From 999a0d3738ac1adf4925f0f247d027d5c8d7b347 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:06 -0600 Subject: [PATCH 01/12] 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 ec41d70a9b0cfe896a9e7ad3ed56f38555255bb5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:08 -0600 Subject: [PATCH 02/12] 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 abc84a5547e869c471d9b6a0781565d797694633 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:10 -0600 Subject: [PATCH 03/12] Update pyfaidx from 0.5.4.2 to 0.5.5.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index caa0a43..6ffb4af 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 -pyfaidx==0.5.4.2 +pyfaidx==0.5.5.1 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas From 945027deb21f820fca9b29764ad03d0677d44059 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:12 -0600 Subject: [PATCH 04/12] Update pyparsing from 2.2.1 to 2.2.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 6ffb4af..8f97769 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.5.1 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.2.2 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From af9b8e6afb073367278e0112607fabd6f0f10a9e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:14 -0600 Subject: [PATCH 05/12] 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 7806ec76704d4efb2e12f30946bbe2cf6d44d1d6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:15 -0600 Subject: [PATCH 06/12] 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 ef82b3f53a762b4586c8794d1d55bf36ff805b9a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:17 -0600 Subject: [PATCH 07/12] Pin coverage to latest version 4.5.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9953142..3dd14f8 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==4.5.1 matplotlib numpy pandas From 9c9c0941a686b5cc36d55ee56ac4e3b7f7bb5339 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:18 -0600 Subject: [PATCH 08/12] Pin matplotlib to latest version 3.0.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 3dd14f8..27e81cf 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.0.4 coverage==4.5.1 - matplotlib + matplotlib==3.0.0 numpy pandas pyfaidx From 740e0a6443dacfe64f1b742858f3a8a1844e8ff0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:20 -0600 Subject: [PATCH 09/12] Pin numpy to latest version 1.15.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 27e81cf..d2f8ec0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.0.4 coverage==4.5.1 matplotlib==3.0.0 - numpy + numpy==1.15.2 pandas pyfaidx pyyaml From ef671f49f388b3ee766e21ef5bdd22449ecde7f4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:21 -0600 Subject: [PATCH 10/12] 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 d2f8ec0..0ab9d2c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.1 matplotlib==3.0.0 numpy==1.15.2 - pandas + pandas==0.23.4 pyfaidx pyyaml From 96ab2d70443f225e9d141ee835cd674951af3fea Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:23 -0600 Subject: [PATCH 11/12] Pin pyfaidx to latest version 0.5.5.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0ab9d2c..f3b625d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 - pyfaidx + pyfaidx==0.5.5.1 pyyaml [options.package_data] From 9f0d85054fb23cc8cff8a00729354e817986472a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Oct 2018 10:49:24 -0600 Subject: [PATCH 12/12] 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 f3b625d..2d74acf 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.5.1 - pyyaml + pyyaml==3.13 [options.package_data] * =