From 6358f5c9ebcc8d9cc81a80b42d02eafb039f82c2 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:08 -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 abd2c295123eab6b3f57ca840b0acec0ff353aed Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:09 -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 0991cc8c46663c62923bb13c15779b051c45958d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:11 -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 27f85f783f1716182013d17381697f91a249e9e1 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:12 -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 ec1a43dcb4a5a64f7ca4766674087e33a8d34577 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:13 -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 8f9fcf93096aafb2cb00676763886da80f7eea02 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:14 -0700 Subject: [PATCH 06/20] Update numpy from 1.15.2 to 1.16.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 60f70c8..162d429 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==1.16.1 pandas==0.23.4 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib From 40e41093f1e2de8339969275050432ad5650dbe4 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:15 -0700 Subject: [PATCH 07/20] Update pandas from 0.23.4 to 0.24.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 162d429..9c84dad 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==1.16.1 -pandas==0.23.4 +pandas==0.24.1 pyfaidx==0.5.4.2 pyparsing==2.2.1 # via matplotlib python-dateutil==2.7.3 # via matplotlib, pandas From d0577a5cd2bfa4d8d4d97a19d9c3da941d29b293 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:16 -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 9c84dad..7c43b62 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ kiwisolver==1.0.1 # via matplotlib matplotlib==3.0.2 numpy==1.16.1 pandas==0.24.1 -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 4510ecef7eba976eb9bc9c8aa0833c5a42a6b454 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:17 -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 7c43b62..9491301 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,7 +14,7 @@ matplotlib==3.0.2 numpy==1.16.1 pandas==0.24.1 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 281e044ae1b91de05874cb807ca47d2adb80c72d Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:18 -0700 Subject: [PATCH 10/20] 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 9491301..0807bfa 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,7 +15,7 @@ numpy==1.16.1 pandas==0.24.1 pyfaidx==0.5.5.2 pyparsing==2.3.1 # 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 731ee296222509d42c963c05a59f4cec26b37692 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:18 -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 0807bfa..58316e6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,6 @@ pandas==0.24.1 pyfaidx==0.5.5.2 pyparsing==2.3.1 # via matplotlib python-dateutil==2.8.0 # 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 a5d2981ec27843fa1ec06b09f7d2b780df12bd42 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:20 -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 58316e6..3ea7cba 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,4 +18,4 @@ pyparsing==2.3.1 # via matplotlib python-dateutil==2.8.0 # 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 64cda590bcac69ce88a4f9763b0cec60bc7ab951 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:21 -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 5d45f4c148208e77c77537790b69fdcf20fa02bb Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:21 -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 b0d0d71ad1d12a410e971fb929a54b39af978c43 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:22 -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 98058a551d5f877049ca38038c7775fa36197afc Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:23 -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 2a121311ad70c4e42a79815d8767f506cd455b36 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:25 -0700 Subject: [PATCH 17/20] Pin numpy to latest version 1.16.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9546d9f..e4859d4 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==1.16.1 pandas pyfaidx pyyaml From 5c49a91a85e1aded8c453681964800535182bdd5 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:25 -0700 Subject: [PATCH 18/20] Pin pandas to latest version 0.24.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index e4859d4..179755f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ install_requires = coverage==4.5.2 matplotlib==3.0.2 numpy==1.16.1 - pandas + pandas==0.24.1 pyfaidx pyyaml From 7319ed4009dde9a9c01dc0276af666f93b080724 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:26 -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 179755f..2cafa73 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ install_requires = matplotlib==3.0.2 numpy==1.16.1 pandas==0.24.1 - pyfaidx + pyfaidx==0.5.5.2 pyyaml [options.package_data] From c91ba937f263bab13b4796605baf130d870ce517 Mon Sep 17 00:00:00 2001 From: pyup-bot Date: Mon, 18 Feb 2019 10:43:27 -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 2cafa73..2c643d8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,7 +53,7 @@ install_requires = numpy==1.16.1 pandas==0.24.1 pyfaidx==0.5.5.2 - pyyaml + pyyaml==3.13 [options.package_data] * =