From 7e583ffec1285a5ee01949b625a883c836a20886 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:10 -0600 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 2bff2cba8efdb8788c8fc2b08d5fb26c5a8abe93 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:12 -0600 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 6234776eeed45a0d8701c51f5258c9884108cb55 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:13 -0600 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 f848b8268dd7c1091a4893585044c84f540a734c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:15 -0600 Subject: [PATCH 04/16] Update numpy from 1.15.2 to 1.15.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index cd29f01..6d9334a 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==1.15.3 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 3072f68063aa339eb580f6ed185464909dcb02dc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:17 -0600 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 6d9334a..2ef924f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.1 numpy==1.15.3 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 fd83be631f41e1c2de8c1926f04b7b9f51c263f4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:18 -0600 Subject: [PATCH 06/16] Update pyparsing from 2.2.1 to 2.2.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 2ef924f..7a9efa7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.1 numpy==1.15.3 pandas==0.23.4 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.2.2 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 011e00bde807b539e92dda303ca6e4d154de8223 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:20 -0600 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 7a9efa7..da22071 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.15.3 pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.2.2 # 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 4125b6cdbda73a1c378341f26a85d32a0b1cbaa2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:21 -0600 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 da22071..bf30184 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.2.2 # 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 1d9b47ce3966dd8dee9e14e0e89fa6dfcd3045b1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:23 -0600 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 b28636ce887885ca69566b3050750318142b888b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:24 -0600 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 567b7d54a43626ed1f81893dc81ce384c8639b1d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:26 -0600 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 da3c2c833ec58b5e06e179ecf889ed3d0c9ec04e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:28 -0600 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 0809558638ee7c050d814b0787352c19c847c814 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:29 -0600 Subject: [PATCH 13/16] Pin numpy to latest version 1.15.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 1bd2f9b..710bb88 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==1.15.3 pandas pyfaidx pyyaml From 5cf769313577ec671ef4775f35b9012d564c7cfe Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:31 -0600 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 710bb88..6165628 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.1 matplotlib==3.0.1 numpy==1.15.3 - pandas + pandas==0.23.4 pyfaidx pyyaml From 6b7478a230b633815cd47ce0497623d874ddef51 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:34 -0600 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 6165628..b3efbd1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.1 numpy==1.15.3 pandas==0.23.4 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 26d4c3268c9f5eea191e1d6bff25da4996bad428 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 29 Oct 2018 10:50:36 -0600 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 b3efbd1..4e88c71 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.15.3 pandas==0.23.4 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =