Merge branch 'feature/compatibility' into 'develop'

Remove python 2 support and move to github actions

See merge request core/sevenbridges-python!77

.github/workflows/python-package.yml

@@ -0,0 +1,57 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+  release:
+    types:
+      - published
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - 3.6
+          - 3.7
+          - 3.8
+          - 3.9
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install -r requirements-dev.txt
+    - name: Test with pytest
+      run: |
+        flake8
+        pytest --verbose --cov-config setup.cfg
+
+  release:
+    needs: tests
+    if: github.event_name == 'release' && github.event.action == 'published'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          pip install wheel twine
+          export PACKAGE_VERSION=${GITHUB_REF:10}
+          echo "__version__ = '$PACKAGE_VERSION'" > sevenbridges/version.py
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

.gitlab-ci.yml

@@ -1,8 +1,4 @@
-image: python:3.8-buster
-
-variables:
-  REQUIREMENTS: "requirements.txt"
-  REQUIREMENTS2: "requirements2.txt"
+image: python:3.9-slim-buster
 
 stages:
   - test
@@ -11,54 +7,40 @@ stages:
 .test: &test
   stage: test
   before_script:
-    - infinity config build-info
     - python --version
-    - pip install -U -r $REQUIREMENTS
+    - pip install -r requirements-dev.txt
     - export PYTHONPATH=$(pwd):$PYTHONPATH
   script:
     - flake8
-    - pytest -v --cov-config setup.cfg
+    - pytest --verbose --cov-config setup.cfg
   artifacts:
     paths:
       - coverage_report/*
 
-# Test with python 2.7
-test:2.7:
-  stage: test
-  before_script:
-    - infinity config build-info
-    - python --version
-    - pip install -U -r $REQUIREMENTS2
-    - export PYTHONPATH=$(pwd):$PYTHONPATH
-  script:
-    - flake8
-    - pytest -v --cov-config setup.cfg
-  image: python:2.7
-
-# Test with python 3.5
-test:3.5:
-  <<: *test
-  image: python:3.5
-
 # Test with python 3.6
 test:3.6:
   <<: *test
-  image: python:3.6
+  image: python:3.6-slim-buster
 
 # Test with python 3.7
 test:3.7:
   <<: *test
-  image: python:3.7-stretch
+  image: python:3.7-slim-buster
 
 # Test with python 3.8
 test:3.8:
   <<: *test
-  image: python:3.8-buster
+  image: python:3.8-slim-buster
+
+# Test with python 3.9
+test:3.9:
+  <<: *test
+  image: python:3.9-slim-buster
 
 sonar:
   stage: sonar
   image: emeraldsquad/sonar-scanner:1.0.0
   script: infinity sonar scanner
   allow_failure: true
   dependencies:
-    - test:3.8
+    - test:3.9

MANIFEST.in

@@ -1 +1,2 @@
-include sevenbridges/VERSION LICENCE README.md requirements*.txt setup.cfg
+include LICENCE
+include README.md

README.md

@@ -1,7 +1,6 @@
 sevenbridges-python
 ===================
 
-[![Travis](https://travis-ci.org/sbg/sevenbridges-python.svg)](https://travis-ci.org/sbg/sevenbridges-python)
 [![PyPI version](https://badge.fury.io/py/sevenbridges-python.svg)](https://pypi.python.org/pypi/sevenbridges-python)
 [![Documentation](https://readthedocs.org/projects/sevenbridges-python/badge/?version=latest)](http://sevenbridges-python.readthedocs.org/en/latest/)
 [![Licence](https://img.shields.io/badge/licence-Apache-orange.svg)](https://github.com/sbg/sevenbridges-python/blob/develop/LICENCE)
@@ -12,7 +11,7 @@ sevenbridges-python is a [Python](http://www.python.org/) library that
 provides an interface for the [Seven Bridges Platform](https://www.sbgenomics.com/) the
 [Cancer Genomics Cloud](http://www.cancergenomicscloud.org/) and
 [Cavatica](http://www.cavatica.org) public APIs. It works with Python
-versions 2.6+ and supports Python 3.
+versions 3.6+.
 
 The [Seven Bridges Platform](https://www.sbgenomics.com/) is a
 cloud-based environment for conducting bioinformatic analyses. It is a
@@ -32,7 +31,7 @@ than a petabyte of multi-dimensional data available immediately to
 authorized researchers. You can add your own data to analyze alongside
 TCGA using predefined analytical workflows or your own tools.
 
-[Cavatica](http://www.cavatica.org/),
+The [Cavatica](http://www.cavatica.org/),
 powered by [Seven Bridges](https://www.sbgenomics.com/), is a data analysis and sharing
 platform designed to accelerate discovery in a scalable, cloud-based
 compute environment where data, results, and workflows are shared among
@@ -48,7 +47,7 @@ The latest documentation can be found on [readthedocs](http://sevenbridges-pytho
 Installation
 ------------
 
-The easiest way to install sevenbridges-python is using pip. :
+The easiest way to install sevenbridges-python is using pip:
 
     $ pip install sevenbridges-python
 
@@ -69,16 +68,15 @@ package, or install it into your site-packages by invoking: :
 
 If you are interested in reviewing this documentation locally, clone
 this repository, position yourself in the docs directory and after
-installing `requirements.txt` (or `requirements2.txt` if using python 2), invoke:
+installing `requirements-dev.txt`, invoke:
 
     $ make html
 
 Run Tests
 ---------
 
 In order to run tests clone this repository, position yourself in the
-root of the cloned project and after installing `requirements.txt` (or
-`requirements2.txt` if using python 2), invoke:
+root of the cloned project and after installing `requirements-dev.txt`, invoke:
 
     $ pytest
 
@@ -116,8 +114,8 @@ before using this library:
 Initialize configuration using the configuration file
 -----------------------------------------------------
 
-Once you obtain your authentication token you can pass it to the Config
-object. You can instantiate your API object by passing the appropriate
+Once you obtain your authentication token, you can pass it to the Config
+object. You can instantiate the API object by passing the appropriate
 configuration. There are three ways you can pass configure the library:
 
 1.  Pass parameters `url` and `token` explicitly when initializing the
@@ -137,9 +135,8 @@ api = sbg.Api(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>')
 ### Initialization via environment variables
 
 ```python
-import sevenbridges as sbg
-
 import os
+import sevenbridges as sbg
 
 # Usually these would be set in the shell beforehand
 os.environ['SB_API_ENDPOINT'] = 'https://api.sbgenomics.com/v2'
@@ -222,7 +219,7 @@ before submitting a pull request.
 Copyright
 ---------
 
-Copyright (c) 2016-2018 Seven Bridges Genomics, Inc. All rights
+Copyright (c) 2020 Seven Bridges Genomics, Inc. All rights
 reserved.
 
 This project is open-source via the [Apache 2.0 License](http://www.apache.org/licenses/LICENSE-2.0).

docs/conf.py

@@ -14,15 +14,15 @@
 
 import os
 import sys
-
+from datetime import datetime
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 extra_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 os.environ['SPHINX_DOC'] = 'True'
 sys.path.append(extra_path)
-from sevenbridges import __version__ as version_pkg
+from sevenbridges import __version__ as version_pkg  # noqa
 
 # -- General configuration ------------------------------------------------
 
@@ -54,9 +54,9 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'sevenbridges-python'
-copyright = u'2018, Seven Bridges Genomics Inc.'
-author = u'Seven Bridges Genomics'
+project = 'sevenbridges-python'
+copyright = f'{datetime.utcnow().year}, Seven Bridges Genomics Inc.'
+author = 'Seven Bridges Genomics'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -227,8 +227,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'sbg.tex', u'sbg Documentation',
-     u'Seven Bridges Genomics', 'manual'),
+    (master_doc, 'sbg.tex', 'sbg Documentation',
+     'Seven Bridges Genomics', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -257,7 +257,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'sbg', u'sbg Documentation',
+    (master_doc, 'sbg', 'sbg Documentation',
      [author], 1)
 ]
 
@@ -271,7 +271,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'sbg', u'sbg Documentation',
+    (master_doc, 'sbg', 'sbg Documentation',
      author, 'sbg', 'One line description of project.',
      'Miscellaneous'),
 ]

requirements-dev.txt

@@ -0,0 +1,9 @@
+-r requirements.txt
+
+flake8==3.8.4
+pytest==6.2.1
+pytest-cov==2.10.1
+requests-mock==1.8.0
+faker==5.0.2
+sphinx==3.4.0
+sphinx_rtd_theme==0.5.0

requirements.txt

@@ -1,10 +1,2 @@
-six>=1.10.0
-requests>=2.20.0
-
-flake8==3.8.4
-pytest==6.1.2
-pytest-cov==2.10.1
-requests-mock==1.8.0
-faker==4.14.2
-sphinx==3.3.0
-sphinx_rtd_theme==0.1.9
+requests>=2.25.1
+urllib3>=1.26.2

setup.cfg

@@ -1,15 +1,3 @@
-[bdist_wheel]
-universal=1
-
-[metadata]
-description-file =
-    README.md
-
-[flake8]
-exclude =
-    docs/conf.py
-    sevenbridges/__init__.py
-
 [tool:pytest]
 addopts =
     --cov=sevenbridges