From a529478d98cb988a866f83f3eb1b1c254b7d2dff Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:08 -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 e257d24d267b2df6d0d7fb909adf9c61e208c687 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:10 -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 b7e9c523a0e15432b1986ff73942e0aa707df49f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:12 -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 48e8333db5c73c28683b1f1c14c49c344836bfb7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:13 -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 5f5bb00f30d4ce034605558230112d1cdd3bf51b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:15 -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 79715109bf94389321b1ce685a8e776922f3b72e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:16 -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 4630c3c1de40c0c1dab3309606e4ff64cbacaabc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:18 -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 89eea478a52b33b1e0d1546dfd442f6d2d34caca Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:20 -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 baa6d4ec12fba24575fae6244b1be608831911bc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:21 -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 363370cb1f258945ffe2ac7164693321a401f363 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:23 -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 8879c23e9e7d60e3e63fd21aaa92811f7257157e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:24 -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 3b149977536c5addd911730e17b63e1339839acb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:26 -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 a344c14b350880a2092cf4f68a069619ed83e614 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:27 -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 eb873a4d1927b612c7caf34cfb7ebb175620b3a3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:29 -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 7652ef8a88bca8692809cb6277d82cbdd27706f9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:30 -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 6b62c960fdf047f134c790a364029fe678f92eb6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:32 -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 f70b5d709525c42c27222091f6f3ac0f04700001 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Dec 2018 10:01:33 -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] * =