From a90855cc955581cbad283c085ddb424418ca0d39 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:05 -0600 Subject: [PATCH 01/22] Update biopython from 1.72 to 1.74 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 161185b..59fde0c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,7 +4,7 @@ # # pip-compile --output-file requirements.txt setup.py # -biopython==1.72 +biopython==1.74 click-plugins==1.0.3 click==6.7 coverage==4.5.1 From c10f3ca6be34ac897c546ee37313ae5cc0149436 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:06 -0600 Subject: [PATCH 02/22] Update click-plugins from 1.0.3 to 1.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 59fde0c..81a16ff 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ # pip-compile --output-file requirements.txt setup.py # biopython==1.74 -click-plugins==1.0.3 +click-plugins==1.1.1 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From 3fb7b8b26009590b21050f1e7add8069faba35ab Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:08 -0600 Subject: [PATCH 03/22] Update click from 6.7 to 7.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 81a16ff..c885cda 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.74 click-plugins==1.1.1 -click==6.7 +click==7.0 coverage==4.5.1 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib From 165ddfb7fbaacb0c3add2353efe2370a0e2a2834 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:09 -0600 Subject: [PATCH 04/22] Update coverage from 4.5.1 to 4.5.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c885cda..4329e1f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.74 click-plugins==1.1.1 click==7.0 -coverage==4.5.1 +coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From e21e04f1acc9af22b88ccc446eaf10c6e1064e8a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:10 -0600 Subject: [PATCH 05/22] Update kiwisolver from 1.0.1 to 1.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4329e1f..4b84855 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ click-plugins==1.1.1 click==7.0 coverage==4.5.4 cycler==0.10.0 # via matplotlib -kiwisolver==1.0.1 # via matplotlib +kiwisolver==1.1.0 # via matplotlib matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 From 84f5d0fb47eb2c25d635da5dcbd120fc4cd47716 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:11 -0600 Subject: [PATCH 06/22] Update matplotlib from 3.0.0 to 3.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4b84855..d6c3c84 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.1.1 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 731e1adb656212b2025f668920a0b32b953ff085 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:12 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.17.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index d6c3c84..566eef3 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 -numpy==1.15.2 +numpy==1.17.1 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 4b76117ed48e433f3d4cd1ab2efa473ef70bac77 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:13 -0600 Subject: [PATCH 08/22] Update pandas from 0.23.4 to 0.25.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 566eef3..d1646af 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.1 -pandas==0.23.4 +pandas==0.25.1 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From caedbe71a00d6b6fd3ecb6aa1b53d2aedd88a037 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:14 -0600 Subject: [PATCH 09/22] Update pyfaidx from 0.5.4.2 to 0.5.5.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index d1646af..4322c48 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.1 pandas==0.25.1 -pyfaidx==0.5.4.2 +pyfaidx==0.5.5.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas From e934025c7d12a1267da1bf72ba36f641daa66700 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:15 -0600 Subject: [PATCH 10/22] Update pyparsing from 2.2.1 to 2.4.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4322c48..49e5cd8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.1 numpy==1.17.1 pandas==0.25.1 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.4.2 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 72c484011e8447af6868a11bda72ec2d42a96793 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:16 -0600 Subject: [PATCH 11/22] Update python-dateutil from 2.7.3 to 2.8.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 49e5cd8..459ee98 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.17.1 pandas==0.25.1 pyfaidx==0.5.5.2 pyparsing==2.4.2 # via matplotlib -python-dateutil==2.7.3 # via matplotlib, pandas +python-dateutil==2.8.0 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From db9573ef03d61c3a745ac5b95555403bb65b1124 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:17 -0600 Subject: [PATCH 12/22] Update pytz from 2018.5 to 2019.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 459ee98..fcd69d8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.25.1 pyfaidx==0.5.5.2 pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2019.2 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From d38fb347043db75f30a5afbd9cf84eb63b4916c1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:19 -0600 Subject: [PATCH 13/22] Update pyyaml from 3.13 to 5.1.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index fcd69d8..35875b0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,5 +17,5 @@ pyfaidx==0.5.5.2 pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.2 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1.2 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 04243b646fbdda1db83b7dbc82597ec7a439c1cd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:20 -0600 Subject: [PATCH 14/22] Update six from 1.11.0 to 1.12.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 35875b0..60558ef 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.2 # via matplotlib, pandas pyyaml==5.1.2 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 278391494a78cc2c8af2f5af116b835b557da345 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:20 -0600 Subject: [PATCH 15/22] Pin biopython to latest version 1.74 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8f7e0f4..b6255cb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,7 +45,7 @@ zip_safe = False include_package_data = True packages = aakbar install_requires = - biopython + biopython==1.74 click>=5.0 click_plugins coverage From 3db064d2d93d65198cef372d060a9e0c807a32f0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:22 -0600 Subject: [PATCH 16/22] 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 b6255cb..f6dfaf3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ packages = aakbar install_requires = biopython==1.74 click>=5.0 - click_plugins + click_plugins==1.1.1 coverage matplotlib numpy From 3e8f3cd6a492c30f234b1f8a1ab8be2903e881fa Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:23 -0600 Subject: [PATCH 17/22] Pin coverage to latest version 4.5.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index f6dfaf3..c271fca 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.74 click>=5.0 click_plugins==1.1.1 - coverage + coverage==4.5.4 matplotlib numpy pandas From 16f7f19a4a115bfd5af03d516d04c4d4d09d6c5d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:24 -0600 Subject: [PATCH 18/22] Pin matplotlib to latest version 3.1.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index c271fca..13cfaa3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.1.1 coverage==4.5.4 - matplotlib + matplotlib==3.1.1 numpy pandas pyfaidx From b99fd2cf73296e60006b0c2097549a9108f912b0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:25 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.17.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 13cfaa3..0c36194 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.4 matplotlib==3.1.1 - numpy + numpy==1.17.1 pandas pyfaidx pyyaml From 8de6ed277bed0569a0c44fdbeb3ce682c93f54d7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:26 -0600 Subject: [PATCH 20/22] Pin pandas to latest version 0.25.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0c36194..18ecbd0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.4 matplotlib==3.1.1 numpy==1.17.1 - pandas + pandas==0.25.1 pyfaidx pyyaml From 1f3273dfbcddd37ba78bd824843655fa2e924c92 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:27 -0600 Subject: [PATCH 21/22] Pin pyfaidx to latest version 0.5.5.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 18ecbd0..a679325 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.1 numpy==1.17.1 pandas==0.25.1 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 014c6618370fc9b2ae607130ad551f3a43e0bb3d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 2 Sep 2019 11:51:28 -0600 Subject: [PATCH 22/22] Pin pyyaml to latest version 5.1.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index a679325..e0dadf9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.17.1 pandas==0.25.1 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1.2 [options.package_data] * =