From ba3521da4eb411e859d4c63a56eb6dea53b4426f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:06 -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 5bf12b4dff7244fa6e9c6f6da4a212717af2e86f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:07 -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 ca348a94828407c527cfceec12e646db6095472a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:08 -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 8b2c1697c10be8fecc7e4ab468690c06c590a1b5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:09 -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 291c427771322acc6cd011b110388ba57e482346 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:10 -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 4cc20575e2c238ff98b5ec0374b2fa2bd04c099f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:11 -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 d6c3d2065072a790a00b674f94cc96fcb59922ec Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:13 -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 682439499136386d994e4d9c23f21c9f804d90a5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:17 -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 b9b7f97c282a55f6bf5173b25e70509883292c61 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:19 -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 90c368db6fa2aaf4d875b9089f2e2a82d80705ee Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:20 -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 aebeca1ae7edf9be5c27e89fd39e9a3afd741c54 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:21 -0600 Subject: [PATCH 11/21] 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 b4aa801..59ed2e0 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 dba8a0212dadbf411ae9e24b5fc90338d1cf7238 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:22 -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 59ed2e0..b1fe0ae 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 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 4a808d2bf13d6813dfa61629bc6f43cb6eec7e43 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:23 -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 b1fe0ae..7a8df5b 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 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From eddcf3263ab204618e558ce4e28367c4ca264a6a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:24 -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 180539f14737b1f3d515e29d28279392900bd9a9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:25 -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 cdf5eedc536898c8f69235e648628132093a15ef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:26 -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 541393be0215c59f232ae81778eb55e606416006 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:29 -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 9ed458a362b9afd33c115b931ac02ab59f54f78e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:31 -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 6c96956889359cc9da9d24e20b42a9c14b7fff31 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:32 -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 07943a693831cc6051ca1eea72d3f3968a38abb0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:33 -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 e6f16fa3ed793934476bfb8a251719855eb01a28 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 15 Apr 2019 11:59:34 -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] * =