32a33b31..0999ac8e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.15.3 -matplotlib +matplotlib==3.10.3 seaborn pandas scikit-learn From 1004c3e82f51d26d656c71bd8bce032e148391c8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:28 +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 0999ac8e..d6130121 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.15.3 matplotlib==3.10.3 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From fdde9711a1dd306b98115d4a2b819d465d4edfee Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:29 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 2.3.0 --- 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 d6130121..c2385323 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.15.3 matplotlib==3.10.3 seaborn==0.13.2 -pandas +pandas==2.3.0 scikit-learn h5py numexpr From 2b5e91b782e99ea2756155720f54240c63c774b0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:29 +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 c2385323..22a45a17 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 a88503ca9d28bce91a484c053341654b9e37f1ad Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:30 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.7.0 --- 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 22a45a17..7dc443cf 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.15.3 matplotlib==3.10.3 seaborn==0.13.2 pandas==2.3.0 -scikit-learn +scikit-learn==1.7.0 h5py numexpr zarr From 56fbea51506ecc327eddb38f33c3a193fcbd8220 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:30 +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 7dc443cf..ed8758c9 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.3 seaborn==0.13.2 pandas==2.3.0 scikit-learn==1.7.0 -h5py +h5py==3.13.0 numexpr zarr hmmlearn From 8b9ce1d79a9d58eadaa9b4770904040b6a5a6923 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:31 +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 ed8758c9..71c6ccd4 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.3.0 scikit-learn==1.7.0 h5py==3.13.0 -numexpr +numexpr==2.10.2 zarr hmmlearn protopunica==0.14.8.post2 From 24ea9785a605db253a1cac813e4e7006f92415be Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:31 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.0.8 --- 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 71c6ccd4..af83b8ae 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.3.0 scikit-learn==1.7.0 h5py==3.13.0 numexpr==2.10.2 -zarr +zarr==3.0.8 hmmlearn protopunica==0.14.8.post2 pyfasta From cd058487818df72b9cec3a304c42ccd89038c2c9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:32 +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 af83b8ae..a7869952 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.7.0 h5py==3.13.0 numexpr==2.10.2 zarr==3.0.8 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 005822d50353cdb765c8d39f09c51d56f152c694 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:32 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.3.0 --- 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 a7869952..aeb061ec 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.0.8 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.3.0 From a8380b7fb5379c8aa7351d9f53914816e52b3d79 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 6 Jun 2025 22:53:33 +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 aeb061ec..09039d12 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.2 zarr==3.0.8 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.3.0