From 9d692c4491b20a155f75385e42b7f92cd2ef9896 Mon Sep 17 00:00:00 2001 From: lc Date: Mon, 22 Mar 2021 17:31:43 +0100 Subject: [PATCH 1/8] changed resistance phenotype from bool to str --- bifrostlib/schemas/bifrost.jsonc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bifrostlib/schemas/bifrost.jsonc b/bifrostlib/schemas/bifrost.jsonc index 4c433b6..0d0d3b3 100644 --- a/bifrostlib/schemas/bifrost.jsonc +++ b/bifrostlib/schemas/bifrost.jsonc @@ -814,7 +814,7 @@ "type": "string" }, "phenotype": { - "type": "boolean" + "type": "string" }, "point_mutations": { "type": "object" From 4d7ab101d3986345749a2c7ddf8cc193c3f55013 Mon Sep 17 00:00:00 2001 From: lc Date: Tue, 23 Mar 2021 10:47:04 +0100 Subject: [PATCH 2/8] removed duration in setup.cfg causing pytest error, removed mkdir line in run_tests causing github actions error --- .github/workflows/run_tests.yml | 2 -- setup.cfg | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 1edb962..2b39845 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -24,8 +24,6 @@ jobs: docker build --build-arg BUILD_ENV=test -t ${{ github.event.repository.name }} . - name: Get_tests_data run: > - mkdir -p /bifrost/; - cd /bifrost/; git clone https://github.com/ssi-dk/bifrost_test_data.git; cd bifrost_test_data/samples; bash download_S1.sh diff --git a/setup.cfg b/setup.cfg index a205b02..4f022bc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -16,6 +16,6 @@ replace = __version__ = '{new_version}' [tool:pytest] minversion = 6.0 -addopts = -ra -q --durations=0 +addopts = -ra -q testpaths = tests From 4a9d626dddac44c72472c5f3d0d422669d435249 Mon Sep 17 00:00:00 2001 From: lc Date: Tue, 23 Mar 2021 11:08:47 +0100 Subject: [PATCH 3/8] =?UTF-8?q?Bump=20version:=202.1.9=20=E2=86=92=202.1.9?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- bifrostlib/__init__.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bifrostlib/__init__.py b/bifrostlib/__init__.py index acfc4d6..98007dc 100644 --- a/bifrostlib/__init__.py +++ b/bifrostlib/__init__.py @@ -4,5 +4,5 @@ 'database_interface' ] -__version__ = '2.1.9' +__version__ = '__version__ = '2.1.9'' diff --git a/setup.py b/setup.py index 80b217f..8444a00 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='bifrostlib', - version='2.1.9', + version='version='2.1.9'', description='Datahandling functions for bifrost (later to be API interface)', url='https://github.com/ssi-dk/bifrostlib', author="Kim Ng, Martin Basterrechea", From e5f43d67eeb8b7bec65696827916c307a95e0efa Mon Sep 17 00:00:00 2001 From: lc Date: Tue, 23 Mar 2021 11:10:19 +0100 Subject: [PATCH 4/8] =?UTF-8?q?Bump=20version:=202.1.9=20=E2=86=92=202.1.9?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- bifrostlib/__init__.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bifrostlib/__init__.py b/bifrostlib/__init__.py index 98007dc..b1d4bd6 100644 --- a/bifrostlib/__init__.py +++ b/bifrostlib/__init__.py @@ -4,5 +4,5 @@ 'database_interface' ] -__version__ = '__version__ = '2.1.9'' +__version__ = '__version__ = '__version__ = '2.1.9''' diff --git a/setup.py b/setup.py index 8444a00..8f22e2b 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='bifrostlib', - version='version='2.1.9'', + version='version='version='2.1.9''', description='Datahandling functions for bifrost (later to be API interface)', url='https://github.com/ssi-dk/bifrostlib', author="Kim Ng, Martin Basterrechea", From aa6d44f73c2bcfbdaf931e3473b34fa3e388fb68 Mon Sep 17 00:00:00 2001 From: lc Date: Tue, 23 Mar 2021 11:12:42 +0100 Subject: [PATCH 5/8] =?UTF-8?q?Bump=20version:=202.1.9=20=E2=86=92=202.1.1?= =?UTF-8?q?0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- bifrostlib/__init__.py | 2 +- setup.cfg | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bifrostlib/__init__.py b/bifrostlib/__init__.py index b1d4bd6..33b8e0e 100644 --- a/bifrostlib/__init__.py +++ b/bifrostlib/__init__.py @@ -4,5 +4,5 @@ 'database_interface' ] -__version__ = '__version__ = '__version__ = '2.1.9''' +__version__ = '__version__ = '__version__ = '2.1.10''' diff --git a/setup.cfg b/setup.cfg index 4f022bc..08e2efb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 2.1.9 +current_version = 2.1.10 commit = True tag = True diff --git a/setup.py b/setup.py index 8f22e2b..89d9d9a 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='bifrostlib', - version='version='version='2.1.9''', + version='version='version='2.1.10''', description='Datahandling functions for bifrost (later to be API interface)', url='https://github.com/ssi-dk/bifrostlib', author="Kim Ng, Martin Basterrechea", From d165f5450be56e4a22a446d6f01da3e99faf9d1c Mon Sep 17 00:00:00 2001 From: lc Date: Tue, 23 Mar 2021 13:23:37 +0100 Subject: [PATCH 6/8] fixing version string screwup --- bifrostlib/__init__.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bifrostlib/__init__.py b/bifrostlib/__init__.py index 33b8e0e..cf6ff11 100644 --- a/bifrostlib/__init__.py +++ b/bifrostlib/__init__.py @@ -4,5 +4,5 @@ 'database_interface' ] -__version__ = '__version__ = '__version__ = '2.1.10''' +__version__ = '2.1.10' diff --git a/setup.py b/setup.py index 89d9d9a..833983a 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='bifrostlib', - version='version='version='2.1.10''', + version='2.1.10', description='Datahandling functions for bifrost (later to be API interface)', url='https://github.com/ssi-dk/bifrostlib', author="Kim Ng, Martin Basterrechea", From 391814f1a606e8ce08a46dc632fd50348a6fc7a0 Mon Sep 17 00:00:00 2001 From: lc Date: Tue, 23 Mar 2021 14:12:36 +0100 Subject: [PATCH 7/8] updated HISTORY.md --- HISTORY.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/HISTORY.md b/HISTORY.md index 0e2ddc8..8cf2714 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -4,6 +4,15 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [2.1.10] - 2020-03-23 +### Notes: +### Changed +- bifrostlib/schemas/bifrost.jsonc + - changed phenotype in resistance category from boolean to string +- setup.cfg + - removed durations flag from the pytest section to avoid crashing +- .github/workflows/run_tests.yml + - removed mkdir -p /bifrost/ which led to permission error when running github actions ## [2.1.9] - 2020-02-12 ### Notes: Issue fixed: [#2](https://github.com/ssi-dk/bifrostlib/issues/2) From 9e95ff907704cfab2474e2dbeddc688e2f8a8eb4 Mon Sep 17 00:00:00 2001 From: PovilasMat Date: Tue, 23 Mar 2021 14:22:56 +0100 Subject: [PATCH 8/8] Update HISTORY.md Added reason for updating bifrostlib --- HISTORY.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/HISTORY.md b/HISTORY.md index 8cf2714..18b8501 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [2.1.10] - 2020-03-23 ### Notes: +Adjusted schema for bifrost_cge_resfinder ### Changed - bifrostlib/schemas/bifrost.jsonc - changed phenotype in resistance category from boolean to string @@ -90,4 +91,4 @@ Changed the whole interface for datahandling from previous. It's now based on a - bifrotslib/\_\_init\_\_.py ### Removed -- mongo_interface.py \ No newline at end of file +- mongo_interface.py