From dbda58bd7097bc4397983a24b10aac736c651f60 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:05 -0600 Subject: [PATCH 01/24] Update click from 7.0 to 7.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4836630..2fdd9d8 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 colorama==0.4.3 contextlib2==0.6.0.post1 # via pytest-shutil coverage==5.0.3 From 40d09b3c5f7d7e36cccfa9985228e39d34aa1f53 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:06 -0600 Subject: [PATCH 02/24] 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 2fdd9d8..5573f2a 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 fb4d4e01d49afa6406c0223b887927d2e210c4e4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:07 -0600 Subject: [PATCH 03/24] Update matplotlib from 3.1.2 to 3.2.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5573f2a..94eed8a 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==3.2.0 mock==3.0.5 # via pytest-shutil more-itertools==8.1.0 # via pytest numpy==1.18.1 From adb50e5aa2c8cd1c2c3ab8a66e3d9ff328652436 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:12 -0600 Subject: [PATCH 04/24] 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 94eed8a..d5cbecc 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==3.2.0 -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 d2652483368093a28606bc92c264b17c961c1e86 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:14 -0600 Subject: [PATCH 05/24] 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 d5cbecc..9e279bd 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==3.2.0 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 e2a06130588e78331750f64a25697956ecd0d0e4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:15 -0600 Subject: [PATCH 06/24] 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 9e279bd..ca2b5a6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.2.0 mock==4.0.1 # via pytest-shutil more-itertools==8.2.0 # via pytest numpy==1.18.1 -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 19e0e4d53bd9cfcbbaa5729db20336663a5c5109 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:16 -0600 Subject: [PATCH 07/24] 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 ca2b5a6..3e6d684 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==20.3 # 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 4386b77e41992ae475070add70126451efe48401 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:17 -0600 Subject: [PATCH 08/24] 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 3e6d684..c1951c2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,7 +18,7 @@ packaging==20.3 # 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 d1fc9946b60a8c9fa424215768bb72dcb5f0fee5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:18 -0600 Subject: [PATCH 09/24] 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 c1951c2..1d2b04a 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 f2923b99b8500366d9a7710ac35bd2a24452b1cd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:22 -0600 Subject: [PATCH 10/24] 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 1d2b04a..dd3ad28 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==3.1.0 # via pytest \ No newline at end of file From eb4f6ce2b0e4451847eb9be8bdb5399ae3f566e2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:24 -0600 Subject: [PATCH 11/24] 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 bb706ae4793c50f931d6dbf4bd77d26821340b6d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:25 -0600 Subject: [PATCH 12/24] 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 6d0bddf31c9ef7f7306ed525fc658fdaef004851 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:26 -0600 Subject: [PATCH 13/24] 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 8e7ee88ee002bca25258134ef5371abfb813e28c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:27 -0600 Subject: [PATCH 14/24] 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 901eb21b92cebbde0bf2249258a50c907e8a8bdb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:29 -0600 Subject: [PATCH 15/24] Pin matplotlib to latest version 3.2.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 20958d0..aac921f 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==3.2.0 numpy pandas path.py<=12.0.2 From 7ce56c76e0115c0aaf560ca53abadbef92881902 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:30 -0600 Subject: [PATCH 16/24] 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 aac921f..dd5534e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = colorama==0.4.3 coverage==5.0.3 matplotlib==3.2.0 - numpy + numpy==1.18.1 pandas path.py<=12.0.2 pyfaidx From a4abbce77e8f677901e27a6a4fa7fe556581050b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:32 -0600 Subject: [PATCH 17/24] 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 dd5534e..20216ae 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = coverage==5.0.3 matplotlib==3.2.0 numpy==1.18.1 - pandas + pandas==1.0.1 path.py<=12.0.2 pyfaidx pyfastaq From c8fade305e6adccd26b93a0380f707825988c07f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:33 -0600 Subject: [PATCH 18/24] 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 20216ae..e140747 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = matplotlib==3.2.0 numpy==1.18.1 pandas==1.0.1 - path.py<=12.0.2 + path.py==12.4.0 pyfaidx pyfastaq pytest From 78126cfb4bbb08b38e47f0a87f29d54c0fd25104 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:34 -0600 Subject: [PATCH 19/24] 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 e140747..b390bd2 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 faae4a07bba054915894b6b1af2b6514d1386aa6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:35 -0600 Subject: [PATCH 20/24] 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 b390bd2..6ebb34c 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 277279a5cfdf2c3823171bb2ecd3ad2c16b169bb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:37 -0600 Subject: [PATCH 21/24] 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 6ebb34c..599a2d2 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 791ccee75f9fc3e5041393d5cb3dc5f4bdca7585 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:38 -0600 Subject: [PATCH 22/24] 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 599a2d2..65a42c7 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 04607f977e405f51f1fb6e8be398bcc711727c55 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:39 -0600 Subject: [PATCH 23/24] 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 65a42c7..4035d9e 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 ee26b27134b3c2e2abd07b1fc389b205c4bdfac0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 9 Mar 2020 12:02:40 -0600 Subject: [PATCH 24/24] 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 4035d9e..0641b31 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] * =