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Update mlst lib #9

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merged 2 commits into from
Apr 16, 2021
Merged

Update mlst lib #9

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c135a12
Json schema phenotype boolean to str (#8)
githubz0r Mar 23, 2021
c6fa6fc
updating jsonc with sequence_type instead of strain
Apr 16, 2021
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2 changes: 0 additions & 2 deletions .github/workflows/run_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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18 changes: 17 additions & 1 deletion HISTORY.md
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Expand Up @@ -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)
Expand Down Expand Up @@ -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
- mongo_interface.py
2 changes: 1 addition & 1 deletion bifrostlib/__init__.py
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Expand Up @@ -4,5 +4,5 @@
'database_interface'
]

__version__ = '2.1.9'
__version__ = '2.1.10'

10 changes: 5 additions & 5 deletions bifrostlib/schemas/bifrost.jsonc
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Expand Up @@ -691,7 +691,7 @@
"summary": {
"type": "object",
"properties": {
"strain": {
"sequence_type": {
"type": "array",
"items": {
"type": "string"
Expand Down Expand Up @@ -726,10 +726,10 @@
"type": "object",
"properties": {
"id": {
"const": "strain"
"const": "sequence_type"
},
"name": {
"const": "strain"
"const": "sequence_type"
}
}
},
Expand All @@ -755,7 +755,7 @@
"db": {
"type": "string"
},
"strain": {
"sequence_type": {
"type": "string"
},
"alleles": {
Expand Down Expand Up @@ -814,7 +814,7 @@
"type": "string"
},
"phenotype": {
"type": "boolean"
"type": "string"
},
"point_mutations": {
"type": "object"
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4 changes: 2 additions & 2 deletions setup.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 2.1.9
current_version = 2.1.10
commit = True
tag = True

Expand All @@ -16,6 +16,6 @@ replace = __version__ = '{new_version}'

[tool:pytest]
minversion = 6.0
addopts = -ra -q --durations=0
addopts = -ra -q
testpaths =
tests
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -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",
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