From 1d532d714a24fb26f0c2f52a7dbe2e5fd0276386 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:08 -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 308149deceb6234e077a64057ad44d967ab233a0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:10 -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 75b6a5c6f524b7e45db95a1123feeca2b3acddba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:12 -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 c71e408264f12bd62b1716ba7a728fda0284ed37 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:13 -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 86ea0f70c1eb0ac54a048b914ff949ce1f4f259e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:14 -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 44471e83383701e8481b114e4777f7718d329780 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:16 -0600 Subject: [PATCH 06/22] Update matplotlib from 3.0.0 to 3.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 9295824..26754c1 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==3.1.0 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 392b2570aadae110432f3326166aac4e91064b08 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:17 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.16.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 26754c1..f819876 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==3.1.0 -numpy==1.15.2 +numpy==1.16.4 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From a2b4ea02b479527ee97cb79d29fb8c6f02e5a5bf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:18 -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 f819876..0e2a3ff 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 numpy==1.16.4 -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 68f9098c06b46d8884d55ecf749e50a378c415d1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:20 -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 0e2a3ff..cac4ba0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 numpy==1.16.4 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 cfc1c9717b828ccb3206d8468044c02ab73c27f4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:21 -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 cac4ba0..1eb47d0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.0 numpy==1.16.4 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 afa589fc8413e110f1ac3c889169446aee6b2c2b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:22 -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 1eb47d0..5cab090 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.4 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 69676c4793a0d972f2900f3b06f88f8ae9f42d2c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:23 -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 5cab090..38c6842 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 ab38e918b159e77b289cbf6752c3f3e7c4acbafd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:24 -0600 Subject: [PATCH 13/22] Update pyyaml from 3.13 to 5.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 38c6842..e2d6c92 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==5.1.1 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 506005a4f5d7580ab1219f7067575561c1594763 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:26 -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 e2d6c92..2dcd297 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==5.1.1 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 2361ced792a648a3d317c27ad45d2f30ee429785 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:27 -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 0c83ced2df2c2e3bcd0a811b8aa74898bc14d2bc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:28 -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 74052c20a45cc56bd783d7664ef5623f3466295a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:29 -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 3066b644def8fb31f985c403ceb7d79477b4123c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:30 -0600 Subject: [PATCH 18/22] Pin matplotlib to latest version 3.1.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5394098..0fc97c1 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==3.1.0 numpy pandas pyfaidx From b2495b5be1776859b750bf67de4f39103862e2aa Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:31 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.16.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0fc97c1..88823a4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.3 matplotlib==3.1.0 - numpy + numpy==1.16.4 pandas pyfaidx pyyaml From 37890ae8bd3d20a24931b6a116e13130e512abd4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:32 -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 88823a4..647b293 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.3 matplotlib==3.1.0 numpy==1.16.4 - pandas + pandas==0.24.2 pyfaidx pyyaml From 8e67acd2b9781a2a57099908d8d8c95c6c6b998d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:33 -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 647b293..6fbe36f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.0 numpy==1.16.4 pandas==0.24.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 875d4f8d33a85d28d7cee76b293fc03bf1ee3ce7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 17 Jun 2019 11:53:34 -0600 Subject: [PATCH 22/22] Pin pyyaml to latest version 5.1.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 6fbe36f..9129ad3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.4 pandas==0.24.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1.1 [options.package_data] * =