Move workflow

README.md

@@ -22,7 +22,7 @@ This will install the oxli library. Right now there is only
 You can also try building it yourself and using it in development mode:
 ```
 mamba env create -f environment.yml -n oxli
-pip install -e .
+pip install -e '.[test]'
 ```
 
 ## Documentation

src/python/tests/test_basic.py

@@ -164,8 +164,9 @@ def test_get_hash_array():
     ), "Hash array counts should match the counts of 'AAA' and 'AAC' and return zero for 'GGG'."
     assert rev_counts == [0, 1, 2], "Count should be in same order as input list"
 
+
 def test_get_array():
     """
     Get vector of counts corresponding to vector of kmers.
     """
-    pass
+    pass

src/python/tests/test_kmer_map.py

@@ -4,5 +4,5 @@
 
 
 def test_kmermap():
-    '''Test option to add kmermap'''
-    pass
+    """Test option to add kmermap"""
+    pass

src/python/tests/test_output.py

@@ -4,21 +4,25 @@
 
 
 def test_serialise():
-    '''Serialise object to JSON '''
+    """Serialise object to JSON"""
     pass
 
+
 def test_deserialise():
-    '''Load object from file.'''
+    """Load object from file."""
     pass
 
+
 def test_dump():
-    '''Write tab delimited kmer:count pairs'''
+    """Write tab delimited kmer:count pairs"""
     pass
 
+
 def test_dump_hash():
-    '''Write tab delimited hash_count pairs '''
+    """Write tab delimited hash_count pairs"""
     pass
 
+
 def test_histo():
-    '''Write frequency counts.'''
+    """Write frequency counts."""
     pass

src/python/tests/test_setops.py

@@ -3,6 +3,7 @@
 
 from test_basic import create_sample_kmer_table
 
+
 # Set operations
 def test_union():
     table1 = create_sample_kmer_table(3, ["AAA", "AAC"])