From d8f01f158105b062b08949ab8dd9119d22b67e07 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:06 -0600 Subject: [PATCH 01/22] 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 1da1d361160cae2f7c848969b2012dc9e56a9997 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:07 -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 3aad626..b73c8ad 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==1.1.1 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From 07942cf561f85bdf580a68670a41ac4b10a2c72c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:08 -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 b73c8ad..a2eaa96 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.73 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 e36b19f450ee5347134b811120dfa37b33ec71e2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:09 -0600 Subject: [PATCH 04/22] Update coverage from 4.5.1 to 4.5.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a2eaa96..73aa2e0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.73 click-plugins==1.1.1 click==7.0 -coverage==4.5.1 +coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From 9c3b0a61f786b110873eb660da462baa06df6ec7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:10 -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 73aa2e0..9295824 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ click-plugins==1.1.1 click==7.0 coverage==4.5.3 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 05013b49686bdafa8270fe57a57da98d584a4cc4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:11 -0600 Subject: [PATCH 06/22] Update matplotlib from 3.0.0 to 3.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 9295824..26754c1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.1.0 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 847623dfa458e479dac51e7e4c55917859c6b7e0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:13 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.16.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 26754c1..f819876 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 -numpy==1.15.2 +numpy==1.16.4 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 31af59213f06faae2133bb8cc6e76a9869167044 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:14 -0600 Subject: [PATCH 08/22] Update pandas from 0.23.4 to 0.24.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f819876..0e2a3ff 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 numpy==1.16.4 -pandas==0.23.4 +pandas==0.24.2 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 37f0fbb0dd515cc3e8be7138c46af087a81ef2f1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:15 -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 0e2a3ff..cac4ba0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.0 numpy==1.16.4 pandas==0.24.2 -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 b1ae99bb87f4b1f57c7893e1b35f2f03c3d95f4b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:16 -0600 Subject: [PATCH 10/22] Update pyparsing from 2.2.1 to 2.4.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index cac4ba0..1eb47d0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.0 numpy==1.16.4 pandas==0.24.2 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.4.0 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From 12a878e6a2052776af270506ece0f01f6feaea4b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:17 -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 1eb47d0..5cab090 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.4 pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.4.0 # 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 a4640d6657aa7b8b935b136344bd7378ae7e1e74 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:18 -0600 Subject: [PATCH 12/22] Update pytz from 2018.5 to 2019.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5cab090..38c6842 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.2 pyfaidx==0.5.5.2 pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2019.1 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From ae9a56cdc0dd5d995957fc80e72e1e1cabd5477e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:19 -0600 Subject: [PATCH 13/22] Update pyyaml from 3.13 to 5.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 38c6842..e2d6c92 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,5 +17,5 @@ pyfaidx==0.5.5.2 pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.1 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1.1 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 365276c8cddecdc103d94c6e49d9a1f64cf586b6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:20 -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 e2d6c92..2dcd297 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.4.0 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.1 # via matplotlib, pandas pyyaml==5.1.1 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 1571f98cffcc526d60542fccc2f30fba55fa314a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:21 -0600 Subject: [PATCH 15/22] 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 eaf6721d2c003c6868ee06a566a9e9cb475ed1df Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:22 -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 83e3fe0..5326ef1 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==1.1.1 coverage matplotlib numpy From 929eff66e5cfe5864900a3cffbcb75e5be362472 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:23 -0600 Subject: [PATCH 17/22] Pin coverage to latest version 4.5.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5326ef1..5394098 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.73 click>=5.0 click_plugins==1.1.1 - coverage + coverage==4.5.3 matplotlib numpy pandas From 732aa7352c89427afd46f8c12d3b6c91ebdfb1e2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:25 -0600 Subject: [PATCH 18/22] Pin matplotlib to latest version 3.1.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5394098..0fc97c1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.1.1 coverage==4.5.3 - matplotlib + matplotlib==3.1.0 numpy pandas pyfaidx From 9bfc6d614af0b845dd2dc7003f4b56931c6d2e41 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:26 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.16.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0fc97c1..88823a4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.3 matplotlib==3.1.0 - numpy + numpy==1.16.4 pandas pyfaidx pyyaml From e7c097c6738410b2df853570c0869a6672d25e4d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:27 -0600 Subject: [PATCH 20/22] Pin pandas to latest version 0.24.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 88823a4..647b293 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.3 matplotlib==3.1.0 numpy==1.16.4 - pandas + pandas==0.24.2 pyfaidx pyyaml From d9eacbe1be235c2b73054a1304b5f5a4dde587ec Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:28 -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 647b293..6fbe36f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.0 numpy==1.16.4 pandas==0.24.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 633a1ccb39738d06b0fd1809d3702da237a10811 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 10 Jun 2019 11:50:29 -0600 Subject: [PATCH 22/22] Pin pyyaml to latest version 5.1.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 6fbe36f..9129ad3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.4 pandas==0.24.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1.1 [options.package_data] * =