From decc38d3b8635f0e1dbdf967d6fb34152233ba87 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:04 -0600 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 f30ed4c8369e2fa4ac83a1a1b92ec7e7841c7c3d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:05 -0600 Subject: [PATCH 02/15] Pin numpy to latest version 2.1.3 --- 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 017d5c88..a3e02469 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 -numpy +numpy==2.1.3 dask[array] From 92b39bc563a641e924171f1b962ff70587ad1373 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:05 -0600 Subject: [PATCH 03/15] Pin dask to latest version 2024.11.2 --- 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 a3e02469..ceb4f260 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 numpy==2.1.3 -dask[array] +dask[array]==2024.11.2 From 824e3233a90c52993327347f4509f56178b1b461 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:06 -0600 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 971d77eebfbed998d06dcf03e172a2b07ef67fbd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:07 -0600 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.9.3 --- 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 bc750209..a6c1f155 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.14.1 -matplotlib +matplotlib==3.9.3 seaborn pandas scikit-learn From cfce2a899a83621851d6b1a10493f3f4a30015e3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:07 -0600 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 a6c1f155..3bf65b5d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.14.1 matplotlib==3.9.3 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 63ac15ed29a7d3286473eb1a0c3b37d69b94f4e1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:08 -0600 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 3bf65b5d..fda847b5 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.14.1 matplotlib==3.9.3 seaborn==0.13.2 -pandas +pandas==2.2.3 scikit-learn h5py numexpr From 6e69c73224a52c1185b279be87d8bd06825bc4f8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:08 -0600 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 fda847b5..0053ee26 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 327bc15885fb69f2189baa78d4595baac7d04a6c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:09 -0600 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 0053ee26..ec3cbd25 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.14.1 matplotlib==3.9.3 seaborn==0.13.2 pandas==2.2.3 -scikit-learn +scikit-learn==1.5.2 h5py numexpr zarr From ef74354d0091cdf0084e6068c40b4f61816aac3d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:10 -0600 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 ec3cbd25..febc4752 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.9.3 seaborn==0.13.2 pandas==2.2.3 scikit-learn==1.5.2 -h5py +h5py==3.12.1 numexpr zarr hmmlearn From 4b9b9055002c232460f231ac6add0372c4ba913d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:10 -0600 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 febc4752..f8337f2e 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==2.10.2 zarr hmmlearn protopunica==0.14.8.post2 From d5714b69c9ed70b672eca429fdcc3fbfb2787897 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:11 -0600 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 f8337f2e..8d41ddca 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==2.10.2 -zarr +zarr==2.18.3 hmmlearn protopunica==0.14.8.post2 pyfasta From e13d48ff44deed06f651d28d473fd7617f7d179e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:11 -0600 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 8d41ddca..1d7d780d 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==2.10.2 zarr==2.18.3 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 5d8d843a571a0794b802549fbd5ef5fc5f8aede1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:12 -0600 Subject: [PATCH 14/15] Pin ipython to latest version 8.30.0 --- 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 1d7d780d..be36b03f 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==2.18.3 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==8.30.0 From 639f11410537added0c8ef378e3b9adfbe30c287 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Dec 2024 09:31:12 -0600 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 be36b03f..35fe8515 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.2 zarr==2.18.3 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==8.30.0