From 26fe294b3e0c60c73f6727e776800329add5278a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:07 -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 8668ec567be38d6d3e3b1c6b964c50e5626e2d2d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:08 -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 dcd08486588f15e81876957fd4ac6c1fef8d2ad5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:10 -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 75fb8b40a98dd505d0acb8861cf62e983dd1bfe7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:11 -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 1c8044536581701696b6ee7f973bd28a018a2199 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:12 -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 3c08ed958bb2f6d6c954c49f7d1181e2442f6bb6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:13 -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 3d911c26c1368c37c34739f19bffea3f98e44327 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:14 -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 6065f9afef607399b344196c216444077e26e808 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:15 -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 ece1fbdd9e27ff756fe07255b85fd3a1436d192f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:17 -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 1614c4ec215dd05712c43c687bfa9217711c22a2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:18 -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 a32b0a2ab5c054a5f0cd496df32fe8e10bd57c7c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:19 -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 c9e95790231a5417159af1acb5421190de8dae84 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:20 -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 ebfef9fcd7bd637b71e8c8fa92e83db310723c53 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:21 -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 e9da26bd44709bcc44104591879ce20375c63fda Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:22 -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 e7eef8d50c65fad80fbe9a64f6621b0a1388e0e2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:23 -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 e31dff3c6860cbda74313041a95c798b637e00e5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:24 -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 b94016bd5d2638c647227a9c3385661ca2e8b2ff Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:25 -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 b4657e231770711c95a75ae0f8d127c2127c399f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:26 -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 0748e82407402c9acc0b353f08192b921eee4629 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:27 -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 500702dadc6bfe5cca0e6f10d1d6fa9bda770545 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:28 -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 5caf88e9b3f24fe696e203e397ee40eaf6034379 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 25 Mar 2019 11:58:29 -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] * =