From c509e61984c7815fc9689bc2953dbd2f88f751bb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:05 -0600 Subject: [PATCH 01/28] Update click from 7.0 to 7.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4836630..0a4b83f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ apipkg==1.5 # via pytest-shutil attrs==19.3.0 # via pytest biopython==1.76 click-plugins==1.1.1 -click==7.0 +click==7.1.1 colorama==0.4.3 contextlib2==0.6.0.post1 # via pytest-shutil coverage==5.0.3 From 1a907bc347c56df7a4fc929ee6207876a88c08b3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:06 -0600 Subject: [PATCH 02/28] Update coverage from 5.0.3 to 5.0.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0a4b83f..e5bc414 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ click-plugins==1.1.1 click==7.1.1 colorama==0.4.3 contextlib2==0.6.0.post1 # via pytest-shutil -coverage==5.0.3 +coverage==5.0.4 cycler==0.10.0 # via matplotlib execnet==1.7.1 # via pytest-shutil importlib-metadata==1.4.0 # via pytest From 20f53971da74a54157cf4d895d727caddb0d08c1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:08 -0600 Subject: [PATCH 03/28] Update importlib-metadata from 1.4.0 to 1.5.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index e5bc414..86b5416 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,7 +8,7 @@ contextlib2==0.6.0.post1 # via pytest-shutil coverage==5.0.4 cycler==0.10.0 # via matplotlib execnet==1.7.1 # via pytest-shutil -importlib-metadata==1.4.0 # via pytest +importlib-metadata==1.5.0 # via pytest kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.2 mock==3.0.5 # via pytest-shutil From 37c3dfc66b2f7eb58df2854c277b3e928d75d13a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:09 -0600 Subject: [PATCH 04/28] Update matplotlib from 3.1.2 to 3.2.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 86b5416..458862b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ cycler==0.10.0 # via matplotlib execnet==1.7.1 # via pytest-shutil importlib-metadata==1.5.0 # via pytest kiwisolver==1.1.0 # via matplotlib -matplotlib==3.1.2 +matplotlib==3.2.1 mock==3.0.5 # via pytest-shutil more-itertools==8.1.0 # via pytest numpy==1.18.1 From bf73c677764097751b19442c534e925387793577 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:10 -0600 Subject: [PATCH 05/28] Update mock from 3.0.5 to 4.0.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 458862b..b7c1e83 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ execnet==1.7.1 # via pytest-shutil importlib-metadata==1.5.0 # via pytest kiwisolver==1.1.0 # via matplotlib matplotlib==3.2.1 -mock==3.0.5 # via pytest-shutil +mock==4.0.2 # via pytest-shutil more-itertools==8.1.0 # via pytest numpy==1.18.1 packaging==20.1 # via pytest From bca02c29f0423fd6db953236f291ebb5a737d152 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:11 -0600 Subject: [PATCH 06/28] Update more-itertools from 8.1.0 to 8.2.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index b7c1e83..7c19ff2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ importlib-metadata==1.5.0 # via pytest kiwisolver==1.1.0 # via matplotlib matplotlib==3.2.1 mock==4.0.2 # via pytest-shutil -more-itertools==8.1.0 # via pytest +more-itertools==8.2.0 # via pytest numpy==1.18.1 packaging==20.1 # via pytest pandas==0.25.3 From bf77f4bf54b4fdc0bd4ac06a9941b64c0b831e9c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:12 -0600 Subject: [PATCH 07/28] Update numpy from 1.18.1 to 1.18.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 7c19ff2..a563358 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.2.1 mock==4.0.2 # via pytest-shutil more-itertools==8.2.0 # via pytest -numpy==1.18.1 +numpy==1.18.2 packaging==20.1 # via pytest pandas==0.25.3 pluggy==0.13.1 # via pytest From 21f7fcd53446811365c79c48b0e200cf3166a84a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:13 -0600 Subject: [PATCH 08/28] Update packaging from 20.1 to 20.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a563358..56a124d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.2.1 mock==4.0.2 # via pytest-shutil more-itertools==8.2.0 # via pytest numpy==1.18.2 -packaging==20.1 # via pytest +packaging==20.3 # via pytest pandas==0.25.3 pluggy==0.13.1 # via pytest py==1.8.1 # via pytest From 67c0e7d004166042efa1c5e9fe1650fe23f8f2a6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:14 -0600 Subject: [PATCH 09/28] Update pandas from 0.25.3 to 1.0.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 56a124d..ad91220 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ mock==4.0.2 # via pytest-shutil more-itertools==8.2.0 # via pytest numpy==1.18.2 packaging==20.3 # via pytest -pandas==0.25.3 +pandas==1.0.3 pluggy==0.13.1 # via pytest py==1.8.1 # via pytest path.py==12.0.2 # via pytest-shutil From 22333272b7f8de94323fac3285715da06152c043 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:15 -0600 Subject: [PATCH 10/28] Update path.py from 12.0.2 to 12.4.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index ad91220..a3b3a13 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,7 +18,7 @@ packaging==20.3 # via pytest pandas==1.0.3 pluggy==0.13.1 # via pytest py==1.8.1 # via pytest -path.py==12.0.2 # via pytest-shutil +path.py==12.4.0 # via pytest-shutil pyfaidx==0.5.8 pyfastaq==3.17.0 # via shell scripts pyparsing==2.4.6 # via matplotlib, pytest From eaf1ad927ce4aa32150e69d83a61180c22a3355f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:16 -0600 Subject: [PATCH 11/28] Update pytest from 5.3.4 to 5.4.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a3b3a13..8a77907 100644 --- a/requirements.txt +++ b/requirements.txt @@ -23,7 +23,7 @@ pyfaidx==0.5.8 pyfastaq==3.17.0 # via shell scripts pyparsing==2.4.6 # via matplotlib, pytest python-dateutil==2.8.1 # via matplotlib, pandas -pytest==5.3.4 +pytest==5.4.1 pytest-shutil==1.7.0 pytz==2019.3 # via pandas pyyaml==5.3 From 54e79276c0c3d868e98d7319f406d3d964450d66 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:17 -0600 Subject: [PATCH 12/28] Update pyyaml from 5.3 to 5.3.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 8a77907..4d61b60 100644 --- a/requirements.txt +++ b/requirements.txt @@ -26,7 +26,7 @@ python-dateutil==2.8.1 # via matplotlib, pandas pytest==5.4.1 pytest-shutil==1.7.0 pytz==2019.3 # via pandas -pyyaml==5.3 +pyyaml==5.3.1 scipy==1.4.1 # via seaborn seaborn==0.10.0 six==1.14.0 # via pyfaidx, python-dateutil, pytest From 85facde926c244bcb84dd5f8bf5989ba7adbf567 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:18 -0600 Subject: [PATCH 13/28] Update wcwidth from 0.1.8 to 0.1.9 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4d61b60..47cf2af 100644 --- a/requirements.txt +++ b/requirements.txt @@ -31,5 +31,5 @@ scipy==1.4.1 # via seaborn seaborn==0.10.0 six==1.14.0 # via pyfaidx, python-dateutil, pytest termcolor==1.1.0 # via pytest-shutil -wcwidth==0.1.8 # via pytest +wcwidth==0.1.9 # via pytest zipp==2.1.0 # via pytest \ No newline at end of file From edaace2dddda4b5e77ed2bf4d1fe08cd7428c3df Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:20 -0600 Subject: [PATCH 14/28] Update zipp from 2.1.0 to 3.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 47cf2af..006fe0b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -32,4 +32,4 @@ seaborn==0.10.0 six==1.14.0 # via pyfaidx, python-dateutil, pytest termcolor==1.1.0 # via pytest-shutil wcwidth==0.1.9 # via pytest -zipp==2.1.0 # via pytest \ No newline at end of file +zipp==3.1.0 # via pytest \ No newline at end of file From 275fdc57dd3fe015af23fe939bd70aa3322b3048 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:21 -0600 Subject: [PATCH 15/28] Pin biopython to latest version 1.76 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index f4dd687..22607c5 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,7 +45,7 @@ zip_safe = False include_package_data = True packages = aakbar install_requires = - biopython + biopython==1.76 click>=5.0 click_plugins colorama From 1fac3872d60c6357a1148a5317597f777d32b81c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:22 -0600 Subject: [PATCH 16/28] 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 22607c5..43a829f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ packages = aakbar install_requires = biopython==1.76 click>=5.0 - click_plugins + click_plugins==1.1.1 colorama coverage matplotlib From cc609c219eac59ce9c19e5527f4d0285dd0c7994 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:23 -0600 Subject: [PATCH 17/28] Pin colorama to latest version 0.4.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 43a829f..d7591e5 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.76 click>=5.0 click_plugins==1.1.1 - colorama + colorama==0.4.3 coverage matplotlib numpy From 09464b06e23843b3ea4b3708a69e3edc06975a65 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:24 -0600 Subject: [PATCH 18/28] Pin coverage to latest version 5.0.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index d7591e5..1cc77f4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.1.1 colorama==0.4.3 - coverage + coverage==5.0.4 matplotlib numpy pandas From eda070dc1c18a113490c1436d7ecc10bbc5b435c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:25 -0600 Subject: [PATCH 19/28] Pin matplotlib to latest version 3.2.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 1cc77f4..0085838 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 colorama==0.4.3 coverage==5.0.4 - matplotlib + matplotlib==3.2.1 numpy pandas path.py<=12.0.2 From 998ad2a155df8ac774a31197a97c9fcf07ed8f9a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:27 -0600 Subject: [PATCH 20/28] Pin numpy to latest version 1.18.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0085838..579fd59 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = colorama==0.4.3 coverage==5.0.4 matplotlib==3.2.1 - numpy + numpy==1.18.2 pandas path.py<=12.0.2 pyfaidx From 2ce0c022d822cd638177fd393d342147659200a4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:28 -0600 Subject: [PATCH 21/28] Pin pandas to latest version 1.0.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 579fd59..576dabc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = coverage==5.0.4 matplotlib==3.2.1 numpy==1.18.2 - pandas + pandas==1.0.3 path.py<=12.0.2 pyfaidx pyfastaq From b8f09a248ed9f1870b0a04ec13568348a0d8bdd8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:29 -0600 Subject: [PATCH 22/28] Pin path.py to latest version 12.4.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 576dabc..cb7d7e6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = matplotlib==3.2.1 numpy==1.18.2 pandas==1.0.3 - path.py<=12.0.2 + path.py==12.4.0 pyfaidx pyfastaq pytest From 824e6fb0ae3beee5aae8924e0de39a8b9af296ab Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:30 -0600 Subject: [PATCH 23/28] Pin pyfaidx to latest version 0.5.8 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index cb7d7e6..6f72f1c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,7 +54,7 @@ install_requires = numpy==1.18.2 pandas==1.0.3 path.py==12.4.0 - pyfaidx + pyfaidx==0.5.8 pyfastaq pytest pytest-shutil From b5e35e475caaa869d29e2ab5bc19db56a5d9421e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:31 -0600 Subject: [PATCH 24/28] Pin pyfastaq to latest version 3.17.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 6f72f1c..2151a18 100644 --- a/setup.cfg +++ b/setup.cfg @@ -55,7 +55,7 @@ install_requires = pandas==1.0.3 path.py==12.4.0 pyfaidx==0.5.8 - pyfastaq + pyfastaq==3.17.0 pytest pytest-shutil pyyaml From 75e87d450b2c9a9765b133f0b70a52ec9202f07c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:32 -0600 Subject: [PATCH 25/28] Pin pytest to latest version 5.4.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 2151a18..53271c1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -56,7 +56,7 @@ install_requires = path.py==12.4.0 pyfaidx==0.5.8 pyfastaq==3.17.0 - pytest + pytest==5.4.1 pytest-shutil pyyaml seaborn From e4f1b363285eeaae717f899af08a9381e0d1e14c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:34 -0600 Subject: [PATCH 26/28] Pin pytest-shutil to latest version 1.7.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 53271c1..2c8f75b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -57,7 +57,7 @@ install_requires = pyfaidx==0.5.8 pyfastaq==3.17.0 pytest==5.4.1 - pytest-shutil + pytest-shutil==1.7.0 pyyaml seaborn From c2304223e7f7b1522fdfcb90708453610d5aeeae Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:35 -0600 Subject: [PATCH 27/28] Pin pyyaml to latest version 5.3.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 2c8f75b..6603f30 100644 --- a/setup.cfg +++ b/setup.cfg @@ -58,7 +58,7 @@ install_requires = pyfastaq==3.17.0 pytest==5.4.1 pytest-shutil==1.7.0 - pyyaml + pyyaml==5.3.1 seaborn [options.package_data] From 92ca494978c8b4fd455e46c5c27c1696e84987f6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Mar 2020 12:04:36 -0600 Subject: [PATCH 28/28] Pin seaborn to latest version 0.10.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 6603f30..bb9eab9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -59,7 +59,7 @@ install_requires = pytest==5.4.1 pytest-shutil==1.7.0 pyyaml==5.3.1 - seaborn + seaborn==0.10.0 [options.package_data] * =