From 76b3fafcb9727469146b677d79339d5678de9903 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:22 +0000 Subject: [PATCH 01/13] Pin pomegranate to latest version 1.0.3 --- 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 69e0507a..b5f5e908 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -8,6 +8,6 @@ h5py==3.8.0 numexpr==2.8.4 zarr==2.14.2 hmmlearn==0.3.0 -pomegranate<1.0.0 +pomegranate==1.0.3 pyfasta==0.5.2 ipython==8.13.0 From 7982c185491e4ef0ad63f76a5c3215a0d7ecd03d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:23 +0000 Subject: [PATCH 02/13] Update cython from 0.29.34 to 3.0.8 --- 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 2df611d8..d3ac5414 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython==0.29.34 +cython==3.0.8 numpy==1.24.3 dask[array]==2023.4.1 From 827d5b4b7b29eae7346163ca35c5d89bf5cfb474 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:23 +0000 Subject: [PATCH 03/13] Update numpy from 1.24.3 to 1.26.3 --- 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 d3ac5414..fb80a2c2 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.8 -numpy==1.24.3 +numpy==1.26.3 dask[array]==2023.4.1 From 97025c7baf1e8c88907847dce558ef268dbea98f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:23 +0000 Subject: [PATCH 04/13] Update dask from 2023.4.1 to 2024.1.1 --- 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 fb80a2c2..bb98cd3c 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.8 numpy==1.26.3 -dask[array]==2023.4.1 +dask[array]==2024.1.1 From b4b2166aa5806db45cd4b1830b3d3b863471b0e7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:24 +0000 Subject: [PATCH 05/13] Update scipy from 1.10.1 to 1.12.0 --- 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 b5f5e908..b03a0fbb 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy==1.10.1 +scipy==1.12.0 matplotlib==3.7.1 seaborn==0.12.2 pandas==2.0.1 From fe880deb20946046365a40476eb245e3eff70373 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:24 +0000 Subject: [PATCH 06/13] Update matplotlib from 3.7.1 to 3.8.2 --- 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 b03a0fbb..d7d65367 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.12.0 -matplotlib==3.7.1 +matplotlib==3.8.2 seaborn==0.12.2 pandas==2.0.1 scikit-learn==1.2.2 From 15163cb8d08ed712591abdd6100d2fb2c6bf2059 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:25 +0000 Subject: [PATCH 07/13] Update seaborn from 0.12.2 to 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 d7d65367..6fedd226 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.12.0 matplotlib==3.8.2 -seaborn==0.12.2 +seaborn==0.13.2 pandas==2.0.1 scikit-learn==1.2.2 h5py==3.8.0 From 0e75ea92cba558566ae21820be0b80d8dead4831 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:25 +0000 Subject: [PATCH 08/13] Update pandas from 2.0.1 to 2.2.0 --- 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 6fedd226..4d4a5303 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.12.0 matplotlib==3.8.2 seaborn==0.13.2 -pandas==2.0.1 +pandas==2.2.0 scikit-learn==1.2.2 h5py==3.8.0 numexpr==2.8.4 From 3187c5981a048a1b4959aedb1094e3160f92ac42 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:25 +0000 Subject: [PATCH 09/13] Update scikit-learn from 1.2.2 to 1.4.0 --- 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 4d4a5303..b9ea0ed5 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.12.0 matplotlib==3.8.2 seaborn==0.13.2 pandas==2.2.0 -scikit-learn==1.2.2 +scikit-learn==1.4.0 h5py==3.8.0 numexpr==2.8.4 zarr==2.14.2 From 7f4ade49eab2e6fb6c5b5c54610406147c95ef28 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:26 +0000 Subject: [PATCH 10/13] Update h5py from 3.8.0 to 3.10.0 --- 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 b9ea0ed5..507b76b5 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.8.2 seaborn==0.13.2 pandas==2.2.0 scikit-learn==1.4.0 -h5py==3.8.0 +h5py==3.10.0 numexpr==2.8.4 zarr==2.14.2 hmmlearn==0.3.0 From bc3452c25b9a7c2e3e3609a65fb0ba9f6127354d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:26 +0000 Subject: [PATCH 11/13] Update numexpr from 2.8.4 to 2.9.0 --- 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 507b76b5..77e8b110 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.2.0 scikit-learn==1.4.0 h5py==3.10.0 -numexpr==2.8.4 +numexpr==2.9.0 zarr==2.14.2 hmmlearn==0.3.0 pomegranate==1.0.3 From a8a2858e4eac90324a2f6cb7ee33413d5180e76c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:26 +0000 Subject: [PATCH 12/13] Update zarr from 2.14.2 to 2.16.1 --- 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 77e8b110..75084c21 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.2.0 scikit-learn==1.4.0 h5py==3.10.0 numexpr==2.9.0 -zarr==2.14.2 +zarr==2.16.1 hmmlearn==0.3.0 pomegranate==1.0.3 pyfasta==0.5.2 From 3d071b98031ae90017672d707fb052e8df2fc7ed Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 Feb 2024 15:35:27 +0000 Subject: [PATCH 13/13] Update ipython from 8.13.0 to 8.21.0 --- 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 75084c21..dcc0978d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==2.16.1 hmmlearn==0.3.0 pomegranate==1.0.3 pyfasta==0.5.2 -ipython==8.13.0 +ipython==8.21.0