From f92edb02ed8da3679698f27e6ec20b4ca5ebf19a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:06 -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 1a4b4bc4009435737a8e28b2a272f7d5439e3e3c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:07 -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 c9f49c59aedfca2c5541d791379a4bf4c516ffb1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:08 -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 045f74af294d03a670d00c3dd00a5567a809d024 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:09 -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 d35568387831567a3a2e5d95879f2493666ecc57 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:10 -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 900375ea332a8b402dca0c8a2a6561018b1ee723 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:11 -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 3d7c3476cc3588f8cc1e22ca49f4faa203509d41 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:13 -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 167e24f608e2d2a3c25162b996342afb1646b1ae Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:14 -0600 Subject: [PATCH 08/30] Update numpy from 1.18.1 to 1.18.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 90f06e5..41dafc9 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==1.18.3 packaging==20.1 # via pytest pandas==0.25.3 pluggy==0.13.1 # via pytest From 5ddbd04c93ff3ff2b265aa917c107fcbc59fe4a5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:15 -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 41dafc9..d63f4b7 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==1.18.3 -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 0cc0093861a86b9e9c460523f63e6b0e8511798c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:16 -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 d63f4b7..04d2e74 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==1.18.3 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 2049aede830bbe02be51d9a98205ad8e63a8b33e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:17 -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 04d2e74..9509dec 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 703ca54476f4e0c69639108dbe7683d589d10cc0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:18 -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 9509dec..a65b914 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 ccf079c251d333f1938417d3fcef3e33d9130600 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:19 -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 a65b914..fe11434 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 15f3c46dafd6e031d77ec76be23710416a5d1b35 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:20 -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 fe11434..daa0d70 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 66f9c20986d963b9ece7776c899942272c43b907 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:21 -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 daa0d70..9a639a7 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 3ed0972d0926778a1f391d234b6a9bdd5b3e647a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:22 -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 9a639a7..fe16e91 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 4ebc53ceabc6b4810e95e59a2618a84843509194 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:23 -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 c62679f28a0e72c1eaf03d79b4f22c2bd9a41a17 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:24 -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 2e588a140b56123171acb67fde8fddf0b5409685 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:25 -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 c0098768854eddeb1c7115e67f116face5b643ce Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:26 -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 3aa62d149b9e843792bd2f1f1e8b5f231a08e80f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:27 -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 a7328d06e90a7e090f778f62be5241b4eabf5f94 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:28 -0600 Subject: [PATCH 22/30] Pin numpy to latest version 1.18.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 155f1b4..39011f8 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==1.18.3 pandas path.py<=12.0.2 pyfaidx From 1fe111d861be1af6cf196031186693773be382fd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:29 -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 39011f8..552ef07 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = coverage==5.1 matplotlib==3.2.1 numpy==1.18.3 - pandas + pandas==1.0.3 path.py<=12.0.2 pyfaidx pyfastaq From eccbabd8daa19ce153e0aa80279cdcf19fd0e596 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:30 -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 552ef07..346743c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = matplotlib==3.2.1 numpy==1.18.3 pandas==1.0.3 - path.py<=12.0.2 + path.py==12.4.0 pyfaidx pyfastaq pytest From a9d54abc631f557385b264b5187a2ebc93b408eb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:32 -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 346743c..22026c1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,7 +54,7 @@ install_requires = numpy==1.18.3 pandas==1.0.3 path.py==12.4.0 - pyfaidx + pyfaidx==0.5.8 pyfastaq pytest pytest-shutil From 86906f662970b1cf5752c090492158c3a2156c59 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:33 -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 22026c1..a32dc49 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 242e6d499305fa49c817c345e853d6945cf882e5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:34 -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 a32dc49..7df0622 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 0440c54b277d244109013229f1fe7d769f89e788 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:35 -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 7df0622..5dc12de 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 ca99e82ab23788e7e9830d9c44f12ede87096241 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:36 -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 5dc12de..6082434 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 406c8551a96eb0174f5017536bca8f88874ead61 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 20 Apr 2020 12:12:37 -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 6082434..4805ea1 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] * =