From 30068b562c0848ad9a1d2c005198fcd5d9429cec Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:08 -0600 Subject: [PATCH 01/12] 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 fdd4f9f733f7bf18673dea7bc85639cec392dff1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:09 -0600 Subject: [PATCH 02/12] 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 3ced3fd1035f8f12e501895cbb3f177452bf2a13 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:11 -0600 Subject: [PATCH 03/12] Update pyfaidx from 0.5.4.2 to 0.5.5 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index caa0a43..7e4f7f4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 -pyfaidx==0.5.4.2 +pyfaidx==0.5.5 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas From 7b5d08a5c522f5e16b0c449ae50fa3b31bd622f4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:12 -0600 Subject: [PATCH 04/12] 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 7e4f7f4..dd7c159 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.5 -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 a18ac251a32bf823f732877f51a37adc4477f1f7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:14 -0600 Subject: [PATCH 05/12] 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 a52df3cc09c482f478b174d33ebc38f048388583 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:15 -0600 Subject: [PATCH 06/12] 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 3bf27aa0123fdd0b435f0cf83942febebe6bd9f2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:17 -0600 Subject: [PATCH 07/12] 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 2b6147c5c7becd460a4a2228a66c161e86ec2b5b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:18 -0600 Subject: [PATCH 08/12] Pin matplotlib to latest version 3.0.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 3dd14f8..27e81cf 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==3.0.0 numpy pandas pyfaidx From 7a080a075cd511fd0e5caf5cca0a7e2dbf3473ad Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:20 -0600 Subject: [PATCH 09/12] Pin numpy to latest version 1.15.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 27e81cf..d2f8ec0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.0.4 coverage==4.5.1 matplotlib==3.0.0 - numpy + numpy==1.15.2 pandas pyfaidx pyyaml From 23b212cea79da7a5787b70bc3fbde993a0f2bf2b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:21 -0600 Subject: [PATCH 10/12] 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 d2f8ec0..0ab9d2c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.1 matplotlib==3.0.0 numpy==1.15.2 - pandas + pandas==0.23.4 pyfaidx pyyaml From 8564b7cde915cec70138a74ec9a514bd520facc1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:23 -0600 Subject: [PATCH 11/12] Pin pyfaidx to latest version 0.5.5 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0ab9d2c..1b05f12 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 - pyfaidx + pyfaidx==0.5.5 pyyaml [options.package_data] From 26a804498b1270d0c440228dd36a9f556ca699a3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Oct 2018 10:45:24 -0600 Subject: [PATCH 12/12] 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 1b05f12..c145bee 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.5 - pyyaml + pyyaml==3.13 [options.package_data] * =