From ec4afd068f2e4a496b73dc1bc248f07cecec3126 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:05 -0600 Subject: [PATCH 01/20] 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 646252041171825e1f1a5791bb008b3a4eb1a4ef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:07 -0600 Subject: [PATCH 02/20] 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 7cb98968c6b49660b9845921d08855619c69d73e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:08 -0600 Subject: [PATCH 03/20] 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 d47394b2777a2e98f60a5a6c7531d3dec35b6240 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:10 -0600 Subject: [PATCH 04/20] 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 e90550f032598db3dbe2e8ccceb3142fd4c066e6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:11 -0600 Subject: [PATCH 05/20] 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 1b8b71c262aaf3fedb2a188c36e5cc1b47237b8a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:12 -0600 Subject: [PATCH 06/20] 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 bc9a601308abd54ef283970d02598fb772f1bc79 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:13 -0600 Subject: [PATCH 07/20] Update pandas from 0.23.4 to 0.24.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f5911a5..d454bc1 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==0.24.1 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 2355a53c5056ab9cbc24ed2973d4dfe7006431ef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:14 -0600 Subject: [PATCH 08/20] 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 d454bc1..360e8e3 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==0.24.1 -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 3c76c747c538134822c9fab98d187e4cdd051ce1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:15 -0600 Subject: [PATCH 09/20] 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 360e8e3..461c276 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.3 numpy==1.16.2 pandas==0.24.1 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 2f8dfd951df3331f6b737c8798d57186b203afdc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:16 -0600 Subject: [PATCH 10/20] 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 461c276..3572410 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.2 pandas==0.24.1 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 69292eeb6173f0aee4c46f72f93bdd1c90f5c891 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:17 -0600 Subject: [PATCH 11/20] 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 3572410..ce7ada0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.1 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 f2d3e37d64bf470331724b8089c5cd90ad540533 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:18 -0600 Subject: [PATCH 12/20] 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 ce7ada0..14b8c12 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==3.13 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From bcc6fcd3d4ff9dbd29d176bdea87ef46cc3d8ce5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:19 -0600 Subject: [PATCH 13/20] 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 0cc59e7cb019a5ce9cf699b4aa8fd35b823e9e60 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:20 -0600 Subject: [PATCH 14/20] 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 ac60bbcae56da03e15b0a10064b667aadca52799 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:22 -0600 Subject: [PATCH 15/20] 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 72727feafd2cf045e293ef423ce784743a134139 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:23 -0600 Subject: [PATCH 16/20] 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 2f1f98ae665e2cfefbbb1f1effc09b47b5067bd6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:27 -0600 Subject: [PATCH 17/20] 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 21c35b3c3326748701c60857a447bab396a03d68 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:28 -0600 Subject: [PATCH 18/20] Pin pandas to latest version 0.24.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 4e8e071..1ff719f 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==0.24.1 pyfaidx pyyaml From 6f1d137612df83ad0d3fda24265327fe1d70b6dd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:29 -0600 Subject: [PATCH 19/20] 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 1ff719f..c464fe3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.3 numpy==1.16.2 pandas==0.24.1 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 39062a02c38fe8804c7c6eba5c3d9552ea835ae1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Mar 2019 11:47:30 -0600 Subject: [PATCH 20/20] 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 c464fe3..a9b41a5 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.2 pandas==0.24.1 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =