From 4f8336b931222314107bdf849d089902e07101a0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:12 -0600 Subject: [PATCH 01/22] 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 021d2dbd12dffd2a09fb681b33c59e5cd425cce5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:13 -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 3aad626..b73c8ad 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==1.1.1 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From 593e2031f94458ef6b6f1c7d01510cdd33a92390 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:14 -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 b73c8ad..a2eaa96 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.73 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 da1765363f7b009db8bd0eeaf0a68dd95ddeabe5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:15 -0600 Subject: [PATCH 04/22] 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 a2eaa96..73aa2e0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.73 click-plugins==1.1.1 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 fc2b1a5edc352f39bba5d1f9e04babac12758320 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:16 -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 73aa2e0..9295824 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ click-plugins==1.1.1 click==7.0 coverage==4.5.3 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 e02ae5c3e60e43006912ba5e9e6c7c7eea1cdf49 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:19 -0600 Subject: [PATCH 06/22] 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 9295824..01b7731 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==1.1.0 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.0.3 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 95c127c311b15460d576d8b95e3a43cf6eca6dfc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:20 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.16.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 01b7731..f6560c0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.0.3 -numpy==1.15.2 +numpy==1.16.3 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From c625c4f856dadb28e6dd3d3a1ef0c5716c40a524 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:21 -0600 Subject: [PATCH 08/22] Update pandas from 0.23.4 to 0.24.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f6560c0..b3178fc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.0.3 numpy==1.16.3 -pandas==0.23.4 +pandas==0.24.2 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 1c3a3735aecb02cd178138b37af54a5cbbcd78fc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:24 -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 b3178fc..5ca9431 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.0.3 numpy==1.16.3 pandas==0.24.2 -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 fb21c64bd2bcc475ce26a35c0dc6400c86d9cbd7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:25 -0600 Subject: [PATCH 10/22] Update pyparsing from 2.2.1 to 2.4.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5ca9431..5a54d1f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.3 numpy==1.16.3 pandas==0.24.2 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.4.0 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 6badc1d08cc07bfa2547625ddc5312121ed7fb57 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:26 -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 5a54d1f..20c09db 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.3 pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.4.0 # 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 e6846f649676c5b98a4442db0e00b706639e10b2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:27 -0600 Subject: [PATCH 12/22] Update pytz from 2018.5 to 2019.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 20c09db..a2c180f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2019.1 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 363bec50afce67a3f2f0599c382ce54c0284a6f3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:31 -0600 Subject: [PATCH 13/22] Update pyyaml from 3.13 to 5.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a2c180f..773d380 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,5 +17,5 @@ pyfaidx==0.5.5.2 pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.1 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 5ed1276bccd71e3afa2875a4242e749524ba22e3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:32 -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 773d380..d4a3655 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.1 # via matplotlib, pandas pyyaml==5.1 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 93d4d46ee16429a92dad7f4cb360503cb3589837 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:33 -0600 Subject: [PATCH 15/22] 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 4ecde483906f17ddf031520ff6a7b128c7c5306f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:35 -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 83e3fe0..5326ef1 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==1.1.1 coverage matplotlib numpy From 817b4aea1375b3f2154b89992296308874a27b5f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:36 -0600 Subject: [PATCH 17/22] 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 5326ef1..5394098 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.73 click>=5.0 click_plugins==1.1.1 - coverage + coverage==4.5.3 matplotlib numpy pandas From 35cdecb99a9d13419c61e6a4bdb6906b888c9e38 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:38 -0600 Subject: [PATCH 18/22] 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 5394098..202556a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.1.1 coverage==4.5.3 - matplotlib + matplotlib==3.0.3 numpy pandas pyfaidx From 53c10c49eb7ffe9f2c729501c2bbc1199053303e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:39 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.16.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 202556a..f4c3ee3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.3 matplotlib==3.0.3 - numpy + numpy==1.16.3 pandas pyfaidx pyyaml From 78ed525cd10e75dfac6b303d8dfa32b72b1a1c61 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:43 -0600 Subject: [PATCH 20/22] Pin pandas to latest version 0.24.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index f4c3ee3..ed11293 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.3 matplotlib==3.0.3 numpy==1.16.3 - pandas + pandas==0.24.2 pyfaidx pyyaml From 248461055c986425d189b215dc0874c582262558 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:44 -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 ed11293..54590de 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.3 numpy==1.16.3 pandas==0.24.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 6b876752586f25e225188de4bb0cdf2e2089776f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 May 2019 12:02:45 -0600 Subject: [PATCH 22/22] Pin pyyaml to latest version 5.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 54590de..4ec7343 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.3 pandas==0.24.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1 [options.package_data] * =