From a35dcd95a8547579a7565bbc27ec7bfaef7d11e5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:04 -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 83e9b860ce211f41ffff2fd18b4abc8b98f6035e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:05 -0600 Subject: [PATCH 02/30] Update coverage from 5.0.3 to 5.0.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0a4b83f..e5bc414 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==5.0.4 cycler==0.10.0 # via matplotlib execnet==1.7.1 # via pytest-shutil importlib-metadata==1.4.0 # via pytest From 02c09a23cfde5bd79e3d02c6a70fcbf1ad55c886 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:06 -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 e5bc414..86a8026 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,7 +8,7 @@ contextlib2==0.6.0.post1 # via pytest-shutil coverage==5.0.4 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 3c19bf8070465fc3ac87fa2e65099c15eb2ae0e3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:07 -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 86a8026..e4932ce 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ coverage==5.0.4 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 1378690ccdc0838d0f474acb3b8abe90945dc8bc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:09 -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 e4932ce..be7749d 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 7efb7c5728ffb889e64c9df6b116e27ae0580f52 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:10 -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 be7749d..f850d10 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 e2a88d13eb5c866aed6225722769472f475069be Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:11 -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 f850d10..37f670a 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 411896343e2133e22058f1701599659b882413cb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:12 -0600 Subject: [PATCH 08/30] Update numpy from 1.18.1 to 1.18.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 37f670a..16c027b 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==1.18.2 packaging==20.1 # via pytest pandas==0.25.3 pluggy==0.13.1 # via pytest From 2bb80e03bd90fca6e5df53062eb6f241d83a5d81 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:13 -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 16c027b..01d935f 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==1.18.2 -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 3380bc01870c02ceec3732d8193da180a84f2ac5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:14 -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 01d935f..5f9dfa4 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==1.18.2 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 8eb1da5e5ef39842f1e6348669f13ea3a820ee90 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:15 -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 5f9dfa4..5424005 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 6b866fb2cb4b0056f567bff89802d1e75dd53601 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:17 -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 5424005..68224e7 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 6c5648bea87d2810619de18bb542eab74a19e3f5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:18 -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 68224e7..c6ca62c 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 8d5f0bae0d324c1566b1400c16ebe74cd4f2a5b2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:19 -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 c6ca62c..65b5881 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 14d00e87f18d18fed73021980be55f15d8615b88 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:20 -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 65b5881..c632661 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 145857125ef8a39013b6551baddf2e9b038cb2d6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:22 -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 c632661..367b1f7 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 f28d3589def90adf55f72ea468a593df5e83faf0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:23 -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 e5ac1b216e425963abc35b2572ac96e2e143df74 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:24 -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 e5be7afd5caf3d26c89d5db369045fac5feea987 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:25 -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 6eceb4785e090b59312d3db72e558199a33bcf9a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:26 -0600 Subject: [PATCH 20/30] Pin coverage to latest version 5.0.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index d7591e5..1cc77f4 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==5.0.4 matplotlib numpy pandas From a5b4711fed970d2e74e5bd391015a7ab5e6a5c8f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:28 -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 1cc77f4..0085838 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 colorama==0.4.3 coverage==5.0.4 - matplotlib + matplotlib==3.2.1 numpy pandas path.py<=12.0.2 From 7e542f5cba5257823f568c870c4f9ad518197448 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:29 -0600 Subject: [PATCH 22/30] Pin numpy to latest version 1.18.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0085838..579fd59 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = colorama==0.4.3 coverage==5.0.4 matplotlib==3.2.1 - numpy + numpy==1.18.2 pandas path.py<=12.0.2 pyfaidx From 07f60ea5e70833b504de3cb8911822fabc8959dd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:30 -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 579fd59..576dabc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = coverage==5.0.4 matplotlib==3.2.1 numpy==1.18.2 - pandas + pandas==1.0.3 path.py<=12.0.2 pyfaidx pyfastaq From e26fa6d8cee45e419fead95835a947bed6be657c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:31 -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 576dabc..cb7d7e6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = matplotlib==3.2.1 numpy==1.18.2 pandas==1.0.3 - path.py<=12.0.2 + path.py==12.4.0 pyfaidx pyfastaq pytest From c7084ef47a58965fb595c6e1b675bea5b0f062ba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:32 -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 cb7d7e6..6f72f1c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,7 +54,7 @@ install_requires = numpy==1.18.2 pandas==1.0.3 path.py==12.4.0 - pyfaidx + pyfaidx==0.5.8 pyfastaq pytest pytest-shutil From fb99e4f2df953e634fe37eb6c815137351736f55 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:33 -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 6f72f1c..2151a18 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 7cd1a629db2239b6ec4b3a8b106528d5110e318e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:34 -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 2151a18..53271c1 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 3ca816a1562f9146ba232c2b8d5866060ae24b19 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:36 -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 53271c1..2c8f75b 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 15fc5ed65523f220e1b157f187d9290d62ea530b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:37 -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 2c8f75b..6603f30 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 098502b729fc3869c617c11218635163626dad21 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 6 Apr 2020 12:10:38 -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 6603f30..bb9eab9 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] * =