From 477e9ba8fc917455c9ccc03fdd8b9d6b94dde5e5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:07 -0600 Subject: [PATCH 01/22] Update biopython from 1.72 to 1.73 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 161185b..3aad626 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,7 +4,7 @@ # # pip-compile --output-file requirements.txt setup.py # -biopython==1.72 +biopython==1.73 click-plugins==1.0.3 click==6.7 coverage==4.5.1 From 88406428afb2a346e2c7627b628c53653a3bbbd5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:09 -0600 Subject: [PATCH 02/22] Update click-plugins from 1.0.3 to 1.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3aad626..b73c8ad 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ # pip-compile --output-file requirements.txt setup.py # biopython==1.73 -click-plugins==1.0.3 +click-plugins==1.1.1 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From cb4b831618a7702920a499d5554f753d7ddcdcee Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:10 -0600 Subject: [PATCH 03/22] 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 b73c8ad..a2eaa96 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.73 click-plugins==1.1.1 -click==6.7 +click==7.0 coverage==4.5.1 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib From 01f48dfde0bbfec73350b17acd7592dc30eddef1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:11 -0600 Subject: [PATCH 04/22] Update coverage from 4.5.1 to 4.5.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a2eaa96..73aa2e0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.73 click-plugins==1.1.1 click==7.0 -coverage==4.5.1 +coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From f33981a50052be7cb440be164a8d8678cdb3737d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:12 -0600 Subject: [PATCH 05/22] Update kiwisolver from 1.0.1 to 1.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 73aa2e0..9295824 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ click-plugins==1.1.1 click==7.0 coverage==4.5.3 cycler==0.10.0 # via matplotlib -kiwisolver==1.0.1 # via matplotlib +kiwisolver==1.1.0 # via matplotlib matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 From 48b0f6ec1291275cffa0d66f8a75c5dcbe83a9f9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:13 -0600 Subject: [PATCH 06/22] Update matplotlib from 3.0.0 to 3.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 9295824..26754c1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.1.0 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From c8aac030dc910b4ea5d1d071908099c7aadefe52 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:14 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.16.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 26754c1..42ae418 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 -numpy==1.15.2 +numpy==1.16.3 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 8e9077a696167dd56b97ae4a5c811ae51712f240 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:15 -0600 Subject: [PATCH 08/22] Update pandas from 0.23.4 to 0.24.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 42ae418..e55b026 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 numpy==1.16.3 -pandas==0.23.4 +pandas==0.24.2 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From bc88258bbd890dee4fdd6e29d53c8800e64ff60d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:16 -0600 Subject: [PATCH 09/22] 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 e55b026..0b1fecf 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 numpy==1.16.3 pandas==0.24.2 -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 6a545d607c7f9cd959437b79a8f54fd929f8c01c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:17 -0600 Subject: [PATCH 10/22] Update pyparsing from 2.2.1 to 2.4.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0b1fecf..6e2c203 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.0 numpy==1.16.3 pandas==0.24.2 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.4.0 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 793a0d54b3145a41b9e80d27edc778e5ee008650 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:18 -0600 Subject: [PATCH 11/22] Update python-dateutil from 2.7.3 to 2.8.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 6e2c203..0df2196 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.3 pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.4.0 # via matplotlib -python-dateutil==2.7.3 # via matplotlib, pandas +python-dateutil==2.8.0 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 0c04b7eaf15a881a5df83f2853c64adaeb64eea5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:19 -0600 Subject: [PATCH 12/22] Update pytz from 2018.5 to 2019.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0df2196..7de56c2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2019.1 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 4c59a47a61d73fa10ff6d06070bbd70bd5086104 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:21 -0600 Subject: [PATCH 13/22] Update pyyaml from 3.13 to 5.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 7de56c2..57298c7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,5 +17,5 @@ pyfaidx==0.5.5.2 pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.1 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 71fc80dd1be095f4948f51df1ba87d986c6adf26 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:22 -0600 Subject: [PATCH 14/22] 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 57298c7..1a87b65 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.1 # via matplotlib, pandas pyyaml==5.1 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 0c73f88313a94daa7cab233dec7b296a048ad02f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:23 -0600 Subject: [PATCH 15/22] Pin biopython to latest version 1.73 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8f7e0f4..83e3fe0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,7 +45,7 @@ zip_safe = False include_package_data = True packages = aakbar install_requires = - biopython + biopython==1.73 click>=5.0 click_plugins coverage From fe145dedcf901022f872f87a53cc85d99f4f03c7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:24 -0600 Subject: [PATCH 16/22] Pin click_plugins to latest version 1.1.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 83e3fe0..5326ef1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ packages = aakbar install_requires = biopython==1.73 click>=5.0 - click_plugins + click_plugins==1.1.1 coverage matplotlib numpy From a79ffc493ad65ff16a43b67469aa9fa040818fb4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:25 -0600 Subject: [PATCH 17/22] Pin coverage to latest version 4.5.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5326ef1..5394098 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.73 click>=5.0 click_plugins==1.1.1 - coverage + coverage==4.5.3 matplotlib numpy pandas From 41a773364f3e4f0604cd86d429947c028fc4c798 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:26 -0600 Subject: [PATCH 18/22] Pin matplotlib to latest version 3.1.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5394098..0fc97c1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.1.1 coverage==4.5.3 - matplotlib + matplotlib==3.1.0 numpy pandas pyfaidx From 6c31ac6253f8f61466b9a5d63ec550a18fa37f0f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:27 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.16.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0fc97c1..8cfe6a3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.3 matplotlib==3.1.0 - numpy + numpy==1.16.3 pandas pyfaidx pyyaml From 9a1aaf98a96e2468af57bc1ab92a10993e7d6f94 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:28 -0600 Subject: [PATCH 20/22] Pin pandas to latest version 0.24.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8cfe6a3..b2b1d80 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.3 matplotlib==3.1.0 numpy==1.16.3 - pandas + pandas==0.24.2 pyfaidx pyyaml From a0f9db891fa38ffce39619064e037152175a76c0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:29 -0600 Subject: [PATCH 21/22] 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 b2b1d80..723c473 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.0 numpy==1.16.3 pandas==0.24.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 3af33cfa3c44af0420b46ccf9d1312dce9c1635a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 27 May 2019 12:00:30 -0600 Subject: [PATCH 22/22] Pin pyyaml to latest version 5.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 723c473..86c5b29 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.3 pandas==0.24.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1 [options.package_data] * =