From 0cb08133bfd247f7ca55cb375459ca404114303f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:08 -0600 Subject: [PATCH 01/21] 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 14436e62ac39d982fc673d57d0288ef0ed7de399 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:12 -0600 Subject: [PATCH 02/21] 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 757480e018d24cf4df57aa16e282200e81da3fd2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:13 -0600 Subject: [PATCH 03/21] 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 3cbd0ed0815bd07853435341221bc9493915d789 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:14 -0600 Subject: [PATCH 04/21] 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 93e90696f194b0a4f7dc8ead824de13ceeeee432 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:15 -0600 Subject: [PATCH 05/21] Update matplotlib from 3.0.0 to 3.0.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 73aa2e0..692fc34 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==1.0.1 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.0.3 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From ca3f698f87d117cb817113eadd1de10d781c4484 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:16 -0600 Subject: [PATCH 06/21] Update numpy from 1.15.2 to 1.16.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 692fc34..8bfc179 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.3 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.3 -numpy==1.15.2 +numpy==1.16.2 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 2acbba21c3c3f9237e1c956067d42e05ef7e500b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:17 -0600 Subject: [PATCH 07/21] 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 8bfc179..7b61035 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.3 numpy==1.16.2 -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 fc22466b7a40f81d77716508f9918d467e820376 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:18 -0600 Subject: [PATCH 08/21] 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 7b61035..49b0af1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.3 numpy==1.16.2 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 67232aa7f21bbbb400b14509c9b69c19522031e5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:19 -0600 Subject: [PATCH 09/21] 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 49b0af1..48c482c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.3 numpy==1.16.2 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 ab4a2a0a792a6da659226099ee459cef5ab2c9fb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:20 -0600 Subject: [PATCH 10/21] 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 48c482c..b4aa801 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.2 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 dc32163d1c4166b366ebaca4999bccdb17768ae6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:21 -0600 Subject: [PATCH 11/21] 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 b4aa801..7c8ee92 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==2018.9 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From d234e69a0be4b9bc41e5c0621d6ad5b2a64663e3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:22 -0600 Subject: [PATCH 12/21] Update pyyaml from 3.13 to 5.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 7c8ee92..38d1bcd 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==2018.9 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From b281abc1a19755de1115c4bb905e497941ea548b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:23 -0600 Subject: [PATCH 13/21] 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 38d1bcd..b2c148a 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==2018.9 # via matplotlib, pandas pyyaml==5.1 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 001cec06f78875c3489088ea67137202f07fb48a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:24 -0600 Subject: [PATCH 14/21] 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 0b47d4eb6786aabd7be3bd85475732337e1375c2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:25 -0600 Subject: [PATCH 15/21] 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 4c562ae904b4be178666ec5f3e9d5a368c4efb61 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:26 -0600 Subject: [PATCH 16/21] 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 c8c4b1a5c1d2f70610f220953bb1ed3daea5262d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:27 -0600 Subject: [PATCH 17/21] Pin matplotlib to latest version 3.0.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5394098..202556a 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==3.0.3 numpy pandas pyfaidx From 0d1daaa1b1e0b602ceea395ea186cf62af9b9fed Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:28 -0600 Subject: [PATCH 18/21] Pin numpy to latest version 1.16.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 202556a..7b7d872 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.3 matplotlib==3.0.3 - numpy + numpy==1.16.2 pandas pyfaidx pyyaml From d14df8db5d26f7ca47060f25616b4fca5834478b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:29 -0600 Subject: [PATCH 19/21] 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 7b7d872..510b54b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.3 matplotlib==3.0.3 numpy==1.16.2 - pandas + pandas==0.24.2 pyfaidx pyyaml From ff8c2cc1b15435d3c2c9804df61ff05143807907 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:30 -0600 Subject: [PATCH 20/21] 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 510b54b..3441506 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.3 numpy==1.16.2 pandas==0.24.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From bd77e8b63bda843bb4a7451872d4be5059c04d6d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 8 Apr 2019 11:57:32 -0600 Subject: [PATCH 21/21] Pin pyyaml to latest version 5.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 3441506..b3a41ac 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.2 pandas==0.24.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1 [options.package_data] * =