From 3fc619672752b13d8821ee8e67098cf25bd6ede6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:05 -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 a9abb85ea9e6f6d3f8f88148469bed51ec00046d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:06 -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 c869746606970d66b14e0b5bbe296a4c05ec48b1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:07 -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 aedf7d961fbe583dc7b5d8f728e82017d1ecc614 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:09 -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 a10a86d4161a0404b9e1bd93c17561d2f04267ce Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:10 -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 036d9c18fc812a55368a04818bc9047b91e1c291 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:11 -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 f48a40535a4beb6b4d65841914f451f9bc7b3948 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:12 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.17.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index d6c3c84..93be16a 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==1.17.3 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 1b24c5965530f94488fb69c8addd92e248afdd48 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:17 -0600 Subject: [PATCH 08/22] Update pandas from 0.23.4 to 0.25.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 93be16a..e662f2b 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==1.17.3 -pandas==0.23.4 +pandas==0.25.2 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 33952bf8164ef2b1c910e0a8b4f716a2d2d39b9e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:18 -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 e662f2b..ac55b1e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.3 pandas==0.25.2 -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 25a687fff04897f5f5c6c2c485b23b7f25a55057 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:19 -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 ac55b1e..0c39011 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.1 numpy==1.17.3 pandas==0.25.2 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 696703cf4f94688d3a60337d549823fd9b249d19 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:20 -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 0c39011..3384e3e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.17.3 pandas==0.25.2 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 34a9bcea52757d4b942584cf219ff23fada0eaa7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:21 -0600 Subject: [PATCH 12/22] Update pytz from 2018.5 to 2019.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3384e3e..f4284aa 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.25.2 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==2019.3 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From c80eb8b3bbf453699c7bea2b1cd3b3d9ae20bb67 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:23 -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 f4284aa..ec56c44 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==2019.3 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1.2 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 9a8685bb6dd3e258e409dc3dfb7f89f729587a07 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:24 -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 ec56c44..a49e837 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==2019.3 # 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 538e1d2ff161fc5f23dc3df9754f2f5502839a4a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:25 -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 e7d472a6227bf3c93bdef0667ce1982bfe5695e5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:26 -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 921959bc1cf395957be91546c96672c0d7734908 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:27 -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 a503fdc1118c5ce20ee727c8c49f6a7eab87a606 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:28 -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 6804826f173170ff7d4f0ad7d1a979a4351b0160 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:30 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.17.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 13cfaa3..47c9c30 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==1.17.3 pandas pyfaidx pyyaml From 762874afff34e7eca01e787c9542062ae86d7316 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:31 -0600 Subject: [PATCH 20/22] Pin pandas to latest version 0.25.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 47c9c30..66c8eb2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.4 matplotlib==3.1.1 numpy==1.17.3 - pandas + pandas==0.25.2 pyfaidx pyyaml From dc4504791e7076d52a11ab1be8e9062b78ff15e5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:32 -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 66c8eb2..568a431 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.1 numpy==1.17.3 pandas==0.25.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From f3ed53d4e7ca90c117e0abb6aca91db950de37c9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Oct 2019 12:03:33 -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 568a431..51d36c9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.17.3 pandas==0.25.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1.2 [options.package_data] * =