From e2d1cf2ceb17d559e5c690d0634ab092a02c666a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:05 -0600 Subject: [PATCH 01/22] Update biopython from 1.72 to 1.74 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 161185b..59fde0c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,7 +4,7 @@ # # pip-compile --output-file requirements.txt setup.py # -biopython==1.72 +biopython==1.74 click-plugins==1.0.3 click==6.7 coverage==4.5.1 From 3f642508af4338f6c78104810d5afa7a77da1e26 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:06 -0600 Subject: [PATCH 02/22] Update click-plugins from 1.0.3 to 1.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 59fde0c..81a16ff 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ # pip-compile --output-file requirements.txt setup.py # biopython==1.74 -click-plugins==1.0.3 +click-plugins==1.1.1 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From ef182eb3407c5c45acddca56c8fde2e8ab339e88 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:08 -0600 Subject: [PATCH 03/22] 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 81a16ff..c885cda 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.74 click-plugins==1.1.1 -click==6.7 +click==7.0 coverage==4.5.1 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib From 50bea6c060d3a316b959c9d06989a74630abdb69 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:09 -0600 Subject: [PATCH 04/22] Update coverage from 4.5.1 to 4.5.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c885cda..4329e1f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.74 click-plugins==1.1.1 click==7.0 -coverage==4.5.1 +coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From 43bf5dc4c1423fa176474948dfd06a9870315625 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:10 -0600 Subject: [PATCH 05/22] Update kiwisolver from 1.0.1 to 1.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4329e1f..4b84855 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ click-plugins==1.1.1 click==7.0 coverage==4.5.4 cycler==0.10.0 # via matplotlib -kiwisolver==1.0.1 # via matplotlib +kiwisolver==1.1.0 # via matplotlib matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 From 41e25495d30ebdbee5366f977886122951bddf24 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:11 -0600 Subject: [PATCH 06/22] Update matplotlib from 3.0.0 to 3.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4b84855..d6c3c84 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.1.1 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 679d91959eb9251096072ad0f5d3821630f6ca95 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:12 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.17.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index d6c3c84..8bf9bbb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 -numpy==1.15.2 +numpy==1.17.0 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 95d7b9a7565a22bd9ffd48f9e56ad20f0e3c4db3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:14 -0600 Subject: [PATCH 08/22] Update pandas from 0.23.4 to 0.25.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 8bf9bbb..1781bb6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.0 -pandas==0.23.4 +pandas==0.25.1 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 0ebe99556b60ceca33af100845e66c29cc59b034 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:15 -0600 Subject: [PATCH 09/22] 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 1781bb6..2ba80da 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.0 pandas==0.25.1 -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 c59d3aa58737c579fcb90f6bcb725b01267683d9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:16 -0600 Subject: [PATCH 10/22] Update pyparsing from 2.2.1 to 2.4.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 2ba80da..b64d4ba 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.1 numpy==1.17.0 pandas==0.25.1 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.4.2 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 97ef884fe119f69a127854aee2cacc6559c69bba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:18 -0600 Subject: [PATCH 11/22] 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 b64d4ba..e57beb2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.17.0 pandas==0.25.1 pyfaidx==0.5.5.2 pyparsing==2.4.2 # 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 8639b17674e22f0ab785f35f6c9a38acc6fae3fd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:19 -0600 Subject: [PATCH 12/22] Update pytz from 2018.5 to 2019.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index e57beb2..a54df1d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.25.1 pyfaidx==0.5.5.2 pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2019.2 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 95b8eec1247ac1fabd0926adc1d97e6207c1299b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:20 -0600 Subject: [PATCH 13/22] Update pyyaml from 3.13 to 5.1.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a54df1d..d15e0b4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,5 +17,5 @@ pyfaidx==0.5.5.2 pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.2 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1.2 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From ccfe29dfd1a7f6f0d018523e05a8c4169f8a17e2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:21 -0600 Subject: [PATCH 14/22] 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 d15e0b4..0d782e7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.2 # via matplotlib, pandas pyyaml==5.1.2 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 5aa6c77f78fb055f7c2341de9b5476f891350042 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:22 -0600 Subject: [PATCH 15/22] Pin biopython to latest version 1.74 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8f7e0f4..b6255cb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,7 +45,7 @@ zip_safe = False include_package_data = True packages = aakbar install_requires = - biopython + biopython==1.74 click>=5.0 click_plugins coverage From 045b7d29e2ca0e59b11cd68108d746f493f93d51 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:23 -0600 Subject: [PATCH 16/22] Pin click_plugins to latest version 1.1.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index b6255cb..f6dfaf3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ packages = aakbar install_requires = biopython==1.74 click>=5.0 - click_plugins + click_plugins==1.1.1 coverage matplotlib numpy From 11c142d315054956f604682bb18104b9d10c6d0c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:24 -0600 Subject: [PATCH 17/22] Pin coverage to latest version 4.5.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index f6dfaf3..c271fca 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.74 click>=5.0 click_plugins==1.1.1 - coverage + coverage==4.5.4 matplotlib numpy pandas From fd5a3c430297de6d78f6e5b6b04bd460873107ab Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:26 -0600 Subject: [PATCH 18/22] Pin matplotlib to latest version 3.1.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index c271fca..13cfaa3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.1.1 coverage==4.5.4 - matplotlib + matplotlib==3.1.1 numpy pandas pyfaidx From 87841dd895eb9486e04c6c7a0cc933e2b6254ead Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:27 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.17.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 13cfaa3..8445685 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.4 matplotlib==3.1.1 - numpy + numpy==1.17.0 pandas pyfaidx pyyaml From 89f447ee4d20711e5cd6f4d07e38c79ae149337f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:28 -0600 Subject: [PATCH 20/22] Pin pandas to latest version 0.25.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8445685..f7944ac 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.4 matplotlib==3.1.1 numpy==1.17.0 - pandas + pandas==0.25.1 pyfaidx pyyaml From f40de33c49283f63ae8709eb912e062e930dd6d1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:29 -0600 Subject: [PATCH 21/22] 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 f7944ac..b004635 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.1 numpy==1.17.0 pandas==0.25.1 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 933473c4acdba49bec0f8a51bbb091678f77dd94 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 26 Aug 2019 11:50:31 -0600 Subject: [PATCH 22/22] Pin pyyaml to latest version 5.1.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index b004635..e9e8576 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.17.0 pandas==0.25.1 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1.2 [options.package_data] * =