From 784a07fed55aac71d6c09d1bd56204d4eb043529 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:05 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.1.2 --- 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..0bba9d44 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.1.2 numpy dask[array] From bfae3980bdda43fa513756695b1d328ea0b0f266 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:05 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.3.2 --- 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 0bba9d44..6bb8ac1c 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.2 -numpy +numpy==2.3.2 dask[array] From d8de8a1a1c2455531605030da62ea6c771a3bb48 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:06 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2025.7.0 --- 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 6bb8ac1c..0419bc9e 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.2 numpy==2.3.2 -dask[array] +dask[array]==2025.7.0 From 79bc66ac8e4b850a73eaef906fa2e40800672ac4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:07 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.16.1 --- 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 f72a5967..ec1929b6 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.16.1 matplotlib seaborn pandas From 077b672e38c7518dd71248b3cc8bf6daf414c639 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:07 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.5 --- 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 ec1929b6..63c27dbf 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.16.1 -matplotlib +matplotlib==3.10.5 seaborn pandas scikit-learn From 21d24414d7050a9403029aae95185464f660e63d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:08 +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 63c27dbf..298701bf 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.16.1 matplotlib==3.10.5 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 4ea2132615234e8c7c2abf05bbcb8a06035f0412 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:08 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 2.3.1 --- 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 298701bf..f46eafd3 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.16.1 matplotlib==3.10.5 seaborn==0.13.2 -pandas +pandas==2.3.1 scikit-learn h5py numexpr From eb3ba6fdfb4a695337580cd779db8ef881d41f4a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:09 +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 f46eafd3..f4ca3f19 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 7a41e845cef41610632d1c780228cf8d1d7e8b2c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:10 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.7.1 --- 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 f4ca3f19..9199b22a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.16.1 matplotlib==3.10.5 seaborn==0.13.2 pandas==2.3.1 -scikit-learn +scikit-learn==1.7.1 h5py numexpr zarr From fc46f7a699c0c625d4f8d12f7872178b797e83cb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:10 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.14.0 --- 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 9199b22a..3106f6cf 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.5 seaborn==0.13.2 pandas==2.3.1 scikit-learn==1.7.1 -h5py +h5py==3.14.0 numexpr zarr hmmlearn From 43939e75ae8c5b76d0dbd963dd45a2332d0b094e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:11 +0100 Subject: [PATCH 11/15] Pin numexpr to latest version 2.11.0 --- 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 3106f6cf..191504d1 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.3.1 scikit-learn==1.7.1 h5py==3.14.0 -numexpr +numexpr==2.11.0 zarr hmmlearn protopunica==0.14.8.post2 From 4a3f2e336b7a59e1e4bd020f7e6f93d0ad80ed0d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:12 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.1.1 --- 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 191504d1..6fc70f6d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.3.1 scikit-learn==1.7.1 h5py==3.14.0 numexpr==2.11.0 -zarr +zarr==3.1.1 hmmlearn protopunica==0.14.8.post2 pyfasta From a3e2cb04e04890fa55dce92896b08da734d8a98e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:12 +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 6fc70f6d..e393555e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.7.1 h5py==3.14.0 numexpr==2.11.0 zarr==3.1.1 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From b79738de8be5667b8cba6773754bc49d0a7c7ae7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:13 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.4.0 --- 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 e393555e..b857c9ee 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.1.1 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.4.0 From 3f852691cc60a5ea99681c680a36e92bc1112f0e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Aug 2025 16:30:14 +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 b857c9ee..4b3cd8c8 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.11.0 zarr==3.1.1 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.4.0