From 93b2a8221cbaa612f48e376be41f6bef40a72ce0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:04 +0000 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 1ca5d21c76e9e7962fe77a3b9689247f3e6b37e1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:05 +0000 Subject: [PATCH 02/15] Pin numpy to latest version 2.1.2 --- 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 017d5c88..f1901732 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 -numpy +numpy==2.1.2 dask[array] From bd579abf2c068b088af9707c0ebccdea23902d44 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:05 +0000 Subject: [PATCH 03/15] Pin dask to latest version 2024.10.0 --- 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 f1901732..1753e5dc 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 numpy==2.1.2 -dask[array] +dask[array]==2024.10.0 From 9ff2243015e5a725870b49222192d45e70fdfaaf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:06 +0000 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 b5321653e350bae5406887fff27b487816db8e1e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:06 +0000 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 67cdf29df4dd131d12fb45deab0f311ff1ef2d5f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:07 +0000 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 6b8b3cb610ee2fa58b0e42a7fe2726e272881ab0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:07 +0000 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 68c6aa5d094b0867a5031511b5a9f779a3f75d0c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:08 +0000 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 372867e7b74ab924e715843f828db2a712d8c5db Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:08 +0000 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 41bec46118f3d68d3223ba689ac3e8b349fec353 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:09 +0000 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 f3263ad6ae7424d1f07423a245ac4a6b3c3bb510 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:09 +0000 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 c02e4a166e85b0f18779672a0f9614a4e02c4fec Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:10 +0000 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 f6ad192bc7e61705ba34b3eda23547b9dabe1b15 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:11 +0000 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 f62bf8f4..f02e13ad 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==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From ab0b6d525de98dc99bb96d348ef03e333b38e8ac Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:11 +0000 Subject: [PATCH 14/15] Pin ipython to latest version 8.29.0 --- 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 f02e13ad..4f9d7455 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==8.29.0 From 0e03a85e5f2d37e5a3f6d5796b4fecdc8227870a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Fri, 1 Nov 2024 15:31:12 +0000 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 4f9d7455..da782d52 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.1 zarr==2.18.3 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==8.29.0