actions ci workflow

.github/workflows/github_actions_test.yml

@@ -0,0 +1,45 @@
+name: Lint and tests
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+  schedule:
+    # ...or run once a month
+    - cron: "0 0 1 * *"
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8"]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+      - name: Install bwa
+        run: conda install bioconda/label/cf201901::bwa
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "setuptools<58.0.0"
+          python -m pip install flake8 pytest
+          pip install src/
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 src/ --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=build
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 src/ --count --exit-zero --max-line-length=127 --statistics --exclude=build
+      - name: Test with pytest
+        run: |
+          pytest

.gitignore

@@ -1 +1,3 @@
 .DS_Store
+__pycache__/
+*.pyc

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')
+    integration

src/CHANGELOG.rst

@@ -1,5 +1,12 @@
 .. _sect_changelog:
 
+Version 1.1.0
+-------------
+
+* Upgrade to Python 3.8
+* Initial wave of integration and unit tests using pytest
+* Implement Continuous integration using GitHub Actions workflow. Build and run linting and tests to succeed. Triggered by PR/Push to master or monthly cron.
+
 Version 1.0
 -----------
 

src/ScaleHD/__backend.py

@@ -1,6 +1,4 @@
 #/usr/bin/python
-__version__ = '1.0'
-__author__ = 'alastair.maxwell@glasgow.ac.uk'
 
 ##
 ## Imports
@@ -453,7 +451,7 @@ def sanitise_inputs(parsed_arguments):
 	## Jobname prefix validity check
 	if parsed_arguments.jobname:
 		for character in parsed_arguments.jobname:
-			if character is ' ' or character is '/':
+			if character == ' ' or character == '/':
 				log.error('{}{}{}{}{}{}'.format(Colour.red,'shd__ ',Colour.end,'Specified Job Name has invalid characters: "', character, '"'))
 				trigger = True
 

src/ScaleHD/__init__.py

@@ -4,5 +4,3 @@
 		   '__alleleface.py',
 		   '__init__.py',
 		   '__main__.py']
-__author__='alastair.maxwell@glasgow.ac.uk'
-__version__='1.0'

src/ScaleHD/__main__.py

@@ -1,3 +1,2 @@
-__version__ = '1.0'
 from .sherpa import main
 main()

src/ScaleHD/align/__alignment.py

@@ -1,6 +1,4 @@
 #/usr/bin/python
-__version__ = '1.0'
-__author__ = 'alastair.maxwell@glasgow.ac.uk'
 
 ##
 ## Generals

src/ScaleHD/genHTML/__generateHTML.py

@@ -1,6 +1,4 @@
 #!/bin/bash/python
-__version__ = '1.0'
-__author__ = 'alastair.maxwell@glasgow.ac.uk'
 
 ## imports
 import os