Merge pull request #5 from ga4gh/release/0.1.2

Release 0.1.2 into main

.github/workflows/test.yml

@@ -0,0 +1,35 @@
+name: Test
+on: [push, pull_request, workflow_dispatch] #workflow_dispatch works only if its active in the main branch
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - 3.7
+          - 3.8
+          - 3.9
+          - '3.10'
+    name: Test on Python v${{ matrix.python-version }} 
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+        architecture: x64
+
+    - name: Install dependencies
+      run: pip install -r requirements.txt
+
+    - name: Run Tests
+      run: python -m pytest --cov
+
+    - name: Submit Coverage
+      if: ${{ matrix.python-version == '3.10' }}
+      env:
+        GITHUB_TOKEN: ${{ secrets.COVERALLS_TOKEN }}
+      run: python -m coveralls

.gitignore

@@ -26,6 +26,9 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+.DS_Store
+
+
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

README.md

@@ -1,2 +1,61 @@
-# ga4gh-testbed-lib
+<img src="https://www.ga4gh.org/wp-content/themes/ga4gh-theme/gfx/GA-logo-horizontal-tag-RGB.svg" alt="GA4GH Logo" style="width: 400px;"/>
+
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=flat-square)](https://opensource.org/licenses/Apache-2.0)
+[![Python](https://img.shields.io/badge/python-3.7|3.8|3.9|3.10-blue.svg?style=flat-square)](https://www.python.org/)
+[![GitHub Actions](https://img.shields.io/github/workflow/status/ga4gh/ga4gh-testbed-lib/Test/main?style=flat-square)](https://github.com/ga4gh/ga4gh-testbed-lib/actions)
+[![Coveralls](https://img.shields.io/coveralls/github/ga4gh/ga4gh-testbed-lib/main?style=flat-square)](https://coveralls.io/github/ga4gh/ga4gh-testbed-lib)
+
+# GA4GH Testbed Lib
+
 Python library for creating GA4GH testbed reports according to a harmonized, cross-workstream schema
+
+## Installation
+
+As a prerequisite, please ensure you have Python 3 installed on your machine.
+`ga4gh-testbed-lib` is tested on the following Python versions:
+* v3.7
+* v3.8
+* v3.9
+* v3.10
+
+`ga4gh-testbed-lib` is a library that can be imported into your Python project.
+To do so, first install it via `pip`:
+
+```
+pip install ga4gh-testbed-lib
+```
+
+Note: We recommend using a Python virtual environment when building any Python project to avoid dependency conflicts with other projects on your system.
+
+## Usage
+
+Once installed, you may import the `ga4gh-testbed-lib` in your Python modules. We recommend only importing the `Report` class directly: 
+```
+from ga4gh.testbed.report.report import Report
+...
+report = Report()
+```
+
+More documentation to come on how to use the report library
+
+## Test
+
+To contribute to the testbed library, you will need to clone the repository:
+```
+git clone https://github.com/ga4gh/ga4gh-testbed-lib.git
+```
+
+To run tests, you will need to install test dependencies (i.e. pytest):
+```
+pip install -r requirements.txt
+```
+
+Tests can be run via `pytest`:
+```
+python -m pytest --cov
+```
+
+## Changelog
+
+### v0.1.2
+* Test level entity now has a `message` attribute for capturing test result summary in a single message

ga4gh/testbed/report/test.py

@@ -7,7 +7,7 @@
 from ga4gh.testbed.mixins.has_message import HasMessage
 from ga4gh.testbed.report.case import Case
 
-class Test(HasTimestamps, HasStatus, HasSummary):
+class Test(HasTimestamps, HasStatus, HasSummary, HasMessage):
     """A single test within the reporting hierarchy, contains multiple cases
 
     Immediate subcomponent of a test "Phase". Represents a single test with
@@ -30,6 +30,7 @@ def __init__(self):
         self._HasTimestamps__initialize_timestamps()
         self._HasStatus__initialize_status()
         self._HasSummary__initialize_summary()
+        self._HasMessage__initialize_message()
 
         self.cases = []
 

requirements_test.txt → requirements.txt

@@ -3,9 +3,10 @@ bleach==4.1.0
 certifi==2021.10.8
 charset-normalizer==2.0.7
 colorama==0.4.4
-coverage==6.0.2
+coverage==6.3.2
+coveralls==3.3.1
+docopt==0.6.2
 docutils==0.18
-ga4gh-testbed-lib==0.1.0
 idna==3.3
 importlib-metadata==4.8.1
 iniconfig==1.1.1

schema/ga4gh-testbed-test.json

@@ -26,6 +26,9 @@
         "summary": {
           "$ref": "ga4gh-testbed-summary.json#/definitions/ga4ghTestbedSummary"
         },
+        "message": {
+          "type": "string"
+        },
         "cases": {
           "type": "array",
           "items": {

setup.py

@@ -1,7 +1,7 @@
 import setuptools
 
 NAME = "ga4gh-testbed-lib"
-VERSION = "0.1.1"
+VERSION = "0.1.2"
 AUTHOR = "Jeremy Adams"
 EMAIL = "jeremy.adams@ga4gh.org"
 

tests/data/e2e/report_finalization_serialization/0.json

@@ -48,6 +48,7 @@
                         "failed": 0,
                         "skipped": 1
                     },
+                    "message": "",
                     "cases": [
                         {
                             "case_name": "Get e. coli",
@@ -82,6 +83,7 @@
                         "failed": 0,
                         "skipped": 0
                     },
+                    "message": "",
                     "cases": [
                         {
                             "case_name": "List bacterial sequences",
@@ -132,6 +134,7 @@
                         "failed": 1,
                         "skipped": 0
                     },
+                    "message": "",
                     "cases": [
                         {
                             "case_name": "Get synonymous mutation",
@@ -166,6 +169,7 @@
                         "failed": 0,
                         "skipped": 2
                     },
+                    "message": "",
                     "cases": [
                         {
                             "case_name": "List synonymous mutations",