Merge pull request #23 from Ulthran/master

Add CI/CD

.github/workflows/codecov.yml

@@ -0,0 +1,35 @@
+name: CodeCov
+
+on:
+  pull_request:
+    branches: [master, main]
+  push:
+    branches: [master, main]
+  schedule:
+    - cron: "0 13 * * 1"
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+      - name: setup-conda
+        uses: s-weigand/[email protected]
+        with:
+          conda-channels: ''
+      - name: Install dependencies
+        run: |
+          conda install -c bioconda vsearch
+          python -m pip install --upgrade pip
+          python -m pip install pytest
+          python -m pip install pytest-cov
+          python -m pip install .
+      - name: Run tests and collect coverage
+        run: pytest --cov tests
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3

.github/workflows/linter.yml

@@ -0,0 +1,28 @@
+name: Super-Linter
+
+on:
+  pull_request:
+    branches: [master, main]
+  push:
+    branches: [master, main]
+
+jobs:
+  super-linter:
+    name: Lint Codebase
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Run Super-Linter
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: true
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+          VALIDATE_PYTHON_BLACK: true
+
+          FILTER_REGEX_EXCLUDE: tests/test_align.py
+          # align.py has some weirdly spaced strings to show alignment
+          # To reformat, `black . --exclude="test_align.py"`

.github/workflows/python-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: PyPi
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Tests
+
+on:
+  pull_request:
+    branches: [master, main]
+  push:
+    branches: [master, main]
+  schedule:
+    - cron: "0 13 * * 1"
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: setup-conda
+      uses: s-weigand/[email protected]
+      with:
+        conda-channels: ''
+    - name: Install dependencies
+      run: |
+        conda install -c bioconda vsearch
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        python -m pip install .
+    - name: Test with pytest
+      run: |
+        pytest -vvl tests/

README.md

@@ -1,5 +1,10 @@
 # Unassigner
 
+[![Tests](https://github.com/Ulthran/unassigner/actions/workflows/tests.yml/badge.svg)](https://github.com/Ulthran/unassigner/actions/workflows/tests.yml)
+[![Super-Linter](https://github.com/Ulthran/unassigner/actions/workflows/linter.yml/badge.svg)](https://github.com/Ulthran/unassigner/actions/workflows/linter.yml)
+[![codecov](https://codecov.io/gh/Ulthran/unassigner/branch/master/graph/badge.svg?token=76YWJFWGON)](https://codecov.io/gh/Ulthran/unassigner)
+[![PyPi](https://github.com/Ulthran/unassigner/actions/workflows/python-publish.yml/badge.svg)](https://github.com/Ulthran/unassigner/actions/workflows/python-publish.yml)
+
 Evaluate consistency with named bacterial species for short 16S rRNA
 marker gene sequences.
 
@@ -54,6 +59,32 @@ sequence alignments.  It's available through
 [conda](https://anaconda.org/bioconda/vsearch), and this is our
 recommended method for installation.
 
+```bash
+conda create --name unassigner
+conda activate unassigner
+conda install -c bioconda vsearch
+pip install unassigner
+```
+
+### Alternative Installation
+
+If `pip install unassigner` isn't working or if you want to use a development 
+version, you can also install via git.
+
+```bash
+conda create --name unassigner
+conda activate unassigner
+conda install -c bioconda vsearch
+git clone https://github.com/kylebittinger/unassigner.git
+cd unassigner
+pip install -r requirements.txt
+pip install .
+```
+
+If you don't want to use conda, see the 
+[vsearch repo](https://github.com/torognes/vsearch) for alternative install 
+methods.
+
 ## Usage
 
 The `unassign` program requires one argument, a FASTA-formatted file
@@ -66,7 +97,8 @@ unassign my_sequences.fasta
 If the program has not been run before, it will automatically download
 the bacterial species data it needs, format its reference files,
 create an output directory named `my_sequences_unassigned`, and write
-a table of results there, along with some auxiliary output files.
+a table of results there, along with some auxiliary output files. Note 
+that the output directory will be in the same directory as `my_sequences.fasta`.
 
 Please see the output of `unassign --help` for a list of the available
 options.

setup.py

@@ -2,38 +2,39 @@
 from setuptools import setup
 
 PACKAGE_DIR = os.path.abspath(os.path.dirname(__file__))
-README_FP = os.path.join(PACKAGE_DIR, 'README.md')
-with open(README_FP, encoding='utf-8') as f:
+README_FP = os.path.join(PACKAGE_DIR, "README.md")
+with open(README_FP, encoding="utf-8") as f:
     long_description = f.read()
 
-setup(name='unassigner',
-      version='0.0.5',
-      description='Bacterial species unassigner',
-      long_description=long_description,
-      long_description_content_type='text/markdown',
-      author='Kyle Bittinger',
-      author_email='[email protected]',
-      url='https://github.com/kylebittinger/unassigner',
-      packages=['unassigner'],
-      install_requires=[
-          'biopython',
-          'scipy',
-      ],
-      entry_points={
-          'console_scripts': [
-              'unassign=unassigner.command:main',
-              'trimragged=unassigner.trim:main',
-              'count_mismatches=unassigner.mismatch_db:main',
-              'pctid_ani_sample=unassigner.ani:main_sampling',
-          ],
-      },
-      classifiers=[
-          'Intended Audience :: Science/Research',
-          'License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)',
-          'Operating System :: POSIX :: Linux',
-          'Operating System :: MacOS :: MacOS X',
-          'Programming Language :: Python :: 3',
-          'Topic :: Scientific/Engineering :: Bio-Informatics',
-      ],
-      license='GPLv2+',
+setup(
+    name="unassigner",
+    version="0.0.5",
+    description="Bacterial species unassigner",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="Kyle Bittinger",
+    author_email="[email protected]",
+    url="https://github.com/kylebittinger/unassigner",
+    packages=["unassigner"],
+    install_requires=[
+        "biopython",
+        "scipy",
+    ],
+    entry_points={
+        "console_scripts": [
+            "unassign=unassigner.command:main",
+            "trimragged=unassigner.trim:main",
+            "count_mismatches=unassigner.mismatch_db:main",
+            "pctid_ani_sample=unassigner.ani:main_sampling",
+        ],
+    },
+    classifiers=[
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+        "Operating System :: POSIX :: Linux",
+        "Operating System :: MacOS :: MacOS X",
+        "Programming Language :: Python :: 3",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
+    license="GPLv2+",
 )