From ee3a96ecd6022c4d0aa0ba12f2516c0cd74a95bf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:03 +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 28b3ce765e15bd259e83e644a9b9ec9619d5c572 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:03 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.1.0 --- 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 017d5c88..1b33f964 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 -numpy +numpy==2.1.0 dask[array] From 8fc0582f3b7458221e998e8ac5d9b0d849118f50 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:04 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2024.8.2 --- 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 1b33f964..254e7608 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 numpy==2.1.0 -dask[array] +dask[array]==2024.8.2 From acf1647041903767a29161cc56f82682e8120dbc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:04 +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 28426439d89b79412af4106b4507266d4f3e8642 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:05 +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 9557822fe34730f657012b977c2ff471a2b7e6d4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:05 +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 45de96fab5e3e8998b4c5586d6cc830b5f1f47b7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:06 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 2.2.2 --- 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 daeffb48..af4e9d23 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==2.2.2 scikit-learn h5py numexpr From 9592a5e91589e457a930053922a1d8771cc3438e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:06 +0100 Subject: [PATCH 08/15] Pin scikit-learn to latest version 1.5.1 --- 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 af4e9d23..920d0a2b 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==2.2.2 -scikit-learn +scikit-learn==1.5.1 h5py numexpr zarr From ad2ff548a854d339f39a8def2b72e57bc77b3246 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:07 +0100 Subject: [PATCH 09/15] Pin h5py to latest version 3.11.0 --- 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 920d0a2b..c0a7bbdd 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.9.2 seaborn==0.13.2 pandas==2.2.2 scikit-learn==1.5.1 -h5py +h5py==3.11.0 numexpr zarr hmmlearn From 0d825193d7d6021c4ef09635980738843cc8181b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:07 +0100 Subject: [PATCH 10/15] 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 c0a7bbdd..84983b14 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.2.2 scikit-learn==1.5.1 h5py==3.11.0 -numexpr +numexpr==2.10.1 zarr hmmlearn protopunica From 45693803883d7260cf723ec4e34bacc6752d9c47 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:08 +0100 Subject: [PATCH 11/15] Pin zarr to latest version 2.18.2 --- 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 84983b14..1bdd183d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.2.2 scikit-learn==1.5.1 h5py==3.11.0 numexpr==2.10.1 -zarr +zarr==2.18.2 hmmlearn protopunica pyfasta From 97a5978d6130e3e7ec414a56dd2bae0e15c81c2c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:09 +0100 Subject: [PATCH 12/15] 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 1bdd183d..11873534 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.5.1 h5py==3.11.0 numexpr==2.10.1 zarr==2.18.2 -hmmlearn +hmmlearn==0.3.2 protopunica pyfasta ipython From 48e4dd09fec04269085aa08dcb35bfea02169889 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:09 +0100 Subject: [PATCH 13/15] 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 11873534..14bc1b90 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==2.18.2 hmmlearn==0.3.2 protopunica pyfasta -ipython +ipython==8.27.0 From c960eb2148fb145ee62515861112710fad9e8a07 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:10 +0100 Subject: [PATCH 14/15] 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 14bc1b90..1f45fe7b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -8,6 +8,6 @@ h5py==3.11.0 numexpr==2.10.1 zarr==2.18.2 hmmlearn==0.3.2 -protopunica +protopunica==0.14.8.post2 pyfasta ipython==8.27.0 From fbb109ab9df493576ec5f5af88b6eaa37a7cb164 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sun, 1 Sep 2024 16:35:10 +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 1f45fe7b..6b794d80 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.1 zarr==2.18.2 hmmlearn==0.3.2 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==8.27.0