Merge branch 'dev' of github.com:Edinburgh-Genome-Foundry/Geneblocks …

…into dev

.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

.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:

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:
      <img src='https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/GeneBlocks/master/examples/complex_sequences.png'
       width='700px'/>
 
-Licence
--------
+License = MIT
+-------------
 
 Geneblocks is an open-source software originally written at the `Edinburgh Genome Foundry
 <http://www.genomefoundry.org>`_ by `Zulko <https://github.com/Zulko>`_
-and `released on Github <https://github.com/Edinburgh-Genome-Foundry/Geneblocks>`_ under the MIT licence (Copyright 2017 Edinburgh Genome Foundry).
+and `released on Github <https://github.com/Edinburgh-Genome-Foundry/Geneblocks>`_ under the MIT license (Copyright 2017 Edinburgh Genome Foundry).
 Everyone is welcome to contribute!

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

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",
+    ],
+)