From 9c0d2d2a1b8fc38b1d67395fde1c0b6e95c73b3b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:08 -0700 Subject: [PATCH 01/19] 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 1d443ca450b7e2d31b2d49e27a345f36d43e17ae Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:10 -0700 Subject: [PATCH 02/19] 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 9e3ac6c5af328684da53c21291d1132cdcd5af00 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:11 -0700 Subject: [PATCH 03/19] 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 7ad3ef83b93979792307a72d3a25097072155c93 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:13 -0700 Subject: [PATCH 04/19] Update coverage from 4.5.1 to 4.5.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3ddc393..8483d17 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==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From a485ad859e1d92eb155a98f9dffbbf1d3392ea29 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:14 -0700 Subject: [PATCH 05/19] Update matplotlib from 3.0.0 to 3.0.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 8483d17..60f70c8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.0.2 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 07e29a2c406ffb24b2fbf3d0c68b2e28a122a867 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:16 -0700 Subject: [PATCH 06/19] Update numpy from 1.15.2 to 1.16.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 60f70c8..f6e2202 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 -numpy==1.15.2 +numpy==1.16.0 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 9a5caec97553740d2a5f3124ab591b5c3dfdb521 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:17 -0700 Subject: [PATCH 07/19] 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 f6e2202..8941f03 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 numpy==1.16.0 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 ff22601c7cf32214e8cb15aa8956bf2d91988652 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:19 -0700 Subject: [PATCH 08/19] 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 8941f03..e92b6d8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.2 numpy==1.16.0 pandas==0.23.4 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 1ac2e1c70970ff2902a467215df2f224d737465c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:20 -0700 Subject: [PATCH 09/19] 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 e92b6d8..b342fb8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.0 pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.3.1 # 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 d1e5aab2b5ca65c7d51dec3afc49a807e41fcf02 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:21 -0700 Subject: [PATCH 10/19] 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 b342fb8..51fbccc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.3.1 # via matplotlib python-dateutil==2.7.5 # 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 3a245f5cb2b59ae3b49cb31381046d386f08e35a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:23 -0700 Subject: [PATCH 11/19] 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 51fbccc..2ae91e8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.3.1 # via matplotlib python-dateutil==2.7.5 # via matplotlib, pandas pytz==2018.9 # via matplotlib, pandas pyyaml==3.13 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 72fac6886f105ca9efe684859fe4eb19fef9ee9d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:25 -0700 Subject: [PATCH 12/19] 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 25ccb5a93dee5e5224fcd3e5eb2f60e3e25ba4fb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:26 -0700 Subject: [PATCH 13/19] 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 3d71dd8b3cb506abbeafbe320e51b23b7d1486a2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:28 -0700 Subject: [PATCH 14/19] Pin coverage to latest version 4.5.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 3749980..abf82c2 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==4.5.2 matplotlib numpy pandas From 3d0822ca6a13909e651c4dd54d254e707c446d4c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:29 -0700 Subject: [PATCH 15/19] Pin matplotlib to latest version 3.0.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index abf82c2..9546d9f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.0.4 coverage==4.5.2 - matplotlib + matplotlib==3.0.2 numpy pandas pyfaidx From 4b0ed684c0860bfb60e96dd3d352f3a7f7b35cbd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:31 -0700 Subject: [PATCH 16/19] Pin numpy to latest version 1.16.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9546d9f..00cede8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.0.4 coverage==4.5.2 matplotlib==3.0.2 - numpy + numpy==1.16.0 pandas pyfaidx pyyaml From bdb63463d72c9691b40a571211d8f311c15880cf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:32 -0700 Subject: [PATCH 17/19] 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 00cede8..3889942 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.2 matplotlib==3.0.2 numpy==1.16.0 - pandas + pandas==0.23.4 pyfaidx pyyaml From 94ada236767649fbca3451a3ada59d1de5c10c12 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:34 -0700 Subject: [PATCH 18/19] 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 3889942..3977548 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.2 numpy==1.16.0 pandas==0.23.4 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 2b18c52abbd1c4b1eec6c1e542b07c0b91bd9964 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 21 Jan 2019 10:17:35 -0700 Subject: [PATCH 19/19] 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 3977548..357e0dc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.0 pandas==0.23.4 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =