From 294d9334e5819f9f2a8787623cd6fda300b6460e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:07 -0600 Subject: [PATCH 01/30] 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 05d1a9ed9433d73e82f2b8f8254970eef8c15aa7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:09 -0600 Subject: [PATCH 02/30] Update coverage from 5.0.3 to 5.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0a4b83f..39d63d1 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==5.1 cycler==0.10.0 # via matplotlib execnet==1.7.1 # via pytest-shutil importlib-metadata==1.4.0 # via pytest From 908c5716ae22ecf415e5da21496425c3dc210d5b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:10 -0600 Subject: [PATCH 03/30] Update importlib-metadata from 1.4.0 to 1.6.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 39d63d1..bd14314 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,7 +8,7 @@ contextlib2==0.6.0.post1 # via pytest-shutil coverage==5.1 cycler==0.10.0 # via matplotlib execnet==1.7.1 # via pytest-shutil -importlib-metadata==1.4.0 # via pytest +importlib-metadata==1.6.0 # via pytest kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.2 mock==3.0.5 # via pytest-shutil From 869b154bcc027994ffa9f58169e5240ebaa25ed8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:11 -0600 Subject: [PATCH 04/30] Update kiwisolver from 1.1.0 to 1.2.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index bd14314..54c7f41 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ coverage==5.1 cycler==0.10.0 # via matplotlib execnet==1.7.1 # via pytest-shutil importlib-metadata==1.6.0 # via pytest -kiwisolver==1.1.0 # via matplotlib +kiwisolver==1.2.0 # via matplotlib matplotlib==3.1.2 mock==3.0.5 # via pytest-shutil more-itertools==8.1.0 # via pytest From 4557ed51b8b3066710dc01f348738ce824de3a9d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:12 -0600 Subject: [PATCH 05/30] 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 54c7f41..1bc604e 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==1.6.0 # via pytest kiwisolver==1.2.0 # 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 d32387af7da70c4308bcddaa9cab91ae5e3e6df9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:13 -0600 Subject: [PATCH 06/30] 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 1bc604e..218c33c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ execnet==1.7.1 # via pytest-shutil importlib-metadata==1.6.0 # via pytest kiwisolver==1.2.0 # 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 19ad491a0d78068fab73957495b99b9d99841199 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:14 -0600 Subject: [PATCH 07/30] 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 218c33c..90f06e5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ importlib-metadata==1.6.0 # via pytest kiwisolver==1.2.0 # 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 8e103bfbca6b71ed8a46d907add419b672118d42 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:15 -0600 Subject: [PATCH 08/30] 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 90f06e5..b4f5fa5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.2.0 # 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 4bb78bb0e62cd1cfec1afb4123f6e5832bb3d72a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:16 -0600 Subject: [PATCH 09/30] 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 b4f5fa5..2211900 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 d8d29e4c909b213c6926bb35952695c215da287f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:17 -0600 Subject: [PATCH 10/30] 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 2211900..055f68c 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 fcc5cb800d9b2c9d8a04163cb10378c5b29e28e6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:18 -0600 Subject: [PATCH 11/30] 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 055f68c..0d66d10 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 ad69b107a5a4fe5fbde22d762734adc3c3e0df51 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:19 -0600 Subject: [PATCH 12/30] Update pyparsing from 2.4.6 to 2.4.7 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0d66d10..094d63e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -21,7 +21,7 @@ py==1.8.1 # via pytest 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 +pyparsing==2.4.7 # via matplotlib, pytest python-dateutil==2.8.1 # via matplotlib, pandas pytest==5.3.4 pytest-shutil==1.7.0 From e321ef131591a8a66881ef9a04a1aa1c26853511 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:20 -0600 Subject: [PATCH 13/30] 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 094d63e..c374df9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -23,7 +23,7 @@ pyfaidx==0.5.8 pyfastaq==3.17.0 # via shell scripts pyparsing==2.4.7 # 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 b9caa3777b23fa3175200fb03df1041305e03452 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:22 -0600 Subject: [PATCH 14/30] 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 c374df9..4000e3f 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 45b9aab6c54f80d3dc3b80bfba3fd493e7dcae9e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:23 -0600 Subject: [PATCH 15/30] 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 4000e3f..2a57e5e 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 c2834f2cc5c77184f28fd7b2c10e3615322fec9e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:24 -0600 Subject: [PATCH 16/30] 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 2a57e5e..31dc016 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 995ee4386b777a2f83bb91228c064223058282d1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:25 -0600 Subject: [PATCH 17/30] 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 0eeb33b692e0b28c55afa37435b73d68cd625cca Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:26 -0600 Subject: [PATCH 18/30] 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 26aec2ac52870797f305cf88c23453a3890b2e1d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:27 -0600 Subject: [PATCH 19/30] 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 498c07c994d1b47b1829d6870dc62bb8f00e7e6a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:28 -0600 Subject: [PATCH 20/30] Pin coverage to latest version 5.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index d7591e5..0e1ba71 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==5.1 matplotlib numpy pandas From 75ee821a2f212e0829337f89bd208e2524654ba2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:29 -0600 Subject: [PATCH 21/30] 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 0e1ba71..155f1b4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 colorama==0.4.3 coverage==5.1 - matplotlib + matplotlib==3.2.1 numpy pandas path.py<=12.0.2 From f5148469fa72b958e949ba093810d01ccc7a4fbe Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:30 -0600 Subject: [PATCH 22/30] 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 155f1b4..06ec09b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = colorama==0.4.3 coverage==5.1 matplotlib==3.2.1 - numpy + numpy==1.18.2 pandas path.py<=12.0.2 pyfaidx From 47dc2d3611d8f0d07424ef8a352580cc2347bd03 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:31 -0600 Subject: [PATCH 23/30] 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 06ec09b..220ec36 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = coverage==5.1 matplotlib==3.2.1 numpy==1.18.2 - pandas + pandas==1.0.3 path.py<=12.0.2 pyfaidx pyfastaq From c89fe2fcf4b6ef04e8547a67097c6d9a3a47ae3e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:32 -0600 Subject: [PATCH 24/30] 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 220ec36..08a5222 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 6c8a92e395163b9bc267f3da67c9b1013d6f6b21 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:33 -0600 Subject: [PATCH 25/30] 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 08a5222..be90059 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 995224cd10920b462205ffb5533c224af9193347 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:35 -0600 Subject: [PATCH 26/30] 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 be90059..bbe91db 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 844ce0dbb06034e7bdeb80ee6ef7c7b83b8100fb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:36 -0600 Subject: [PATCH 27/30] 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 bbe91db..7e152ba 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 af2fed55cfb2c00d73c5fa920c4bad7bb57436e9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:37 -0600 Subject: [PATCH 28/30] 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 7e152ba..f39309f 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 9a64d34b5b9a0831e5bacf70d70ce2f671a5280b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:38 -0600 Subject: [PATCH 29/30] 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 f39309f..56d113b 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 8e586d8f3ba634409169ac476114e8fd00852299 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 13 Apr 2020 12:13:39 -0600 Subject: [PATCH 30/30] 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 56d113b..e3a6b3f 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] * =