biocommons#741 small refactoring to update directory structure, based…

… on PR comments, also disabling slow running unit test

src/hgvs/pretty/console/chrom_seq_renderer.py

@@ -9,7 +9,7 @@ def legend(self) -> str:
 
     def display(self, data: VariantData) -> str:
         """colors the ref sequences with adenine (A, green), thymine (T, red), cytosine (C, yellow), and guanine (G, blue)"""
-        from hgvs.pretty.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+        from hgvs.pretty.console.constants import ENDC, TBLUE, TGREEN, TRED, TYELLOW
 
         var_seq = ""
         for p in data.position_details:

src/hgvs/pretty/console/chrom_seq_reverse_renderer.py

@@ -11,7 +11,7 @@ def legend(self) -> str:
 
     def display(self, data: VariantData) -> str:
         """colors the ref sequences with adenine (A, green), thymine (T, red), cytosine (C, yellow), and guanine (G, blue)"""
-        from hgvs.pretty.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+        from hgvs.pretty.console.constants import ENDC, TBLUE, TGREEN, TRED, TYELLOW
 
         var_seq = ""
         for p in data.position_details:

src/hgvs/pretty/console/prot_mapping_renderer.py

@@ -3,7 +3,7 @@
 
 
 class ProtMappingRenderer(BasicRenderer):
-    """prints the position in p (amino acid) coordinates."""
+    """Prints the position in p (amino acid) coordinates."""
 
     def legend(self):
         return "aa pos    : "

src/hgvs/pretty/console/prot_seq_renderer.py

@@ -14,7 +14,7 @@ def display(self, data: VariantData) -> str:
         if not data.var_c_or_n:
             return ""
 
-        from hgvs.pretty.pretty_print import ENDC, TGREEN, TRED
+        from hgvs.pretty.console.constants import ENDC, TGREEN, TRED
 
         var_str = ""
         for pdata in data.position_details:

src/hgvs/pretty/console/shuffled_variant.py

@@ -17,7 +17,7 @@ def legend(self) -> str:
 
     def display(self, data: VariantData) -> str:
 
-        from hgvs.pretty.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+        from hgvs.pretty.console.constants import ENDC, TRED
 
         seq_start = data.display_start
         seq_end = data.display_end

src/hgvs/pretty/console/tx_alig_renderer.py

@@ -17,7 +17,7 @@ def display(self, data: VariantData) -> str:
         if not data.var_c_or_n:
             return ""
 
-        from hgvs.pretty.pretty_print import ENDC, TPURPLE, TYELLOW
+        from hgvs.pretty.console.constants import ENDC, TPURPLE, TYELLOW
 
         var_str = ""
 

src/hgvs/pretty/console/tx_ref_disagree_renderer.py

@@ -6,16 +6,15 @@ class TxRefDisagreeRenderer(BasicRenderer):
     """Display tx-ref-disagree positions"""
 
     def legend(self) -> str:
-
-        return f"tx ref dif: "
+        return "tx ref dif: "
 
     def display(self, data: VariantData) -> str:
         """show differences between tx and ref genome, if there are any"""
 
         if not data.var_c_or_n:
             return ""
 
-        from hgvs.pretty.pretty_print import ENDC, TRED
+        from hgvs.pretty.console.constants import ENDC, TRED
 
         var_str = ""
         counter = -1

src/hgvs/pretty/datacompiler.py

@@ -24,6 +24,7 @@ def __init__(self, config: PrettyConfig):
         self.config = config
 
     def get_shuffled_variant(self, var_g: SequenceVariant, direction: int) -> VariantCoords:
+        """ Takes a sequence variant and returns VariantCoords that have been shuffled accordingly."""
 
         # get shuffled representation:
         if direction == 5:

tests/test_pretty_print.py

@@ -7,6 +7,7 @@
 from hgvs.pretty.pretty_print import PrettyPrint
 
 
+@pytest.mark.skip("The pretty print tests are data hungry. If we were to add the data to the test cache, we would inflate the size of the cache. As such only running when necessary.")
 @pytest.mark.quick
 @pytest.mark.models
 class Test_SimplePosition(unittest.TestCase):