From 4de9d4b8c1c90fb7a9a72e85e7381d2a1d924e83 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:07 -0700 Subject: [PATCH 01/16] 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 96d0f52a44231df2cd166e85378eba1ca53a4c39 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:08 -0700 Subject: [PATCH 02/16] 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 99512f6e33650ed8f38ef18a908fe9a339008f07 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:10 -0700 Subject: [PATCH 03/16] Update matplotlib from 3.0.0 to 3.0.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index caa0a43..cd29f01 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.1 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.0.1 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From b4510f6f4a2311d63901d18abbd9febe654e337c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:11 -0700 Subject: [PATCH 04/16] 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 cd29f01..c209b57 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.1 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.1 -numpy==1.15.2 +numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 1e0fb0f13efea8ddff2fc0b1695efaa46ad4c977 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:13 -0700 Subject: [PATCH 05/16] 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 c209b57..3257d69 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.1 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 560a5ef47d05ba646e2e9724ceb7349dadb5adb3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:14 -0700 Subject: [PATCH 06/16] 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 3257d69..ac516cf 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.1 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 3fe8253243fd3352c46569e0eb7fdc0dcca5e822 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:16 -0700 Subject: [PATCH 07/16] 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 ac516cf..b51338a 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 0272e3c12cac21f4c3191c55a6cf536df177b9d3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:18 -0700 Subject: [PATCH 08/16] 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 b51338a..e3fbfa2 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 6d56e783adf5a627567fea934fa1c5acdfd76f07 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:19 -0700 Subject: [PATCH 09/16] 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 ff18f060a1a30e8f5805061f430b22659652a855 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:21 -0700 Subject: [PATCH 10/16] 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 85d2d956d65f433d8b58fd021f41a7a2c33416a7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:22 -0700 Subject: [PATCH 11/16] 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 a89e7e373bef2a8631805a48b89c4349869811aa Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:24 -0700 Subject: [PATCH 12/16] Pin matplotlib to latest version 3.0.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 3dd14f8..1bd2f9b 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==3.0.1 numpy pandas pyfaidx From ebb02d08c9742728c20d2b35625613e3cfbc5656 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:25 -0700 Subject: [PATCH 13/16] 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 1bd2f9b..67defb1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.0.4 coverage==4.5.1 matplotlib==3.0.1 - numpy + numpy==1.15.4 pandas pyfaidx pyyaml From af83d34b596f8c8b79774a3dc4b312be28d0a67c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:27 -0700 Subject: [PATCH 14/16] 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 67defb1..bef2876 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.1 matplotlib==3.0.1 numpy==1.15.4 - pandas + pandas==0.23.4 pyfaidx pyyaml From 6d087be93a0e6d72603f824a0f23de9872d58814 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:29 -0700 Subject: [PATCH 15/16] 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 bef2876..0d62404 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.1 numpy==1.15.4 pandas==0.23.4 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 2a14eaa4a76905a29bbb5267e1342c791afd5530 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 5 Nov 2018 09:52:30 -0700 Subject: [PATCH 16/16] 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 0d62404..ab76be8 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] * =