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/HISTORY.md b/HISTORY.md index 0e2ddc8..ecc538d 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -4,6 +4,22 @@ 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). +## [2.1.11] - 2021-04-16 +### Notes: +Adjusted schema for bifrost_cge_mlst +### Changed +- bifrostlib/schemas/bifrost.jsonc + - changed 'strain' to 'sequence_type' in summary and report +## [2.1.10] - 2021-03-23 +### Notes: +Adjusted schema for bifrost_cge_resfinder +### 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) @@ -81,4 +97,4 @@ 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 diff --git a/bifrostlib/__init__.py b/bifrostlib/__init__.py index acfc4d6..cf6ff11 100644 --- a/bifrostlib/__init__.py +++ b/bifrostlib/__init__.py @@ -4,5 +4,5 @@ 'database_interface' ] -__version__ = '2.1.9' +__version__ = '2.1.10' diff --git a/bifrostlib/schemas/bifrost.jsonc b/bifrostlib/schemas/bifrost.jsonc index 4c433b6..4d881dc 100644 --- a/bifrostlib/schemas/bifrost.jsonc +++ b/bifrostlib/schemas/bifrost.jsonc @@ -691,7 +691,7 @@ "summary": { "type": "object", "properties": { - "strain": { + "sequence_type": { "type": "array", "items": { "type": "string" @@ -726,10 +726,10 @@ "type": "object", "properties": { "id": { - "const": "strain" + "const": "sequence_type" }, "name": { - "const": "strain" + "const": "sequence_type" } } }, @@ -755,7 +755,7 @@ "db": { "type": "string" }, - "strain": { + "sequence_type": { "type": "string" }, "alleles": { @@ -814,7 +814,7 @@ "type": "string" }, "phenotype": { - "type": "boolean" + "type": "string" }, "point_mutations": { "type": "object" diff --git a/setup.cfg b/setup.cfg index a205b02..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 @@ -16,6 +16,6 @@ replace = __version__ = '{new_version}' [tool:pytest] minversion = 6.0 -addopts = -ra -q --durations=0 +addopts = -ra -q testpaths = tests diff --git a/setup.py b/setup.py index 80b217f..833983a 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='bifrostlib', - version='2.1.9', + 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",