From 82985ab6994d79b768bfb5795721ab18a9065f2f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:04 -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 2c08948128ab52f8a3dd83f1934db3acf9b1c80f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:05 -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 4ffc694953857b7e269bdcd0225d58bfbcc97e44 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:06 -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 608d874007d538e6025343790589429e6da1ba9a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:07 -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 86e5c3f85741a5cf4e7a23ade9592cbbb4b54a7a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:08 -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 467c57c74c0b888f1d8ef156cc8bebde1ad590c8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:09 -0600 Subject: [PATCH 06/21] Update numpy from 1.15.2 to 1.16.3 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 692fc34..7d889fb 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==1.16.3 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 14ce0005349eb26fab91840b59ab033084a07f12 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:10 -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 7d889fb..a5133c2 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==1.16.3 -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 510ce2accf21d4a90337a675ce45453c6d3f4fb8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:11 -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 a5133c2..0d9c15a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.3 numpy==1.16.3 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 3898925e4f947ddb1927122d73211171cc0b42dd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:12 -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 0d9c15a..ac2722d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.3 numpy==1.16.3 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 eb4834a1bdbad5dea601d0fc716a3c7b6c414682 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:13 -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 ac2722d..e79ea1b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.3 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 0696341afc5ee6f1089a5b17d4fcce45fa81d867 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:14 -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 e79ea1b..c666f1e 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 73fc411476b9a869a6b45baa85a44ab215e8b803 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:15 -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 c666f1e..4a2fb2d 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 a0dce85857d900339a539338f99c66f0d4c94ac5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:17 -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 4a2fb2d..7c6a6f9 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 093a853aa024a18aab2d6fc5a4318a45abdd56bf Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:18 -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 a60e5612283e7789a746447de3fc9f1fff3a1517 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:19 -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 cf1c93f314335ac18fd6bdcbdaf2bd60f018ba9a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:20 -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 b0ef793a0e855f469430d638330ee8cd0477e9a0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:20 -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 7acb5a5f1be457b1ea18391a9ea787036b79aa8a Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:21 -0600 Subject: [PATCH 18/21] Pin numpy to latest version 1.16.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 202556a..f4c3ee3 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==1.16.3 pandas pyfaidx pyyaml From 69ee5135dc4488bd1c519137f4f49f47fe83f22b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:22 -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 f4c3ee3..ed11293 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.3 matplotlib==3.0.3 numpy==1.16.3 - pandas + pandas==0.24.2 pyfaidx pyyaml From b87b9225f21adc5ec459be2c1248be5f28cea225 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:24 -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 ed11293..54590de 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.3 numpy==1.16.3 pandas==0.24.2 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 7490d81490b94dc7e2970f34851071ff33335ceb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 22 Apr 2019 11:54:25 -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 54590de..4ec7343 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.3 pandas==0.24.2 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1 [options.package_data] * =