Update README

Author: Ulthran

README.md

@@ -1,7 +1,26 @@
 # 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.