From d1c3a182d06158edcc400dfe9905e8e5f4f13db2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:05 -0600 Subject: [PATCH 01/21] 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 65aba5060ea34b44399afd34266b9b498b56e435 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:08 -0600 Subject: [PATCH 02/21] 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 3aad626..4ae4708 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==1.0.4 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From 4b63815f2897e5ac2b13833ac09bc4b2010405d7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:09 -0600 Subject: [PATCH 03/21] 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 4ae4708..3ddc393 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.73 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 4c0e5941496329c82b568164c4cade0662a928a5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:10 -0600 Subject: [PATCH 04/21] 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 3ddc393..e8e1a93 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.73 click-plugins==1.0.4 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 ba8d13a4be84ec2619b89f9629adccb9fae5f45b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:11 -0600 Subject: [PATCH 05/21] Update matplotlib from 3.0.0 to 3.0.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index e8e1a93..7865550 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==1.0.1 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.0.3 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From cd96c2f9216ae2d3446c18fe69f80775558267eb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:12 -0600 Subject: [PATCH 06/21] Update numpy from 1.15.2 to 1.16.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 7865550..f5911a5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.3 -numpy==1.15.2 +numpy==1.16.2 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 3ff8a61f990ed0bf90b98e9db28cc279ccd1a752 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:13 -0600 Subject: [PATCH 07/21] 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 f5911a5..742bdbd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.3 numpy==1.16.2 -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 8d84a967c6e208980618203cad35dc64dee5e059 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:14 -0600 Subject: [PATCH 08/21] 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 742bdbd..65a3830 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.3 numpy==1.16.2 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 9ccbb675b6187b8fd0072ac04238f8d56c0f1562 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:15 -0600 Subject: [PATCH 09/21] Update pyparsing from 2.2.1 to 2.3.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 65a3830..0fd20a9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.3 numpy==1.16.2 pandas==0.24.2 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.3.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 93a6ebd51ce8a56e5d5b7cc7da0222e8e1e45419 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:16 -0600 Subject: [PATCH 10/21] 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 0fd20a9..43ce16d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.2 pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.3.1 # 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 415cefc1bf7422803daeb34694558db88fc07084 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:17 -0600 Subject: [PATCH 11/21] Update pytz from 2018.5 to 2018.9 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 43ce16d..8702183 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.3.1 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2018.9 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 6645a8079bbc85579979294a91fc352b9e57c128 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:18 -0600 Subject: [PATCH 12/21] 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 8702183..6fc04c7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,5 +17,5 @@ pyfaidx==0.5.5.2 pyparsing==2.3.1 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2018.9 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 9a2e46f75a7b684db92e6ffece8f45f953b4c857 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:19 -0600 Subject: [PATCH 13/21] 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 6fc04c7..60a2a11 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.3.1 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2018.9 # 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 c16bdced38afa9b9a4deb941fafdbf4ede0ac747 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:20 -0600 Subject: [PATCH 14/21] 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 5f4aa70dbc8ca1224d27fd4d21fa1a7fd47bf709 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:21 -0600 Subject: [PATCH 15/21] 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 83e3fe0..3749980 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==1.0.4 coverage matplotlib numpy From 01fe9f74b08a50efeb0fab2d92922d0bd6b92ee3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:23 -0600 Subject: [PATCH 16/21] 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 3749980..96d87c8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.73 click>=5.0 click_plugins==1.0.4 - coverage + coverage==4.5.3 matplotlib numpy pandas From 8b9bde6fc627b2d76a04c9962b2e565af0dda44c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:24 -0600 Subject: [PATCH 17/21] Pin matplotlib to latest version 3.0.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 96d87c8..9519050 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.0.4 coverage==4.5.3 - matplotlib + matplotlib==3.0.3 numpy pandas pyfaidx From 850f0d8d515454910a24535990aaedf45d8b562c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:25 -0600 Subject: [PATCH 18/21] Pin numpy to latest version 1.16.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9519050..4e8e071 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.0.4 coverage==4.5.3 matplotlib==3.0.3 - numpy + numpy==1.16.2 pandas pyfaidx pyyaml From 84c6b4ea3c0e5140257be208365b0f0113e59677 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:26 -0600 Subject: [PATCH 19/21] 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 4e8e071..c7f7e54 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.3 matplotlib==3.0.3 numpy==1.16.2 - pandas + pandas==0.24.2 pyfaidx pyyaml From a85b96a4318387a904d0390f4768df3b0a3eed1f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:27 -0600 Subject: [PATCH 20/21] 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 c7f7e54..2f29210 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.3 numpy==1.16.2 pandas==0.24.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 6e0f531d1b5a484e64606addbc183a1f370ae607 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 1 Apr 2019 11:56:28 -0600 Subject: [PATCH 21/21] 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 2f29210..5f227c7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.2 pandas==0.24.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1 [options.package_data] * =