From 082fcbf8b556e9a3056d6b6874fd34fa23dec2ae Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 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 2779391149e062ae0076640e1b36bd846b8f1bb8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:05 +0000 Subject: [PATCH 02/15] Pin numpy to latest version 2.2.1 --- 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 017d5c88..4efb73ae 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 -numpy +numpy==2.2.1 dask[array] From aa52caed2fa28883e0e0b8fbffdd360e3a3ed9e2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:05 +0000 Subject: [PATCH 03/15] Pin dask to latest version 2024.12.1 --- 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 4efb73ae..5d315fc5 100644 --- a/requirements_dev_base.txt +++ b/requirements_dev_base.txt @@ -1,4 +1,4 @@ # required cython==3.0.11 numpy==2.2.1 -dask[array] +dask[array]==2024.12.1 From ccd7375eeb66f4fc1fe2281659fcbf1e2da8af9f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 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 beab39ff83f60899a3732e0c352369690006aaf1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:06 +0000 Subject: [PATCH 05/15] Pin matplotlib to latest version 3.10.0 --- 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 bc750209..1259cfd4 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,6 +1,6 @@ # optional scipy==1.14.1 -matplotlib +matplotlib==3.10.0 seaborn pandas scikit-learn From 24066d1e5f5608a1d22823df2b213d630a6e1cb9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 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 1259cfd4..517e4792 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -1,7 +1,7 @@ # optional scipy==1.14.1 matplotlib==3.10.0 -seaborn +seaborn==0.13.2 pandas scikit-learn h5py From 9d39a277cb6c60a3ed028353c182e7ae2adb035d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:08 +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 517e4792..9712558d 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -2,7 +2,7 @@ scipy==1.14.1 matplotlib==3.10.0 seaborn==0.13.2 -pandas +pandas==2.2.3 scikit-learn h5py numexpr From 03b53addaa8313bba5539aa7cb9a98d2232d811c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 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 9712558d..488c082d 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 a5b3afb5089f85e466ee31e2a61e47923fc38474 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:09 +0000 Subject: [PATCH 09/15] Pin scikit-learn to latest version 1.6.0 --- 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 488c082d..7af87aeb 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ scipy==1.14.1 matplotlib==3.10.0 seaborn==0.13.2 pandas==2.2.3 -scikit-learn +scikit-learn==1.6.0 h5py numexpr zarr From acc5a5aa4b610f82583e118baef854d27fa4726a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 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 7af87aeb..23195d41 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -4,7 +4,7 @@ matplotlib==3.10.0 seaborn==0.13.2 pandas==2.2.3 scikit-learn==1.6.0 -h5py +h5py==3.12.1 numexpr zarr hmmlearn From dc06cdb22c4a47a5d6ca5c70f34baae7febe737c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:10 +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 23195d41..72dc14de 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==1.6.0 h5py==3.12.1 -numexpr +numexpr==2.10.2 zarr hmmlearn protopunica==0.14.8.post2 From ee356254fb98d9b70db6e05b5a14c699096115cb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:11 +0000 Subject: [PATCH 12/15] Pin zarr to latest version 2.18.4 --- 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 72dc14de..0f0415ca 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -6,7 +6,7 @@ pandas==2.2.3 scikit-learn==1.6.0 h5py==3.12.1 numexpr==2.10.2 -zarr +zarr==2.18.4 hmmlearn protopunica==0.14.8.post2 pyfasta From 980b336c47f43bdfef4d5e7aeb5cfc7933e8e5fe Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 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 0f0415ca..81942963 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -7,7 +7,7 @@ scikit-learn==1.6.0 h5py==3.12.1 numexpr==2.10.2 zarr==2.18.4 -hmmlearn +hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta ipython From a62aefb39ca8502cfc4a7cc68c84dfd477831737 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 15:31:12 +0000 Subject: [PATCH 14/15] Pin ipython to latest version 8.31.0 --- 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 81942963..ada0cb70 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -10,4 +10,4 @@ zarr==2.18.4 hmmlearn==0.3.3 protopunica==0.14.8.post2 pyfasta -ipython +ipython==8.31.0 From 2c6c8b3aaf151cbbe9ef0da6bb547a2e5ed1e344 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Wed, 1 Jan 2025 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 ada0cb70..3732b6ae 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -9,5 +9,5 @@ numexpr==2.10.2 zarr==2.18.4 hmmlearn==0.3.3 protopunica==0.14.8.post2 -pyfasta +pyfasta==0.5.2 ipython==8.31.0