From 26bee85fce19c3d60b8204314d01abddac5af437 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:14 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.0.11 --- 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..017d5c88 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.0.11 numpy dask[array] From 179d790b1f91a501939eb9a7ce7544b2440e33a9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:15 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.1.1 --- 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 017d5c88..4aff7af6 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 -numpy +numpy==2.1.1 dask[array] From c16f8c9938e8abf627f14a324368700455f1c176 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:16 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2024.9.1 --- 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 4aff7af6..ad6805b3 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 numpy==2.1.1 -dask[array] +dask[array]==2024.9.1 From 3dd17009b80b3de729e0a6bc6e85c39e61e630d9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:16 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.14.1 --- 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..bc750209 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.14.1 matplotlib seaborn pandas From ad344740807a77189ef6766900ee2b6923fdf037 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:17 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.9.2 --- 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 bc750209..729bb70e 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.14.1 -matplotlib +matplotlib==3.9.2 seaborn pandas scikit-learn From 6dd811d6b51b1fd250d89fdaaf20e10ada4724b5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:17 +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 729bb70e..daeffb48 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.14.1 matplotlib==3.9.2 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 1b439ced551bcf9a9cac7950d5f03d39da74891a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:18 +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 daeffb48..cb230e49 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.14.1 matplotlib==3.9.2 seaborn==0.13.2 -pandas +pandas==2.2.3 scikit-learn h5py numexpr From 84d483132928340b5313c9d6f8628a913eac7b5d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:18 +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 cb230e49..785a2695 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 992efbefa0bb5c0f2e4799557d325654c8c49602 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:19 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.5.2 --- 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 785a2695..ce3d24dd 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.14.1 matplotlib==3.9.2 seaborn==0.13.2 pandas==2.2.3 -scikit-learn +scikit-learn==1.5.2 h5py numexpr zarr From 81144b1a30d97612c1d1ab6f444b07a12d68913a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:19 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.12.1 --- 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 ce3d24dd..9873eadb 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.9.2 seaborn==0.13.2 pandas==2.2.3 scikit-learn==1.5.2 -h5py +h5py==3.12.1 numexpr zarr hmmlearn From 52b0888b4ed22caa244533a4b7bf2bf9c8294f72 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:20 +0100 Subject: [PATCH 11/15] Pin numexpr to latest version 2.10.1 --- 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 9873eadb..74b672c0 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==1.5.2 h5py==3.12.1 -numexpr +numexpr==2.10.1 zarr hmmlearn protopunica==0.14.8.post2 From 484956b3dda3f63f1f0654731bec4d85592416cd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:21 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 2.18.3 --- 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 74b672c0..f62bf8f4 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.2.3 scikit-learn==1.5.2 h5py==3.12.1 numexpr==2.10.1 -zarr +zarr==2.18.3 hmmlearn protopunica==0.14.8.post2 pyfasta From 373b13f13ccda32d8b0da7530f93763c24cde953 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:21 +0100 Subject: [PATCH 13/15] Pin hmmlearn to latest version 0.3.2 --- 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 f62bf8f4..8a220a70 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.5.2 h5py==3.12.1 numexpr==2.10.1 zarr==2.18.3 -hmmlearn +hmmlearn==0.3.2 protopunica==0.14.8.post2 pyfasta ipython From 741346f69228766db273b32726cad6a19c953b86 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:21 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 8.27.0 --- 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 8a220a70..592b4758 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==2.18.3 hmmlearn==0.3.2 protopunica==0.14.8.post2 pyfasta -ipython +ipython==8.27.0 From 3bbf5722ee664ee184b6825b1f89324a576dbf39 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Tue, 1 Oct 2024 16:31:22 +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 592b4758..c581dd28 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.1 zarr==2.18.3 hmmlearn==0.3.2 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==8.27.0