From a855e682fdb181a08b8a38def9b797d5febba815 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:05 -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 044e530ba4f61732111ea5dcb474b780d6aeaab2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:07 -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 8804058c9abb0acc262b6ac71ffa78f3c62b15b0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:08 -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 64da790f68175b739522b4d070ffa5a49af8db12 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:09 -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 9b41a57204b8a743fcb6f0255980610d07308e5d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:11 -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 6c4649d6fcc654f411338c57b4ae3bd8ffde81d1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:12 -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 69557eb03e691ba48aeac955ac6cac681339866a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:13 -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 595bc14794ef58d7eb9c049491ef89ee69eb0936 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:14 -0700 Subject: [PATCH 08/22] Update zipp from 2.1.0 to 3.0.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 2c6ded5..7317876 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==3.0.0 # via pytest \ No newline at end of file From d75f2ad24c578ce7afb0a3766166ab31f2d01f8d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:15 -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 18a74764f4dcdf2271de942bd415bb5948c71ca5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:16 -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 44be17cf752d05c82992f5657ecf2c1a9f62b588 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:17 -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 542900cd70e69a61fb196ebfc7dc896278ac995d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:18 -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 6f4a373a91d77a477121dc2ef2a4b0b4b954d66e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:20 -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 a2e98120194fcc9963ff7a43014c23f35c9b59be Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:21 -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 fa5480577815bd9b76ed6bc3638fb442d6161bc4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:22 -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 c7b4f6015483515cf6078aef96f64635f3315a5d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:23 -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 dd7801f96ecfb1a834748fce292547a40aedd41b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:24 -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 ec591a8825d2c8ac5984f6565edac72514d93396 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:25 -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 0b037dee03e593a4e75f812cd9ff1801284d53e0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:26 -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 aa1732f43f687433c8645cc198e08c0dd6206059 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:27 -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 edde495bef757a31aa61c29b5532c600f6c28d46 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:28 -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 46c696b01b8e43d2e7b1ce4370e60371a8abbc8c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Mar 2020 11:02:30 -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] * =