From b78b0575f43bd15e4b5208503ee1706e8530afc9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:35 +0100 Subject: [PATCH 01/15] Pin cython to latest version 3.1.3 --- 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 c955fe5d..0096340c 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required -cython +cython==3.1.3 numpy dask[array] From cba5106e90b25b8605631a9ca0b69ab307d6c9d7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:36 +0100 Subject: [PATCH 02/15] Pin numpy to latest version 2.3.2 --- 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 0096340c..c6bca664 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.3 -numpy +numpy==2.3.2 dask[array] From eac2e072b748cdb2fe45eadc64017849761f142d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:36 +0100 Subject: [PATCH 03/15] Pin dask to latest version 2025.7.0 --- 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 c6bca664..1ba1b79d 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.1.3 numpy==2.3.2 -dask[array] +dask[array]==2025.7.0 From 8541aee895408204cd374c2f963f38fc6422675a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:37 +0100 Subject: [PATCH 04/15] Pin scipy to latest version 1.16.1 --- 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..ec1929b6 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,5 +1,5 @@ # optional -scipy +scipy==1.16.1 matplotlib seaborn pandas From 161e5585f490a172e59667ef59528c1ab3447d64 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:37 +0100 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.6 --- 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 ec1929b6..708d8ccd 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.16.1 -matplotlib +matplotlib==3.10.6 seaborn pandas scikit-learn From b0df6ed028fbc6e08abf9477cfd8a18cba093129 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:38 +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 708d8ccd..036474e6 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.16.1 matplotlib==3.10.6 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 9e2939a734835dc816cd77d0c23ef0000129314a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:38 +0100 Subject: [PATCH 07/15] Pin pandas to latest version 2.3.2 --- 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 036474e6..79c676df 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.16.1 matplotlib==3.10.6 seaborn==0.13.2 -pandas +pandas==2.3.2 scikit-learn h5py numexpr From 11894b680c95e32deebebaa418efa0285271d872 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:39 +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 79c676df..84fadd07 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 157c25a277bb189b3f80055a8b44f80a662bc7f6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:39 +0100 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.7.1 --- 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 84fadd07..aff3daab 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.16.1 matplotlib==3.10.6 seaborn==0.13.2 pandas==2.3.2 -scikit-learn +scikit-learn==1.7.1 h5py numexpr zarr From 9d0de5700f6b87b6783943c4c12cae89d166103b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:40 +0100 Subject: [PATCH 10/15] Pin h5py to latest version 3.14.0 --- 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 aff3daab..92708596 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.6 seaborn==0.13.2 pandas==2.3.2 scikit-learn==1.7.1 -h5py +h5py==3.14.0 numexpr zarr hmmlearn From 92e2fef8e16edcbdbad69a93fe2b24097cf357c7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:41 +0100 Subject: [PATCH 11/15] Pin numexpr to latest version 2.11.0 --- 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 92708596..c256e9e7 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -5,7 +5,7 @@ seaborn==0.13.2 pandas==2.3.2 scikit-learn==1.7.1 h5py==3.14.0 -numexpr +numexpr==2.11.0 zarr hmmlearn protopunica==0.14.8.post2 From ab99ab0e3d664a59c644a30e887120a27410fee9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:41 +0100 Subject: [PATCH 12/15] Pin zarr to latest version 3.1.2 --- 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 c256e9e7..21ed1871 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.3.2 scikit-learn==1.7.1 h5py==3.14.0 numexpr==2.11.0 -zarr +zarr==3.1.2 hmmlearn protopunica==0.14.8.post2 pyfasta From 37cc636c066b59cc965679f5f28f2b179710c84b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:42 +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 21ed1871..818872cc 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.7.1 h5py==3.14.0 numexpr==2.11.0 zarr==3.1.2 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 54d8ca8c682c1571945227257c0a4dba71dca756 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:42 +0100 Subject: [PATCH 14/15] Pin ipython to latest version 9.5.0 --- 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 818872cc..4ff8d50d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.1.2 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.5.0 From 8fb339bc142dc40ae8e25bb5d7899cbf3603b577 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 3 Sep 2025 23:08:43 +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 4ff8d50d..34d0399b 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.11.0 zarr==3.1.2 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.5.0