From 82e0de974284a8cad824807d14676c6a73c9cc44 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:05 -0600 Subject: [PATCH 01/22] Update biopython from 1.72 to 1.74 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 161185b..59fde0c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,7 +4,7 @@ # # pip-compile --output-file requirements.txt setup.py # -biopython==1.72 +biopython==1.74 click-plugins==1.0.3 click==6.7 coverage==4.5.1 From 6bf7e61ab4a918bb5a4d44567ff9f6030eb54dc3 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:07 -0600 Subject: [PATCH 02/22] 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 59fde0c..81a16ff 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ # pip-compile --output-file requirements.txt setup.py # biopython==1.74 -click-plugins==1.0.3 +click-plugins==1.1.1 click==6.7 coverage==4.5.1 cycler==0.10.0 # via matplotlib From 148dc825fbc158ad5024b61f1b32c915ab6e3286 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:08 -0600 Subject: [PATCH 03/22] 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 81a16ff..c885cda 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ # biopython==1.74 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 a0430ae8e493ec0d4afecb415f80ac44fe6ab0d6 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:09 -0600 Subject: [PATCH 04/22] Update coverage from 4.5.1 to 4.5.4 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c885cda..4329e1f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ biopython==1.74 click-plugins==1.1.1 click==7.0 -coverage==4.5.1 +coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.0 From 9635282ec0de4eeebc9bd903af76d75136d213e8 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:10 -0600 Subject: [PATCH 05/22] Update kiwisolver from 1.0.1 to 1.1.0 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4329e1f..4b84855 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ click-plugins==1.1.1 click==7.0 coverage==4.5.4 cycler==0.10.0 # via matplotlib -kiwisolver==1.0.1 # via matplotlib +kiwisolver==1.1.0 # via matplotlib matplotlib==3.0.0 numpy==1.15.2 pandas==0.23.4 From 31a244a9f2fd42548eb3513e8a9e041115ccf741 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:11 -0600 Subject: [PATCH 06/22] Update matplotlib from 3.0.0 to 3.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 4b84855..d6c3c84 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ click==7.0 coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib -matplotlib==3.0.0 +matplotlib==3.1.1 numpy==1.15.2 pandas==0.23.4 pyfaidx==0.5.4.2 From 481c4e4799dbea924e2f1b4e21c528279ab8d7a7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:13 -0600 Subject: [PATCH 07/22] Update numpy from 1.15.2 to 1.17.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index d6c3c84..5c2f504 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ coverage==4.5.4 cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 -numpy==1.15.2 +numpy==1.17.2 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 3bb222cea6b08e75c89391ea4e935de587a65c2d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:14 -0600 Subject: [PATCH 08/22] Update pandas from 0.23.4 to 0.25.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5c2f504..d360c79 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ cycler==0.10.0 # via matplotlib kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.2 -pandas==0.23.4 +pandas==0.25.1 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From 81cae2cec0071aa08564b72f29f7065fa499e34f Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:15 -0600 Subject: [PATCH 09/22] 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 d360c79..12337dc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.1.0 # via matplotlib matplotlib==3.1.1 numpy==1.17.2 pandas==0.25.1 -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 8942e670dba300daa73c2cdd08f5aec086309748 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:16 -0600 Subject: [PATCH 10/22] Update pyparsing from 2.2.1 to 2.4.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 12337dc..0f723ed 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.1.1 numpy==1.17.2 pandas==0.25.1 pyfaidx==0.5.5.2 -pyparsing==2.2.1 # via matplotlib +pyparsing==2.4.2 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas pytz==2018.5 # via matplotlib, pandas pyyaml==3.13 From b5c23f63bbb6626c462fdfa33d3e47d2f8e5c9ac Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:17 -0600 Subject: [PATCH 11/22] 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 0f723ed..d4bcda6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.17.2 pandas==0.25.1 pyfaidx==0.5.5.2 pyparsing==2.4.2 # 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 52a9257bdb0cfdcb193fc7c149357f50746b38ca Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:18 -0600 Subject: [PATCH 12/22] Update pytz from 2018.5 to 2019.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index d4bcda6..40b5a40 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.25.1 pyfaidx==0.5.5.2 pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas -pytz==2018.5 # via matplotlib, pandas +pytz==2019.2 # via matplotlib, pandas pyyaml==3.13 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From 862e404351f9ebc6aa3afead5db26b5d94b3ee43 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:19 -0600 Subject: [PATCH 13/22] Update pyyaml from 3.13 to 5.1.2 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 40b5a40..1f59421 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,5 +17,5 @@ pyfaidx==0.5.5.2 pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.2 # via matplotlib, pandas -pyyaml==3.13 +pyyaml==5.1.2 six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil From ec5f04651609ca85a2e074eb5a6fce5b577482c0 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:21 -0600 Subject: [PATCH 14/22] 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 1f59421..b5c7773 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.4.2 # via matplotlib python-dateutil==2.8.0 # via matplotlib, pandas pytz==2019.2 # via matplotlib, pandas pyyaml==5.1.2 -six==1.11.0 # via cycler, matplotlib, pyfaidx, python-dateutil +six==1.12.0 # via cycler, matplotlib, pyfaidx, python-dateutil From bda80168eb3a320de6376c10748d57aeb8e3a8bb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:22 -0600 Subject: [PATCH 15/22] Pin biopython to latest version 1.74 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8f7e0f4..b6255cb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,7 +45,7 @@ zip_safe = False include_package_data = True packages = aakbar install_requires = - biopython + biopython==1.74 click>=5.0 click_plugins coverage From f4de8b7b462a08e9ac77cf28641f9578f67cfc56 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:23 -0600 Subject: [PATCH 16/22] 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 b6255cb..f6dfaf3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ packages = aakbar install_requires = biopython==1.74 click>=5.0 - click_plugins + click_plugins==1.1.1 coverage matplotlib numpy From bc83180c81c696b72f03cb03022283647f422fcd Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:25 -0600 Subject: [PATCH 17/22] Pin coverage to latest version 4.5.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index f6dfaf3..c271fca 100644 --- a/setup.cfg +++ b/setup.cfg @@ -48,7 +48,7 @@ install_requires = biopython==1.74 click>=5.0 click_plugins==1.1.1 - coverage + coverage==4.5.4 matplotlib numpy pandas From ab9bc531c931856ee8ec0145be281ace5334fb1b Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:26 -0600 Subject: [PATCH 18/22] Pin matplotlib to latest version 3.1.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index c271fca..13cfaa3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,7 +49,7 @@ install_requires = click>=5.0 click_plugins==1.1.1 coverage==4.5.4 - matplotlib + matplotlib==3.1.1 numpy pandas pyfaidx From 1e24bc25bfc538d219c7af34e3853faaeefff4d5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:27 -0600 Subject: [PATCH 19/22] Pin numpy to latest version 1.17.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 13cfaa3..8ae62b7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ install_requires = click_plugins==1.1.1 coverage==4.5.4 matplotlib==3.1.1 - numpy + numpy==1.17.2 pandas pyfaidx pyyaml From dbb6746ff531f97db5a286d36f8402994f8f0bc7 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:28 -0600 Subject: [PATCH 20/22] Pin pandas to latest version 0.25.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 8ae62b7..e35f666 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.4 matplotlib==3.1.1 numpy==1.17.2 - pandas + pandas==0.25.1 pyfaidx pyyaml From f4bcc016ff274dff3c70d611dbf32bb3857fa8ac Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:29 -0600 Subject: [PATCH 21/22] 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 e35f666..9bfffc6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.1.1 numpy==1.17.2 pandas==0.25.1 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From 5192013e931330dfd9cbf68007e210925068db8d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 23 Sep 2019 11:59:30 -0600 Subject: [PATCH 22/22] Pin pyyaml to latest version 5.1.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9bfffc6..ae30504 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.17.2 pandas==0.25.1 pyfaidx==0.5.5.2 - pyyaml + pyyaml==5.1.2 [options.package_data] * =