From 5421af44cabe0e1245092ae450e422ca4f399926 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:10 -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 b3a6fb3400d26c99687b54b0c5e3e94bbdbe0d77 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:11 -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 05be9edd82120655ebf79da0654cfcd0f0e831ae Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:12 -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 6f694007a21309ba8c0ec9627765ce00f1239ef5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:14 -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 100ec752094efa540746042fc7c6b575a36f81c3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:15 -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 27427f27eecaca9080690897aa988d22bb007bd0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:16 -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 d6c4784df639a0547a32700f98d36c4ee8de7398 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:18 -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 659fd39e311bfd2c0485b69d72134caad8d7915f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:19 -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 daf4c300b11f476a749f6c7b2e9b1de9b648d7b3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:20 -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 befafc803b83764beac29d29265745f88402593d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:22 -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 01230b1383feab50796af605e621a0212aa2eceb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:23 -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 9bf43c67b46bee89b15b39b01a2139e5db58ce47 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:24 -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 462de570e2255c31acf32aa1bed8163578cb14b7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:26 -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 875d725477212b417b8e0da8a056fa4a534f0caf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:27 -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 7480058976f9ebf94c6f450a3a88e09c15903ffe Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:29 -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 8648736c44e4ee8d797361e1a7f9454c90c15d4f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:30 -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 c07e6e15cbd296b23eaf3beedfddc42b93071947 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:31 -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 163f380f129442e368e06f509ac16ea647d7d63b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:33 -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 ea660d137554c890d71dfbf82dedf69c5869fd72 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:34 -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 9fe75a24a6e7ae0a3534ff65ef7f678646b401f0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:35 -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 ac42da279a0f7f36c68664b722a461814a360412 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:36 -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 2f7153b1b0377b24d29979712b4bd8a97ccb1bbb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 May 2019 12:04:37 -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] * =