diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..d710f21 --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,31 @@ +name: build + +on: [push] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: "3.9" + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install pytest pytest-cov coveralls + sudo apt-get -qq update + sudo apt-get install ncbi-blast+ + - name: Install + run: | + pip install -e . + - name: Test with pytest + run: | + python -m pytest --cov geneblocks --cov-report term-missing + - name: Coveralls + run: coveralls + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + COVERALLS_SERVICE_NAME: github diff --git a/.travis.yml b/.travis.yml index 6f4f4a5..49375c3 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,12 +1,12 @@ language: python python: - - "3.6" + - "3.9" # command to install dependencies before_install: - sudo apt-get -qq update - sudo apt-get install ncbi-blast+ install: - - pip install coveralls pytest-cov==2.6 pytest==3.2.3 + - pip install coveralls pytest-cov pytest - pip install -e . # command to run tests script: diff --git a/README.rst b/README.rst index c2db6ad..aafee9d 100644 --- a/README.rst +++ b/README.rst @@ -8,9 +8,9 @@ GeneBlocks ========== -.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/Geneblocks.svg?branch=master - :target: https://travis-ci.org/Edinburgh-Genome-Foundry/Geneblocks - :alt: Travis CI build status +.. image:: https://github.com/Edinburgh-Genome-Foundry/Geneblocks/actions/workflows/build.yml/badge.svg + :target: https://github.com/Edinburgh-Genome-Foundry/Geneblocks/actions/workflows/build.yml + :alt: GitHub CI build status .. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/Geneblocks/badge.svg :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/Geneblocks @@ -40,20 +40,20 @@ The CommonBlocks feature requires NCBI BLAST+. On Ubuntu, install it with .. code:: shell - (sudo) apt-get install ncbi-blast+ + apt-get install ncbi-blast+ You can install GeneBlocks through PIP: .. code:: shell - (sudo) pip install geneblocks + pip install geneblocks Alternatively, you can unzip the sources in a folder and type: .. code:: shell - (sudo) python setup.py install + python setup.py install Usage @@ -180,10 +180,10 @@ of modifications brought to the second sequence: -Licence -------- +License = MIT +------------- Geneblocks is an open-source software originally written at the `Edinburgh Genome Foundry `_ by `Zulko `_ -and `released on Github `_ under the MIT licence (Copyright 2017 Edinburgh Genome Foundry). +and `released on Github `_ under the MIT license (Copyright 2017 Edinburgh Genome Foundry). Everyone is welcome to contribute! diff --git a/pypi-readme.rst b/pypi-readme.rst index 6b51784..b4eb8e0 100644 --- a/pypi-readme.rst +++ b/pypi-readme.rst @@ -1,9 +1,9 @@ GeneBlocks -============= +========== -.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/DnaChisel.svg?branch=master - :target: https://travis-ci.org/Edinburgh-Genome-Foundry/Geneblocks - :alt: Travis CI build status +.. image:: https://github.com/Edinburgh-Genome-Foundry/Geneblocks/actions/workflows/build.yml/badge.svg + :target: https://github.com/Edinburgh-Genome-Foundry/Geneblocks/actions/workflows/build.yml + :alt: GitHub CI build status .. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/Geneblocks/badge.svg :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/Geneblocks diff --git a/setup.py b/setup.py index 8f8abd8..defcdd6 100644 --- a/setup.py +++ b/setup.py @@ -1,19 +1,26 @@ import ez_setup + ez_setup.use_setuptools() from setuptools import setup, find_packages -exec(open('geneblocks/version.py').read()) # loads __version__ +exec(open("geneblocks/version.py").read()) # loads __version__ setup( - name='geneblocks', + name="geneblocks", version=__version__, - author='Zulko', - description='Library to compare DNA sequences (diff, common blocks, etc.)', - long_description=open('pypi-readme.rst').read(), - license='MIT', - url='https://github.com/Edinburgh-Genome-Foundry/geneblocks', + author="Zulko", + description="Library to compare DNA sequences (diff, common blocks, etc.)", + long_description=open("pypi-readme.rst").read(), + license="MIT", + url="https://github.com/Edinburgh-Genome-Foundry/geneblocks", keywords="DNA sequence blocks diff synthetic-biology bioinformatics", - packages=find_packages(exclude='docs'), - install_requires=['numpy', 'Biopython', 'dna_features_viewer', - 'networkx', 'python-Levenshtein']) + packages=find_packages(exclude="docs"), + install_requires=[ + "numpy", + "Biopython", + "dna_features_viewer", + "networkx", + "python-Levenshtein", + ], +)