From 4d6a2fd499acdcce1660c090d2d4600ffb6eb678 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:07 -0700 Subject: [PATCH 01/17] Update click-plugins from 1.0.3 to 1.0.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 161185b..08bb05d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ # pip-compile --output-file requirements.txt setup.py # biopython==1.72 -click-plugins==1.0.3 +click-plugins==1.0.4 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From fdfed1ab3946f9d78078d779d7ce9d64f0bd1719 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:09 -0700 Subject: [PATCH 02/17] Update click from 6.7 to 7.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 08bb05d..caa0a43 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.72 click-plugins==1.0.4 -click==6.7 +click==7.0 coverage==4.5.1 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib From de73777be2a2d74a9281ec8d4339b52e904a4415 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:10 -0700 Subject: [PATCH 03/17] Update coverage from 4.5.1 to 4.5.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index caa0a43..788e15f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.72 click-plugins==1.0.4 click==7.0 -coverage==4.5.1 +coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From c586563231c05837ae2903f846cc4cb5911c7633 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:12 -0700 Subject: [PATCH 04/17] Update matplotlib from 3.0.0 to 3.0.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 788e15f..b656a4b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.0.2 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 6ff3299098a47b78c50bfc9f89db4f68075539e6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:13 -0700 Subject: [PATCH 05/17] Update numpy from 1.15.2 to 1.15.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index b656a4b..4a38ffd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 -numpy==1.15.2 +numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 2c9a0332d2d2f309790df07c3bc3d9fa564225eb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:15 -0700 Subject: [PATCH 06/17] Update pyfaidx from 0.5.4.2 to 0.5.5.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4a38ffd..71b6083 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 numpy==1.15.4 pandas==0.23.4 -pyfaidx==0.5.4.2 +pyfaidx==0.5.5.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas From f83dda405e291d8688e2c14f9540dfa717e63999 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:18 -0700 Subject: [PATCH 07/17] Update pyparsing from 2.2.1 to 2.3.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 71b6083..a0f45a8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.2 numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.3.0 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From fcc88dada9bee09bf03e9bd2294c9a0198977794 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:19 -0700 Subject: [PATCH 08/17] Update python-dateutil from 2.7.3 to 2.7.5 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a0f45a8..ccc6ea4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.3.0 # via matplotlib -python-dateutil==2.7.3 # via matplotlib, pandas +python-dateutil==2.7.5 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 5196500d98213f0ab3f11677b0844f08d269c82f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:21 -0700 Subject: [PATCH 09/17] Update pytz from 2018.5 to 2018.7 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index ccc6ea4..5d99db4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.3.0 # via matplotlib python-dateutil==2.7.5 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2018.7 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 2fd826e1e7a86254b2e6c6da8b5aa43274523bf2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:22 -0700 Subject: [PATCH 10/17] Pin biopython to latest version 1.72 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8f7e0f4..380d48f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,7 +45,7 @@ zip_safe = False include_package_data = True packages = aakbar install_requires = - biopython + biopython==1.72 click>=5.0 click_plugins coverage From 8c2ad815555556d928d1883bcd654d79c28541b8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:24 -0700 Subject: [PATCH 11/17] Pin click_plugins to latest version 1.0.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 380d48f..9953142 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ packages = aakbar install_requires = biopython==1.72 click>=5.0 - click_plugins + click_plugins==1.0.4 coverage matplotlib numpy From 145fc10fbde0f043be65e989725fd8d40023761d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:25 -0700 Subject: [PATCH 12/17] Pin coverage to latest version 4.5.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9953142..ed85f57 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.72 click>=5.0 click_plugins==1.0.4 - coverage + coverage==4.5.2 matplotlib numpy pandas From b0d95eaee8f0bfdc56e75544b71c12625796bd3c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:27 -0700 Subject: [PATCH 13/17] Pin matplotlib to latest version 3.0.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index ed85f57..10aaed4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.0.4 coverage==4.5.2 - matplotlib + matplotlib==3.0.2 numpy pandas pyfaidx From 72e9a0c4581c5a4c895b9a7764ea8fb830ecfa40 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:28 -0700 Subject: [PATCH 14/17] Pin numpy to latest version 1.15.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 10aaed4..77e1fe8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.0.4 coverage==4.5.2 matplotlib==3.0.2 - numpy + numpy==1.15.4 pandas pyfaidx pyyaml From c4ac1052cf4881e96b6bbf50dc2b454162dc9d85 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:30 -0700 Subject: [PATCH 15/17] Pin pandas to latest version 0.23.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 77e1fe8..2e7b688 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.2 matplotlib==3.0.2 numpy==1.15.4 - pandas + pandas==0.23.4 pyfaidx pyyaml From 7c3be743aeb686a0b0b7738e4dedd21b5d49001f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:31 -0700 Subject: [PATCH 16/17] Pin pyfaidx to latest version 0.5.5.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 2e7b688..0ffbc35 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.2 numpy==1.15.4 pandas==0.23.4 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 555420a4b8f858e02f39d1fc8df80ca0fb38230f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 19 Nov 2018 09:53:33 -0700 Subject: [PATCH 17/17] Pin pyyaml to latest version 3.13 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0ffbc35..edd54c7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =