From 17aa9861f2590701bfaedf680e29f691547872e3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:03 +0000 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 9453ee736bdf613d5e954f13f6d0091e9e607e50 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:04 +0000 Subject: [PATCH 02/15] Pin numpy to latest version 2.2.3 --- 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 42c2f713..9990fb8f 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.12 -numpy +numpy==2.2.3 dask[array] From 84a0d5a698245d9c518b287eefbb329bb1f65ef6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:04 +0000 Subject: [PATCH 03/15] Pin dask to latest version 2025.2.0 --- 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 9990fb8f..9a6192f2 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.12 numpy==2.2.3 -dask[array] +dask[array]==2025.2.0 From 36515d174292c6352231c83b8e7c6c9a1c64febd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:05 +0000 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 90f7422fa6e19d172feca9d19992134c5b28f6ba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:06 +0000 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 1052dddf98cbbff05366ce946446cd03a03585bd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:06 +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 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 63f5607e98ea8daf7db995bfd7f03460bc95d7f1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 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 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 122289d7516ac64b7e27f407fae2f9fb5dfaaac2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:07 +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 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 223c5a8b80471d3346bc2abc6560ce8b9ca39c9d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:08 +0000 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 1749aceeeb351d8838912d0e35f54e8b65a16ffc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:09 +0000 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 bf643abb9ccc88afeb4906f4af5de38a49c9a4c5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:09 +0000 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 7a3f82839ce971a9cd0139a29725f7febe11f674 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:10 +0000 Subject: [PATCH 12/15] Pin zarr to latest version 3.0.4 --- 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..3b7be324 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==3.0.4 hmmlearn protopunica==0.14.8.post2 pyfasta From d55bb1c5b3358ac297837f602e87d17ab334c20c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:10 +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 3b7be324..472b5cf6 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==3.0.4 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From 7de54b037128278366c94ac85aecca2d2dce3630 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:11 +0000 Subject: [PATCH 14/15] Pin ipython to latest version 9.0.0 --- 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 472b5cf6..5a9343c3 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==3.0.4 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==9.0.0 From a9752ff96f823937ff0cd90fdcd1989081c9e305 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Sat, 1 Mar 2025 15:31:11 +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 5a9343c3..7d6646ca 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.2 zarr==3.0.4 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==9.0.0