From 7f144f04c29037777bace2a3af5b3e91974ac08c Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:07 -0700 Subject: [PATCH 01/19] 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 c37fd684ed73df01a1c893d98021909f1db612b2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:10 -0700 Subject: [PATCH 02/19] 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 9874baec4e600be20fbb55ae94dc148c91142cf3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:12 -0700 Subject: [PATCH 03/19] 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 7d8492fe0df237ba39cb273d82a44404d80b481e Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:13 -0700 Subject: [PATCH 04/19] 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 8143cbcab12a0cbafd742d3523cfe7b2fddb7af1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:15 -0700 Subject: [PATCH 05/19] 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 c67ce2c1350ec255b4f6e639f7b60f726becfe21 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:16 -0700 Subject: [PATCH 06/19] Update numpy from 1.15.2 to 1.15.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 60f70c8..2764c4e 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==1.15.4 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 29eff53184782ad92a07850ee1fba1840c16eb39 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:18 -0700 Subject: [PATCH 07/19] 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 2764c4e..f9ba474 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 numpy==1.15.4 pandas==0.23.4 -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 5079a8948e410cd12784b5df40979beb29d25e2b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:19 -0700 Subject: [PATCH 08/19] Update pyparsing from 2.2.1 to 2.3.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f9ba474..bde8226 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.2 numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.3.0 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From fdafbfaadef0a17761fd160c1aae2d4d1f7ce04b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:21 -0700 Subject: [PATCH 09/19] 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 bde8226..c837f37 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.3.0 # 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 3ec6979dee2dcc59e0b4b755b2a704dde95265e4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:23 -0700 Subject: [PATCH 10/19] 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 c837f37..099bb72 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.23.4 pyfaidx==0.5.5.2 pyparsing==2.3.0 # 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 1ad34ddaaade75a2e6dcd8e6c218be37ea9c790a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:24 -0700 Subject: [PATCH 11/19] 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 099bb72..c936513 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.3.0 # 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 ca88ebba5d1defa8423617006fdb6b8c12813a6a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:26 -0700 Subject: [PATCH 12/19] 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 e80812b8b06496d1922e6493a2f6cb10bc9ea210 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:27 -0700 Subject: [PATCH 13/19] 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 dbbb055b99585b63a87ec3c3f8178a7f22890ceb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:29 -0700 Subject: [PATCH 14/19] 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 5dfe558bbcaf97efefaecbe46c9d486e9b2813ba Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:30 -0700 Subject: [PATCH 15/19] 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 51c0c7a0dabcbf62a99d4cc9082e9043dedcb5cd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:32 -0700 Subject: [PATCH 16/19] Pin numpy to latest version 1.15.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9546d9f..d745abd 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==1.15.4 pandas pyfaidx pyyaml From 461f7429242f2370e99993cda336372291e01bc5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:34 -0700 Subject: [PATCH 17/19] Pin pandas to latest version 0.23.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index d745abd..d53fa2c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.2 matplotlib==3.0.2 numpy==1.15.4 - pandas + pandas==0.23.4 pyfaidx pyyaml From 0031f0092b628305ccdde7224cd4c388da8f86f9 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:35 -0700 Subject: [PATCH 18/19] 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 d53fa2c..e906935 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.2 numpy==1.15.4 pandas==0.23.4 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 4de3d32eeba2e4a5481b38f8b87a2ec72790d63d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 7 Jan 2019 10:16:37 -0700 Subject: [PATCH 19/19] 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 e906935..c4cdf63 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.15.4 pandas==0.23.4 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =