From bfcbf194162c2e740bb5d019842a6746d3b2dea0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:06 -0700 Subject: [PATCH 01/20] 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 4836630..987b8dd 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 254ac8867accdb5e2715b371e41d6000e0c9a30c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:07 -0700 Subject: [PATCH 02/20] Update matplotlib from 3.1.2 to 3.1.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 987b8dd..13ff956 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==3.1.3 mock==3.0.5 # via pytest-shutil more-itertools==8.1.0 # via pytest numpy==1.18.1 From 129fc65f1ff7d17a995fc4898c09dbc33aba4e72 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:08 -0700 Subject: [PATCH 03/20] 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 13ff956..4816c1a 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==3.1.3 mock==3.0.5 # 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 6f2220a2092216f5acefbe37bbd25026c9c288ff Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:09 -0700 Subject: [PATCH 04/20] Update pandas from 0.25.3 to 1.0.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4816c1a..98f68f1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ mock==3.0.5 # via pytest-shutil more-itertools==8.2.0 # via pytest numpy==1.18.1 packaging==20.1 # via pytest -pandas==0.25.3 +pandas==1.0.0 pluggy==0.13.1 # via pytest py==1.8.1 # via pytest path.py==12.0.2 # via pytest-shutil From 85613465a398df694851ebeaf97da4cf1d4a7877 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:10 -0700 Subject: [PATCH 05/20] 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 98f68f1..b3e5a94 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,7 +18,7 @@ packaging==20.1 # via pytest pandas==1.0.0 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 d18a54392f8b4b2c2cbf740c72e95a7e2d7715e7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:11 -0700 Subject: [PATCH 06/20] Update pytest from 5.3.4 to 5.3.5 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index b3e5a94..6329ea9 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==5.3.5 pytest-shutil==1.7.0 pytz==2019.3 # via pandas pyyaml==5.3 From bda6e1e23f41f2ca9018a07254a3a0072490f2bd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:12 -0700 Subject: [PATCH 07/20] 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 0ba19d2b3c9f0a26fd513a4c651450f67cd8539c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:13 -0700 Subject: [PATCH 08/20] 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 f782b8fe2584c690839a6b44c61b86de89b36cde Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:14 -0700 Subject: [PATCH 09/20] 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 9edad6c011257daf75dd84c19e4b19743a58bc26 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:16 -0700 Subject: [PATCH 10/20] 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 787fa17e14cccac24c493417d4816941a514ea24 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:17 -0700 Subject: [PATCH 11/20] Pin matplotlib to latest version 3.1.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 20958d0..18a69dd 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==3.1.3 numpy pandas path.py<=12.0.2 From 59b950969cb778496a2646d3e786ca655a3bb682 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:18 -0700 Subject: [PATCH 12/20] 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 18a69dd..b17a91e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = colorama==0.4.3 coverage==5.0.3 matplotlib==3.1.3 - numpy + numpy==1.18.1 pandas path.py<=12.0.2 pyfaidx From 3723ca6585fe2235c560a1544f3eab1dee6283c6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:20 -0700 Subject: [PATCH 13/20] Pin pandas to latest version 1.0.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index b17a91e..a65bdc7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = coverage==5.0.3 matplotlib==3.1.3 numpy==1.18.1 - pandas + pandas==1.0.0 path.py<=12.0.2 pyfaidx pyfastaq From caea06a4c614047f224d173dfdf602d6b251f97f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:21 -0700 Subject: [PATCH 14/20] 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 a65bdc7..98b16b9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = matplotlib==3.1.3 numpy==1.18.1 pandas==1.0.0 - path.py<=12.0.2 + path.py==12.4.0 pyfaidx pyfastaq pytest From 970589b25ac4a87ad98e3601c6817329fbdde9eb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:22 -0700 Subject: [PATCH 15/20] 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 98b16b9..a1508a6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,7 +54,7 @@ install_requires = numpy==1.18.1 pandas==1.0.0 path.py==12.4.0 - pyfaidx + pyfaidx==0.5.8 pyfastaq pytest pytest-shutil From 8df6343287c9c7cf30224aefd6f6b0976dead68c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:23 -0700 Subject: [PATCH 16/20] 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 a1508a6..5b679dd 100644 --- a/setup.cfg +++ b/setup.cfg @@ -55,7 +55,7 @@ install_requires = pandas==1.0.0 path.py==12.4.0 pyfaidx==0.5.8 - pyfastaq + pyfastaq==3.17.0 pytest pytest-shutil pyyaml From e07f0bcbf050796ad359a1c217b62db12b7fd0c8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:24 -0700 Subject: [PATCH 17/20] Pin pytest to latest version 5.3.5 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5b679dd..26a0aa4 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==5.3.5 pytest-shutil pyyaml seaborn From e62771bd147112b49731844789dfad99fe40f1c5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:26 -0700 Subject: [PATCH 18/20] 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 26a0aa4..7cf3e1e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -57,7 +57,7 @@ install_requires = pyfaidx==0.5.8 pyfastaq==3.17.0 pytest==5.3.5 - pytest-shutil + pytest-shutil==1.7.0 pyyaml seaborn From 7a25f23418d7b4492f0dd73cef362744e77be208 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:27 -0700 Subject: [PATCH 19/20] 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 7cf3e1e..97f2876 100644 --- a/setup.cfg +++ b/setup.cfg @@ -58,7 +58,7 @@ install_requires = pyfastaq==3.17.0 pytest==5.3.5 pytest-shutil==1.7.0 - pyyaml + pyyaml==5.3 seaborn [options.package_data] From b4428eb7b0b230435d4804666d194715c169392e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 3 Feb 2020 11:05:28 -0700 Subject: [PATCH 20/20] 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 97f2876..57e7828 100644 --- a/setup.cfg +++ b/setup.cfg @@ -59,7 +59,7 @@ install_requires = pytest==5.3.5 pytest-shutil==1.7.0 pyyaml==5.3 - seaborn + seaborn==0.10.0 [options.package_data] * =