From 671ab2a0d0b481c8eafefe16124305ec193c5f57 Mon Sep 17 00:00:00 2001 From: Jeremy Adams Date: Tue, 22 Mar 2022 13:13:53 -0400 Subject: [PATCH] update README and remove extraneous files --- .travis.yml | 16 ------------- README.md | 56 ++++++++++++++++++++++++++++++++++++++++++- requirements.txt | 1 - requirements_test.txt | 36 ---------------------------- 4 files changed, 55 insertions(+), 54 deletions(-) delete mode 100644 .travis.yml delete mode 100644 requirements_test.txt diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 49efc7a..0000000 --- a/.travis.yml +++ /dev/null @@ -1,16 +0,0 @@ -dist: xenial -language: python -python: - - "3.7" - - "3.8" - - "3.9" -install: - - python -m pip install --upgrade pip - - python setup.py install - - python -m pip install -r requirements_test.txt -before_script: - - export PYTHONPATH=`pwd` -script: - - pytest --cov ga4gh/ --cov-report=term-missing tests/ -after_success: - - coveralls diff --git a/README.md b/README.md index 38bdd7d..f6e485d 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,56 @@ -# ga4gh-testbed-lib +GA4GH Logo + +[![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 +``` diff --git a/requirements.txt b/requirements.txt index e560130..1b2552a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,6 @@ coverage==6.3.2 coveralls==3.3.1 docopt==0.6.2 docutils==0.18 -ga4gh-testbed-lib==0.1.2 idna==3.3 importlib-metadata==4.8.1 iniconfig==1.1.1 diff --git a/requirements_test.txt b/requirements_test.txt deleted file mode 100644 index ba9dd91..0000000 --- a/requirements_test.txt +++ /dev/null @@ -1,36 +0,0 @@ -attrs==21.2.0 -bleach==4.1.0 -certifi==2021.10.8 -charset-normalizer==2.0.7 -colorama==0.4.4 -coverage==6.0.2 -docutils==0.18 -ga4gh-testbed-lib==0.1.2 -idna==3.3 -importlib-metadata==4.8.1 -iniconfig==1.1.1 -jsonschema==4.1.2 -keyring==23.2.1 -packaging==21.0 -pkginfo==1.7.1 -pluggy==1.0.0 -py==1.10.0 -Pygments==2.10.0 -pyparsing==2.4.7 -pyrsistent==0.18.0 -pytest==6.2.5 -pytest-cov==3.0.0 -python-coveralls==2.9.3 -PyYAML==6.0 -readme-renderer==30.0 -requests==2.26.0 -requests-toolbelt==0.9.1 -rfc3986==1.5.0 -six==1.16.0 -toml==0.10.2 -tomli==1.2.1 -tqdm==4.62.3 -twine==3.4.2 -urllib3==1.26.7 -webencodings==0.5.1 -zipp==3.6.0