From 30ab022e93456165710d965e7c5cfbbf453a5d18 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:05 -0600 Subject: [PATCH 01/24] 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 2f97108082138ed9efa4f1c8d8eab5735a7d561f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:06 -0600 Subject: [PATCH 02/24] 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 0a4b83f..9c7eed2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,7 +8,7 @@ contextlib2==0.6.0.post1 # via pytest-shutil coverage==5.0.3 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 cd4087285057cb37877f2f6eadb01f1bafed4663 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:07 -0600 Subject: [PATCH 03/24] Update matplotlib from 3.1.2 to 3.2.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 9c7eed2..868cea8 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==3.2.0 mock==3.0.5 # via pytest-shutil more-itertools==8.1.0 # via pytest numpy==1.18.1 From b5a3ca2c80417efe7ccee20fca05329e05633e75 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:08 -0600 Subject: [PATCH 04/24] 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 868cea8..c1fd5ac 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==3.2.0 -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 0d38f993fdc55400e2dc45876a21f8f6ec2139be Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:09 -0600 Subject: [PATCH 05/24] 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 c1fd5ac..fc3f090 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==3.2.0 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 59d934e06414f14be69db400b2007ba01e067376 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:10 -0600 Subject: [PATCH 06/24] 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 fc3f090..91b35b9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.2.0 mock==4.0.2 # via pytest-shutil more-itertools==8.2.0 # via pytest numpy==1.18.1 -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 ac3baba324b7a159a7974d8b8f360feba2caf8ef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:11 -0600 Subject: [PATCH 07/24] Update pandas from 0.25.3 to 1.0.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 91b35b9..bfb1204 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==1.18.1 packaging==20.3 # via pytest -pandas==0.25.3 +pandas==1.0.2 pluggy==0.13.1 # via pytest py==1.8.1 # via pytest path.py==12.0.2 # via pytest-shutil From d28f9dc06c43b112033d0a4d8d461ca9962f4b7f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:13 -0600 Subject: [PATCH 08/24] 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 bfb1204..cf0e878 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,7 +18,7 @@ packaging==20.3 # via pytest pandas==1.0.2 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 289b75e80b11ad14974152e47786797085cfbe7f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:14 -0600 Subject: [PATCH 09/24] 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 cf0e878..adff29d 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 ef8163bd4a1a43cbae4040e01997ba3e547b62a0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:15 -0600 Subject: [PATCH 10/24] 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 adff29d..d1c5e2d 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==0.1.8 # 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 23b27142491769fac55c81a8275af9bb85f23274 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:16 -0600 Subject: [PATCH 11/24] 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 da1e04d7ed6e7537c1202afd645be76f1a264cbc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:17 -0600 Subject: [PATCH 12/24] 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 15b1af5096ffc14b6e820b545f53d70c307187ed Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:18 -0600 Subject: [PATCH 13/24] 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 7a49ca240ca4e36018318423326867da66ef0932 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:19 -0600 Subject: [PATCH 14/24] Pin coverage to latest version 5.0.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index d7591e5..20958d0 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==5.0.3 matplotlib numpy pandas From c3e193f8b6053a990f661d67088a5bc2ed7c5d6a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:20 -0600 Subject: [PATCH 15/24] Pin matplotlib to latest version 3.2.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 20958d0..aac921f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 colorama==0.4.3 coverage==5.0.3 - matplotlib + matplotlib==3.2.0 numpy pandas path.py<=12.0.2 From af4ebc424c1fb79b134a7631f23e1688b06909ec Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:22 -0600 Subject: [PATCH 16/24] Pin numpy to latest version 1.18.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index aac921f..dd5534e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = colorama==0.4.3 coverage==5.0.3 matplotlib==3.2.0 - numpy + numpy==1.18.1 pandas path.py<=12.0.2 pyfaidx From de835afc59e70c94ea49500b8113b6144fa9b606 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:23 -0600 Subject: [PATCH 17/24] Pin pandas to latest version 1.0.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index dd5534e..734d498 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = coverage==5.0.3 matplotlib==3.2.0 numpy==1.18.1 - pandas + pandas==1.0.2 path.py<=12.0.2 pyfaidx pyfastaq From c21247ecd098261f9ef936f64de47a983c972e93 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:24 -0600 Subject: [PATCH 18/24] 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 734d498..50ebd70 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = matplotlib==3.2.0 numpy==1.18.1 pandas==1.0.2 - path.py<=12.0.2 + path.py==12.4.0 pyfaidx pyfastaq pytest From 06bd70a8d2e22be1b79510246dce010cf3c10751 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:25 -0600 Subject: [PATCH 19/24] 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 50ebd70..a018d29 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,7 +54,7 @@ install_requires = numpy==1.18.1 pandas==1.0.2 path.py==12.4.0 - pyfaidx + pyfaidx==0.5.8 pyfastaq pytest pytest-shutil From dc54ee66b6ee44bacd7e5a5eb56f88df38dcf0ff Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:26 -0600 Subject: [PATCH 20/24] 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 a018d29..77b817a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -55,7 +55,7 @@ install_requires = pandas==1.0.2 path.py==12.4.0 pyfaidx==0.5.8 - pyfastaq + pyfastaq==3.17.0 pytest pytest-shutil pyyaml From 6051918dc8db8733275a611e3393a60094936844 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:27 -0600 Subject: [PATCH 21/24] 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 77b817a..4f3c869 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 0322c7091e476cd4e0e3f0d4ff153a28f68d3e61 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:28 -0600 Subject: [PATCH 22/24] 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 4f3c869..50b78b0 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 d5ce08ae23dc42c880771bb54d62c9a8ccb8dcca Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:29 -0600 Subject: [PATCH 23/24] Pin pyyaml to latest version 5.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 50b78b0..a3861f1 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 seaborn [options.package_data] From cf74010764276887eb44b21a00e756b9ca3ad012 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 16 Mar 2020 12:03:30 -0600 Subject: [PATCH 24/24] 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 a3861f1..1158263 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 - seaborn + seaborn==0.10.0 [options.package_data] * =