Refactor IlluminaFastq class for broad machine type support

.github/workflows/pr.yml

@@ -0,0 +1,14 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+
+  workflow_dispatch:
+
+jobs:
+  run-tests:
+    uses: ./.github/workflows/test.yml
+    secrets: inherit

.github/workflows/test.yml

@@ -0,0 +1,50 @@
+name: Tests
+
+on:
+  workflow_call:
+
+  workflow_dispatch:
+
+jobs:
+  tests:
+    name: Run Tests
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest
+          python -m pip install .
+
+      - name: Run tests
+        run: pytest -s -vvvv -l --tb=long test
+
+  lint:
+    name: Lint Code Base
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install Dependencies
+        run: pip install black
+
+      - name: Lint Code Base
+        run: |
+          black --check .

.gitignore

@@ -1,14 +1,27 @@
+# Editors
+.vscode/
+.idea/
+
+# Vagrant
+.vagrant/
+
+# Mac/OSX
+.DS_Store
+
+# Windows
+Thumbs.db
+
+# Source for the following rules: https://raw.githubusercontent.com/github/gitignore/master/Python.gitignore
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
-*~
+*$py.class
 
 # C extensions
 *.so
 
 # Distribution / packaging
 .Python
-env/
 build/
 develop-eggs/
 dist/
@@ -20,9 +33,11 @@ lib64/
 parts/
 sdist/
 var/
+wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -37,26 +52,74 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
+.hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
 *.pot
 
 # Django stuff:
 *.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
 
 # Sphinx documentation
 docs/_build/
 
 # PyBuilder
 target/
 
-# data files
-*.fasta
-*.fastq
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json

README.md

@@ -1,7 +1,30 @@
 # seqBackup
 
-`python -m unittests` to run tests.
+Logic for parsing Illumina headers and folders as well as for archiving reads.
 
-## TODO:
+## Dev
 
--make backup_illumina.py able to take relative paths for --forward-reads argument
+```
+git clone https://github.com/PennChopMicrobiomeProgram/seqBackup.git
+cd seqBackup/
+python -m venv env
+source env/bin/activate
+pip install -e .
+pip install black pytest
+```
+
+Before commits, make sure everything is well formatted and working:
+
+```
+black .
+pytest test/
+git commit ...
+```
+
+### Adding a new machine type
+
+To add a new machine type, add the new machine code to the `MACHINE_TYPES` map in `seqBackuplib/illumina.py`. In some cases, you may have to add machine specific parsing in `_parse_header` or `_parse_folder`. In `test/test_illumina.py`, we have a mechanism for requiring tests for each supported machine type. Add the new machine type to the `machine_fixtures` map and then create the fixture that it points to in `test/conftest.py`. Follow the pattern laid out by other fixtures and try to make the test data as realistic as possible.
+
+### Incorporting new version
+
+This software is the "source of truth" for Illumina file handling logic. Other software in our ecosystem depend on this logic including the sample registry and the automation pipeline. When you update this software you will have to then update the installed versions wherever it is deployed as a dependency. We don't bother with official GitHub releases and instead just point directly at the `master` branch, so usually it is a matter of running `pip install git+https://github.com/PennChopMicrobiomeProgram/seqBackup.git@master` from the host machine.

scripts/backup_illumina.py

@@ -1,3 +1,4 @@
 #!/usr/bin/env python
 from seqBackupLib.backup import main
+
 main()