From fc1564b37015dea871423617837c927eb27a8d7a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:06 -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 2667636d97b1a66714ab2fe877010ad94a532a64 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:08 -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 0feada4c0b160271635a209da47360279f5f1d4c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:09 -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 b51fa6d7bb1b25f0727eae9a81a98aa50306579e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:11 -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 75007d623c388a4b4f36b6022cbd834c71689b84 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:13 -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 0f47fdb39a4363857061bbefbff69cffe89b5770 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:14 -0700 Subject: [PATCH 06/20] Update numpy from 1.15.2 to 1.16.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 60f70c8..f6e2202 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==1.16.0 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From f965f1f68bcdfecdc76fd0275e07c023d82302cd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:16 -0700 Subject: [PATCH 07/20] Update pandas from 0.23.4 to 0.24.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f6e2202..58cab06 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==1.16.0 -pandas==0.23.4 +pandas==0.24.0 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 778be7ad19a10f5287c82c513762ab580a54f805 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:19 -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 58cab06..7eadef3 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 numpy==1.16.0 pandas==0.24.0 -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 e01ae66557f96b0ca3e68b22207374fe5fa40cef Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:20 -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 7eadef3..da5a62c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.2 numpy==1.16.0 pandas==0.24.0 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 1d3f0c548e057e09c5f1eed253120680631c09ee Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:22 -0700 Subject: [PATCH 10/20] Update python-dateutil from 2.7.3 to 2.7.5 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index da5a62c..49c946f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.0 pandas==0.24.0 pyfaidx==0.5.5.2 pyparsing==2.3.1 # via matplotlib -python-dateutil==2.7.3 # via matplotlib, pandas +python-dateutil==2.7.5 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 49cc8707fefd1a85bed46d19a13aba05a89ad69c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:23 -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 49c946f..151169f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.0 pyfaidx==0.5.5.2 pyparsing==2.3.1 # via matplotlib python-dateutil==2.7.5 # 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 a5d53b3cef9a300cc789a43602fb53e6c9fe1dd6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:25 -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 151169f..81f5fcf 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.3.1 # via matplotlib python-dateutil==2.7.5 # 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 712bcf34a1df7708e116769ad8dc7f27feb63385 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:27 -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 843b10c07698aad5accac224ebfcab057299f6bb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:28 -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 d28d11a43a94bd580bbc5d2bde2b911d2a193758 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:30 -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 9fd72d6489653ef51cf7abd63cc453e69219eb93 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:31 -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 b36170337869f2f79b9eac9f73bf03e56ab3ed4a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:33 -0700 Subject: [PATCH 17/20] Pin numpy to latest version 1.16.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9546d9f..00cede8 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==1.16.0 pandas pyfaidx pyyaml From 93e3ca8022955897751076604d493fac83b36e05 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:34 -0700 Subject: [PATCH 18/20] Pin pandas to latest version 0.24.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 00cede8..6c57662 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.2 matplotlib==3.0.2 numpy==1.16.0 - pandas + pandas==0.24.0 pyfaidx pyyaml From edc454918ffc58259345b7c228d477e27ed04f57 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:36 -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 6c57662..3e8434e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.2 numpy==1.16.0 pandas==0.24.0 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 3e72e3aa2bd8d771a81fd03fe2b58bd641c4cd0a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 28 Jan 2019 10:17:37 -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 3e8434e..1fe9e6c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.0 pandas==0.24.0 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =