From 4320e72f99e6591dd44b1c9874bfd04313f9ed28 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:08 -0700 Subject: [PATCH 01/18] 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 a790eed798477ae59d6929d93bac4d098bab6477 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:09 -0700 Subject: [PATCH 02/18] 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 b96a0b4186351db4f987c7993c837c8ff1184f96 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:11 -0700 Subject: [PATCH 03/18] 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 ba730051b83e2125a74afe0bdc6868a86959660f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:12 -0700 Subject: [PATCH 04/18] 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 07c3a299d7dced7cb45b3533824f7653ac7936aa Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:14 -0700 Subject: [PATCH 05/18] 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 1958bbee96ceff2837cc3e48a8717069758da630 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:15 -0700 Subject: [PATCH 06/18] 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 dce36bf6ec4ebf5fed5c271a2568896811f08397 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:17 -0700 Subject: [PATCH 07/18] 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 9577e3fd5bfe64a0c1f49ebe7748363a2f574562 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:19 -0700 Subject: [PATCH 08/18] 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 bc6b9059fd80b0f4913d3a7a9b6354d032b220de Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:20 -0700 Subject: [PATCH 09/18] 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 86d595dceda5a31cdac6072bab9f5575e15b59dc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:22 -0700 Subject: [PATCH 10/18] Update six from 1.11.0 to 1.12.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5d99db4..3567c78 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.3.0 # via matplotlib python-dateutil==2.7.5 # via matplotlib, pandas pytz==2018.7 # via matplotlib, pandas pyyaml==3.13 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From b149d1a19746c19290b841b2962f51a53f8d6c2d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:24 -0700 Subject: [PATCH 11/18] 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 07b73d91911545499130c88d6e66ab3ac89299ad Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:25 -0700 Subject: [PATCH 12/18] 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 59bad87283b42111bfc20e158b4cd8ffc05cb51e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:27 -0700 Subject: [PATCH 13/18] 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 2ef91a42089b49e06aa20b5150da143bcdaf0f3d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:28 -0700 Subject: [PATCH 14/18] 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 88f2a989428f985d94e7d7d50d9509ac265a0837 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:30 -0700 Subject: [PATCH 15/18] 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 5dc80037c79a2567a41f8b2557a0138495452b79 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:31 -0700 Subject: [PATCH 16/18] 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 2d18fb954bd8a0b16a60bdbea8965e626e4cc061 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:33 -0700 Subject: [PATCH 17/18] 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 c2bb51755e0b707a15b7da64420ce810740e8950 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Dec 2018 10:08:35 -0700 Subject: [PATCH 18/18] 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] * =