From 4c24ecf2e66e4b48fe4fdc1f405d8a70d2d0b1a8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:05 -0700 Subject: [PATCH 01/22] 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 500e305b70f6c7a0ef5393cfd992e5e65756f6f4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:06 -0700 Subject: [PATCH 02/22] 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 93af029b73626b1669d21a2bc01b640991815863 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:07 -0700 Subject: [PATCH 03/22] Update mock from 3.0.5 to 4.0.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 13ff956..c182a0c 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==3.1.3 -mock==3.0.5 # via pytest-shutil +mock==4.0.1 # via pytest-shutil more-itertools==8.1.0 # via pytest numpy==1.18.1 packaging==20.1 # via pytest From ceb220abe310d97ab670cd2f1376b8bc79a47318 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:09 -0700 Subject: [PATCH 04/22] 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 c182a0c..6c14973 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==4.0.1 # 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 330129ca38d9eb3857cfda2e24c929f5b41ece16 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:10 -0700 Subject: [PATCH 05/22] Update pandas from 0.25.3 to 1.0.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 6c14973..d96b3f4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ mock==4.0.1 # via pytest-shutil more-itertools==8.2.0 # via pytest numpy==1.18.1 packaging==20.1 # via pytest -pandas==0.25.3 +pandas==1.0.1 pluggy==0.13.1 # via pytest py==1.8.1 # via pytest path.py==12.0.2 # via pytest-shutil From f36d9533352945a5b64a5fd8eb97e72194dd32c6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:11 -0700 Subject: [PATCH 06/22] 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 d96b3f4..11f247d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,7 +18,7 @@ packaging==20.1 # via pytest pandas==1.0.1 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 78c1b3dc0e7050410017cee12b64cac543e99a63 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:12 -0700 Subject: [PATCH 07/22] 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 11f247d..2c6ded5 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 22cad1ef3623ccd07f4458faec95bfe2254488b1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:13 -0700 Subject: [PATCH 08/22] Update zipp from 2.1.0 to 2.2.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 2c6ded5..473d8e5 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==2.2.0 # via pytest \ No newline at end of file From c59a3cfd58257aa3c1b650da3b232ccb32e73d72 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:14 -0700 Subject: [PATCH 09/22] 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 509ec999d172b041b30fe0ef0accb30aa038e41a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:15 -0700 Subject: [PATCH 10/22] 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 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 c446cad537de37b42b3fd7332dd7e261c2ae8898 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:16 -0700 Subject: [PATCH 11/22] 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 465d245f0fca947fb739f08ae8224f9ba84309fe Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:17 -0700 Subject: [PATCH 12/22] 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 61a4156923729528e94b677d2e54528e36fe2554 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:18 -0700 Subject: [PATCH 13/22] 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 c2685f148fb8382dc856c52bf0e5ca28382cdbd4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:19 -0700 Subject: [PATCH 14/22] 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 440302fe4d4644c09cdf86a5cee96f97ada3615b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:21 -0700 Subject: [PATCH 15/22] Pin pandas to latest version 1.0.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index b17a91e..928b4a6 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==1.0.1 path.py<=12.0.2 pyfaidx pyfastaq From 395ae6061e00c48906bafcbd22198a3b8b655db0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:22 -0700 Subject: [PATCH 16/22] 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 928b4a6..a98b809 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = matplotlib==3.1.3 numpy==1.18.1 pandas==1.0.1 - path.py<=12.0.2 + path.py==12.4.0 pyfaidx pyfastaq pytest From 1a914cf5e33d0415b92f567aadef1b5098f19036 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:23 -0700 Subject: [PATCH 17/22] 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 a98b809..e85e04d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,7 +54,7 @@ install_requires = numpy==1.18.1 pandas==1.0.1 path.py==12.4.0 - pyfaidx + pyfaidx==0.5.8 pyfastaq pytest pytest-shutil From 6150a6fb6d9911a803f3d94c6904fac21ae51217 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:24 -0700 Subject: [PATCH 18/22] 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 e85e04d..1b35a90 100644 --- a/setup.cfg +++ b/setup.cfg @@ -55,7 +55,7 @@ install_requires = pandas==1.0.1 path.py==12.4.0 pyfaidx==0.5.8 - pyfastaq + pyfastaq==3.17.0 pytest pytest-shutil pyyaml From f0220d443a89a6591b8cf4ce02a89e48f3bc006d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:25 -0700 Subject: [PATCH 19/22] 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 1b35a90..455c262 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 1bc0ba611a497b308faebeff3ccc01419c2ac865 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:27 -0700 Subject: [PATCH 20/22] 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 455c262..0070068 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 937bc5de5449459a4b08b579c924ca728a5cba57 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:28 -0700 Subject: [PATCH 21/22] 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 0070068..f3b93a9 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 c2f5f347a67d3b425ab28dec65090d4a76423776 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Feb 2020 11:03:29 -0700 Subject: [PATCH 22/22] 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 f3b93a9..e1a99b0 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] * =