Format a wide samplesheet in Preprocess helper and move to poetry (#34)

* Format a wide samplesheet with each read-pair on a row

* Initial test scaffold

* Test with and without lane

* Add newline at end of file

* Remove whitespace

* Remove whitespace

* Add tests to github actions

* Add pytest dependency

* Switch to poetry package management

* Add poetry run prefix

* update working dir

Co-authored-by: Nathan Thorpe <[email protected]>

Author: sminot

.github/workflows/lint.yml

@@ -25,9 +25,14 @@ jobs:
       - name: Install deps
         run: |
           python -m pip install --upgrade pip
-          pip install flake8
-          python setup.py install
+          pip install poetry
+          poetry install --all-extras
 
       - name: Run lint
         run: |
-          flake8 pubweb
+          poetry run flake8 pubweb
+
+      - name: Run Tests
+        working-directory: tests
+        run: |
+          poetry run pytest --cov --cov-report=xml --cov-branch -o junit_family=xunit2 --junitxml=junit/test-results.xml

.github/workflows/package.yml

@@ -28,16 +28,16 @@ jobs:
       - name: Install deps
         run: |
           python -m pip install --upgrade pip
-          pip install wheel
+          pip install poetry
 
       - name: Test install
         run: |
-          python setup.py install
-          pubweb-cli
+          poetry install --all-extras
+          poetry run pubweb-cli
 
       - name: Build python package
         run: |
-          python setup.py bdist_wheel
+          poetry build
 
       - name: Publish package
         if: github.event_name == 'release'

.sonarcloud.properties

@@ -1 +1,4 @@
 sonar.python.version=3
+sonar.python.xunit.reportPath=**/junit/test-results.xml
+sonar.python.coverage.reportPaths=**/coverage.xml
+sonar.exclusions=**/tests/*.py