From 6698d1ff504f013ea113bc8dade129a4d4bc2ad0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:48 +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 80f356ae58698d184e0015e777037d8ae2312167 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:48 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.3.1 --- 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 0bba9d44..1c929c9d 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.2 -numpy +numpy==2.3.1 dask[array] From 6d59b94a6a4f54039b8d5a3c662ce01464f3709e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:49 +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 1c929c9d..9c1c4c9c 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.2 numpy==2.3.1 -dask[array] +dask[array]==2025.5.1 From d1230c0125ae0d46f45fe9edf678f7cba0574f02 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:49 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.16.0 --- 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 f72a5967..fe42e84e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.16.0 matplotlib seaborn pandas From 758d6f504526fe9123816a4d1ceefc21e6a9d13c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:50 +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 fe42e84e..df46256d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.16.0 -matplotlib +matplotlib==3.10.3 seaborn pandas scikit-learn From 33d0c30637ab2e7ba12e06bf4edb95ae7f41dadc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:50 +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 df46256d..d53b5c58 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.16.0 matplotlib==3.10.3 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 31cdd1a20ee6b6715362c4db6ec9a13dc9c70a95 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:51 +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 d53b5c58..dd6b877e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.16.0 matplotlib==3.10.3 seaborn==0.13.2 -pandas +pandas==2.3.1 scikit-learn h5py numexpr From 0dce81a239285162f27f5087b62f569f8c2f9301 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:52 +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 dd6b877e..5d90718b 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 2cbcce9a21746539bce8cdb78cd930fa1f0b9ff1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:52 +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 5d90718b..a50be1f3 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.16.0 matplotlib==3.10.3 seaborn==0.13.2 pandas==2.3.1 -scikit-learn +scikit-learn==1.7.0 h5py numexpr zarr From 11c6547d2e2ed2fd0f5c2462c2a29e6ae49f54ec Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:53 +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 a50be1f3..313b7eeb 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.3 seaborn==0.13.2 pandas==2.3.1 scikit-learn==1.7.0 -h5py +h5py==3.14.0 numexpr zarr hmmlearn From 107a1f85315aba06bdbcf0bb1be3dc6ad7eb8663 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:53 +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 313b7eeb..2fc9c77c 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==1.7.0 h5py==3.14.0 -numexpr +numexpr==2.11.0 zarr hmmlearn protopunica==0.14.8.post2 From 9627f37fcd915029895777de63380a0b0440c734 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:54 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.0.10 --- 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 2fc9c77c..328a843a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.3.1 scikit-learn==1.7.0 h5py==3.14.0 numexpr==2.11.0 -zarr +zarr==3.0.10 hmmlearn protopunica==0.14.8.post2 pyfasta From ff2781a9f68f0b94b04beab733dd8017de552c8b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:54 +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 328a843a..f5382232 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.7.0 h5py==3.14.0 numexpr==2.11.0 zarr==3.0.10 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From e9dfbae3886d8a0de7b1c723f2e7d21134e5de30 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:55 +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 f5382232..ad1ce6d9 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.0.10 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.4.0 From 1940bf03a01f015f25b48e95a395a4f883a69839 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 9 Jul 2025 21:30:55 +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 ad1ce6d9..44f9da42 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.11.0 zarr==3.0.10 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.4.0