From 5cfd835dd26a689091888fdcb039dd246e3d28a9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:12 -0700 Subject: [PATCH 01/20] Update biopython from 1.72 to 1.73 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 161185b..3aad626 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,7 +4,7 @@ # # pip-compile --output-file requirements.txt setup.py # -biopython==1.72 +biopython==1.73 click-plugins==1.0.3 click==6.7 coverage==4.5.1 From 98cfb444304f8a93046b0f858d88f3aa2754281c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:19 -0700 Subject: [PATCH 02/20] Update click-plugins from 1.0.3 to 1.0.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3aad626..4ae4708 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ # pip-compile --output-file requirements.txt setup.py # biopython==1.73 -click-plugins==1.0.3 +click-plugins==1.0.4 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From 74a6fb1aa9954e7cd153d25da909da93e0289bcc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:21 -0700 Subject: [PATCH 03/20] 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 4ae4708..3ddc393 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.73 click-plugins==1.0.4 -click==6.7 +click==7.0 coverage==4.5.1 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib From d7241465ec4f7b7cdeec629cbe2bbb786c87aeea Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:23 -0700 Subject: [PATCH 04/20] Update coverage from 4.5.1 to 4.5.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3ddc393..8483d17 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.73 click-plugins==1.0.4 click==7.0 -coverage==4.5.1 +coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From 873bf0fcd10fa5cbbefcb85cf71f89ebdc8bdda9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:25 -0700 Subject: [PATCH 05/20] Update matplotlib from 3.0.0 to 3.0.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 8483d17..60f70c8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.0.2 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From dcc62bfd18e5079e9211332ac1fc8973a494cb51 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:30 -0700 Subject: [PATCH 06/20] Update numpy from 1.15.2 to 1.16.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 60f70c8..162d429 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.2 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 -numpy==1.15.2 +numpy==1.16.1 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 004f3fadf8b57c8ca7f4e103dbf261e2cd58afaf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:32 -0700 Subject: [PATCH 07/20] Update pandas from 0.23.4 to 0.24.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 162d429..9c84dad 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 numpy==1.16.1 -pandas==0.23.4 +pandas==0.24.1 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 31ddd1849b8421943bd39644dae942d3a19dd2c6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:33 -0700 Subject: [PATCH 08/20] 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 9c84dad..7c43b62 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 numpy==1.16.1 pandas==0.24.1 -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 95af9f934597aaa24c681114c5f42092fb5eb4c7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:35 -0700 Subject: [PATCH 09/20] Update pyparsing from 2.2.1 to 2.3.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 7c43b62..9491301 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.2 numpy==1.16.1 pandas==0.24.1 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.3.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 6a484a85d39c123a8f51c921a77954e4fe42be46 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:39 -0700 Subject: [PATCH 10/20] 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 9491301..0807bfa 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.1 pandas==0.24.1 pyfaidx==0.5.5.2 pyparsing==2.3.1 # 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 ef20b039a36f53c9f37e18a7071f4a0728dd357c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:41 -0700 Subject: [PATCH 11/20] Update pytz from 2018.5 to 2018.9 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0807bfa..58316e6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.1 pyfaidx==0.5.5.2 pyparsing==2.3.1 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2018.9 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From e02116579e1d667b9ccb163c0df5ea74a48fc85e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:43 -0700 Subject: [PATCH 12/20] 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 58316e6..3ea7cba 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.3.1 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2018.9 # via matplotlib, pandas pyyaml==3.13 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From d71c5606b50f76ff0b7692c4b7aa00a221c09492 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:47 -0700 Subject: [PATCH 13/20] Pin biopython to latest version 1.73 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8f7e0f4..83e3fe0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,7 +45,7 @@ zip_safe = False include_package_data = True packages = aakbar install_requires = - biopython + biopython==1.73 click>=5.0 click_plugins coverage From 2ea50ed761cf0dadc4259114c1bea72992d58dc6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:48 -0700 Subject: [PATCH 14/20] Pin click_plugins to latest version 1.0.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 83e3fe0..3749980 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ packages = aakbar install_requires = biopython==1.73 click>=5.0 - click_plugins + click_plugins==1.0.4 coverage matplotlib numpy From 16f4c57bbcf723f64dbfb387a83f399396c813ef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:50 -0700 Subject: [PATCH 15/20] Pin coverage to latest version 4.5.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 3749980..abf82c2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.73 click>=5.0 click_plugins==1.0.4 - coverage + coverage==4.5.2 matplotlib numpy pandas From 2631818eae8a6185ef7e812c5d7f1f4d969f0e14 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:51 -0700 Subject: [PATCH 16/20] Pin matplotlib to latest version 3.0.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index abf82c2..9546d9f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.0.4 coverage==4.5.2 - matplotlib + matplotlib==3.0.2 numpy pandas pyfaidx From f8c9de9509e0776f462a418579524d8d898137a3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:53 -0700 Subject: [PATCH 17/20] Pin numpy to latest version 1.16.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9546d9f..e4859d4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.0.4 coverage==4.5.2 matplotlib==3.0.2 - numpy + numpy==1.16.1 pandas pyfaidx pyyaml From 4d8c137863bc309fc48c9641bf351fa044576b36 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:55 -0700 Subject: [PATCH 18/20] Pin pandas to latest version 0.24.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index e4859d4..179755f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.2 matplotlib==3.0.2 numpy==1.16.1 - pandas + pandas==0.24.1 pyfaidx pyyaml From 586617ddc5cf2645439ae527a4192a79d33d77e3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:57 -0700 Subject: [PATCH 19/20] 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 179755f..2cafa73 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.2 numpy==1.16.1 pandas==0.24.1 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 28298d44070e1429bd7479ad43794ea86311ac08 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 11 Feb 2019 10:26:58 -0700 Subject: [PATCH 20/20] Pin pyyaml to latest version 3.13 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 2cafa73..2c643d8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.1 pandas==0.24.1 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =