From 99f103b63945b5e4685548761e907ea58acff49e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:04 -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 3c51516ac2e52faa5380f2607a8debc424d1d481 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:05 -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 f861837aff55c0f46d3580211a307bd9a25853eb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:07 -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 d753a977024918d4792c880fd24eb366ea7c0aab Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:08 -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 14ec16822098136deddf10bd694e7f9e6a2b80e9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:09 -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 9038e754b69bd32ffb6927698bb446d6c13896b9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:10 -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 66476c01fe368152332c9470e756c9f8ee95a44d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:11 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.17.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index d6c3c84..5c2f504 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==1.17.2 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 1d0abfe4d88768486de2f5563c4421bdc5ca2e82 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:12 -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 5c2f504..d360c79 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==1.17.2 -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 7532499676697a6e6f5d75dc5b0f3ccbca2fa96e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:13 -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 d360c79..12337dc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.2 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 044cb9ceb3f8a81425254b8bbbeb7bd0dac3223f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:14 -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 12337dc..0f723ed 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.1 numpy==1.17.2 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 24600e1055339bf27f43d2201a32c7f43f96ed03 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:15 -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 0f723ed..d4bcda6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.17.2 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 a652b1c29b58ae708b2540b09219838eba685824 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:16 -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 d4bcda6..40b5a40 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 6a5c00dfdbbbcfb28929b61b1ee6b25f32fa94ff Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:18 -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 40b5a40..1f59421 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 7d42c586203b9ca571ceb628388299ed1cb5f5be Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:19 -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 1f59421..b5c7773 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 58ee01db2059c7960824801939fb05ed05670119 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:20 -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 46ed62ac924bf7e875d9b9728082900f778dde41 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:21 -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 6d33b41a41430e8e77c7cff347010d69925f882b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:22 -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 8e63df0df1f813d44612690f747f9cac26cb45e0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:23 -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 f7da4c064c4a311e9c412b3ee7a009f8bd1dcd30 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:24 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.17.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 13cfaa3..8ae62b7 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==1.17.2 pandas pyfaidx pyyaml From a523a072b27d85f8a702f19a54e6941b4868fb19 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:25 -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 8ae62b7..e35f666 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.4 matplotlib==3.1.1 numpy==1.17.2 - pandas + pandas==0.25.1 pyfaidx pyyaml From 18da17e9199f98506326a84f5067623f507a6774 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:26 -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 e35f666..9bfffc6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.1 numpy==1.17.2 pandas==0.25.1 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From a5ea3806d8af8645afccfd88551885d63a834946 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Sep 2019 11:53:27 -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 9bfffc6..ae30504 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.17.2 pandas==0.25.1 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1.2 [options.package_data] * =