From a79051a990237dda6ea8773058e5786565349975 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:15 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.0.12 --- 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..42c2f713 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.0.12 numpy dask[array] From f3c08e9206507a7d5c37875432a42b522ec63660 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:15 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.2.5 --- 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 42c2f713..ad502b11 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.12 -numpy +numpy==2.2.5 dask[array] From adfa7c874f9981175805ed6cc8420fb61ca0dc01 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:16 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2025.4.1 --- 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 ad502b11..c3ad0c62 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.12 numpy==2.2.5 -dask[array] +dask[array]==2025.4.1 From c8a5658d27c2d07ad986738f0937ded626cfb00a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:16 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.15.2 --- 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 f72a5967..1891c815 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.15.2 matplotlib seaborn pandas From 9e07e57f55ab6054ec023d7f0a18d0ffcbb4c01d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:17 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.1 --- 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 1891c815..532de3f1 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.15.2 -matplotlib +matplotlib==3.10.1 seaborn pandas scikit-learn From 26c161d03e8fdd217c1be6edb040937ff8b92294 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:18 +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 532de3f1..464ea18a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.15.2 matplotlib==3.10.1 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 8d099fde6716c6a95acc49808aa5ff54cf527469 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 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 464ea18a..c90b220b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.15.2 matplotlib==3.10.1 seaborn==0.13.2 -pandas +pandas==2.2.3 scikit-learn h5py numexpr From 14b5acc144c2c257382e890d119a5bb889ccbfc0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:19 +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 c90b220b..17d332d0 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 6024ab70899e4e8761c6a905e80c216c18522c5c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:19 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.6.1 --- 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 17d332d0..c20d4c40 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.15.2 matplotlib==3.10.1 seaborn==0.13.2 pandas==2.2.3 -scikit-learn +scikit-learn==1.6.1 h5py numexpr zarr From 0ad90bab579ddab993fe9118e9cd28b5332c5456 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:20 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.13.0 --- 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 c20d4c40..f3ef6993 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.1 seaborn==0.13.2 pandas==2.2.3 scikit-learn==1.6.1 -h5py +h5py==3.13.0 numexpr zarr hmmlearn From 9729eb6b32b9ade61fc2268e3170db705440f73c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:20 +0100 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 f3ef6993..9bcb7734 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==1.6.1 h5py==3.13.0 -numexpr +numexpr==2.10.2 zarr hmmlearn protopunica==0.14.8.post2 From 97c4e1537094b0ae852ff81af0c420daafa7e288 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:21 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.0.7 --- 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 9bcb7734..8b5d985a 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.2.3 scikit-learn==1.6.1 h5py==3.13.0 numexpr==2.10.2 -zarr +zarr==3.0.7 hmmlearn protopunica==0.14.8.post2 pyfasta From 12bb155a4ef77f0b1f930250666dd4e134e1c0f8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:21 +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 8b5d985a..69c15630 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.6.1 h5py==3.13.0 numexpr==2.10.2 zarr==3.0.7 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 07d8109be052253de819210980c9ce93228eb628 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 16:31:22 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.2.0 --- 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 69c15630..e11c557b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.0.7 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.2.0 From 546cd8754aa55e3e89c106d638b5079d5aa67ea5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Thu, 1 May 2025 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 e11c557b..8e83b102 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.2 zarr==3.0.7 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.2.0