#741 small refactoring to update directory structure, based on PR com…

…ments

src/hgvs/easy.py

@@ -37,7 +37,7 @@
 from hgvs.dataproviders.uta import connect
 from hgvs.normalizer import Normalizer
 from hgvs.parser import Parser
-from hgvs.pretty_print import PrettyPrint
+from hgvs.pretty.pretty_print import PrettyPrint
 from hgvs.validator import Validator
 from hgvs.variantmapper import VariantMapper
 

src/hgvs/pretty/renderer/chrom_seq_renderer.py → src/hgvs/pretty/console/chrom_seq_renderer.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class ChromSeqRendered(BasicRenderer):
@@ -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_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+        from hgvs.pretty.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
 
         var_seq = ""
         for p in data.position_details:

src/hgvs/pretty/renderer/chrom_seq_reverse_renderer.py → src/hgvs/pretty/console/chrom_seq_reverse_renderer.py

@@ -1,7 +1,7 @@
 from bioutils.sequences import reverse_complement
 
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class ChromReverseSeqRendered(BasicRenderer):
@@ -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_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+        from hgvs.pretty.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
 
         var_seq = ""
         for p in data.position_details:

src/hgvs/pretty/console/constants.py

@@ -0,0 +1,14 @@
+### Color constants for rendering text on the console
+
+TGREEN = "\033[32m"  # Green Text
+TGREENBG = "\033[30;42m"
+TRED = "\033[31m"  # Red Text
+TREDBG = "\033[30;41m"
+TBLUE = "\033[34m"  # Blue Text
+TBLUEBG = "\033[30;44m"
+TPURPLE = "\033[35m"  # Purple Text
+TPURPLEBG = "\033[30;45m"
+TYELLOW = "\033[33m"  # Yellow Text
+TYELLOWBG = "\033[30;43m"
+
+ENDC = "\033[m"  # reset to the defaults

src/hgvs/pretty/renderer/pos_info.py → src/hgvs/pretty/console/pos_info.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class ChrPositionInfo(BasicRenderer):

src/hgvs/pretty/renderer/prot_mapping_renderer.py → src/hgvs/pretty/console/prot_mapping_renderer.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class ProtMappingRenderer(BasicRenderer):

src/hgvs/pretty/renderer/prot_ruler_renderer.py → src/hgvs/pretty/console/prot_ruler_renderer.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class ProtRulerRenderer(BasicRenderer):

src/hgvs/pretty/renderer/prot_seq_renderer.py → src/hgvs/pretty/console/prot_seq_renderer.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class ProtSeqRenderer(BasicRenderer):
@@ -14,7 +14,7 @@ def display(self, data: VariantData) -> str:
         if not data.var_c_or_n:
             return ""
 
-        from hgvs.pretty_print import ENDC, TGREEN, TRED
+        from hgvs.pretty.pretty_print import ENDC, TGREEN, TRED
 
         var_str = ""
         for pdata in data.position_details:

src/hgvs/pretty/console/renderer.py

@@ -0,0 +1,32 @@
+from abc import ABC, abstractmethod
+
+from hgvs.pretty.console.constants import ENDC, TPURPLE, TYELLOW
+
+
+def colorize_hgvs(hgvs_str: str) -> str:
+    """ Takes a string representation of a hgvs Sequence Variant and renders it with console colors.
+    """
+
+    spl = hgvs_str.split(":")
+    var_str = TPURPLE + spl[0] + ENDC
+    var_str += ":"
+
+    sec = spl[1].split(".")
+    var_str += TYELLOW + sec[0] + ENDC
+    var_str += "."
+    var_str += sec[1]
+
+    return var_str
+
+class BasicRenderer(ABC):
+    def __init__(self, config, orientation: int):
+        self.config = config
+        self.orientation = orientation
+
+    @abstractmethod
+    def legend(self):
+        pass
+
+    @abstractmethod
+    def display(self):
+        pass

src/hgvs/pretty/renderer/ruler.py → src/hgvs/pretty/console/ruler.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class ChrRuler(BasicRenderer):

src/hgvs/pretty/renderer/shuffled_variant.py → src/hgvs/pretty/console/shuffled_variant.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantCoords, VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 from hgvs.sequencevariant import SequenceVariant
 
 
@@ -17,7 +17,7 @@ def legend(self) -> str:
 
     def display(self, data: VariantData) -> str:
 
-        from hgvs.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+        from hgvs.pretty.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
 
         seq_start = data.display_start
         seq_end = data.display_end

src/hgvs/pretty/renderer/tx_alig_renderer.py → src/hgvs/pretty/console/tx_alig_renderer.py

@@ -1,7 +1,7 @@
 import math
 
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class TxAligRenderer(BasicRenderer):
@@ -17,7 +17,7 @@ def display(self, data: VariantData) -> str:
         if not data.var_c_or_n:
             return ""
 
-        from hgvs.pretty_print import ENDC, TPURPLE, TYELLOW
+        from hgvs.pretty.pretty_print import ENDC, TPURPLE, TYELLOW
 
         var_str = ""
 

src/hgvs/pretty/renderer/tx_mapping_renderer.py → src/hgvs/pretty/console/tx_mapping_renderer.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class TxMappingRenderer(BasicRenderer):

src/hgvs/pretty/renderer/tx_pos.py → src/hgvs/pretty/console/tx_pos.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class TxRulerRenderer(BasicRenderer):

src/hgvs/pretty/renderer/tx_ref_disagree_renderer.py → src/hgvs/pretty/console/tx_ref_disagree_renderer.py

@@ -1,5 +1,5 @@
 from hgvs.pretty.models import VariantData
-from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.pretty.console.renderer import BasicRenderer
 
 
 class TxRefDisagreeRenderer(BasicRenderer):
@@ -15,7 +15,7 @@ def display(self, data: VariantData) -> str:
         if not data.var_c_or_n:
             return ""
 
-        from hgvs.pretty_print import ENDC, TRED
+        from hgvs.pretty.pretty_print import ENDC, TRED
 
         var_str = ""
         counter = -1

src/hgvs/pretty/datacompiler.py

@@ -1,4 +1,4 @@
-from typing import List, Optional, Tuple
+from typing import List, Tuple
 
 from bioutils.normalize import normalize
 from bioutils.sequences import aa1_to_aa3_lut

src/hgvs/pretty/models.py

@@ -94,7 +94,7 @@ class VariantData:
 
 @dataclass
 class PrettyConfig:
-    """acontainer for various configurations."""
+    """A container for various configurations."""
 
     hdp: Interface
     am37: AssemblyMapper

src/hgvs/pretty_print.py → src/hgvs/pretty/pretty_print.py

@@ -2,35 +2,25 @@
 
 import hgvs
 from hgvs.assemblymapper import AssemblyMapper
+from hgvs.pretty.console.renderer import colorize_hgvs
 from hgvs.pretty.datacompiler import DataCompiler
 from hgvs.pretty.models import PrettyConfig
-from hgvs.pretty.renderer.chrom_seq_renderer import ChromSeqRendered
-from hgvs.pretty.renderer.chrom_seq_reverse_renderer import ChromReverseSeqRendered
-from hgvs.pretty.renderer.pos_info import ChrPositionInfo
-from hgvs.pretty.renderer.prot_mapping_renderer import ProtMappingRenderer
-from hgvs.pretty.renderer.prot_ruler_renderer import ProtRulerRenderer
-from hgvs.pretty.renderer.prot_seq_renderer import ProtSeqRenderer
-from hgvs.pretty.renderer.ruler import ChrRuler
-from hgvs.pretty.renderer.shuffled_variant import ShuffledVariant
-from hgvs.pretty.renderer.tx_alig_renderer import TxAligRenderer
-from hgvs.pretty.renderer.tx_mapping_renderer import TxMappingRenderer
-from hgvs.pretty.renderer.tx_pos import TxRulerRenderer
-from hgvs.pretty.renderer.tx_ref_disagree_renderer import TxRefDisagreeRenderer
+from hgvs.pretty.console.chrom_seq_renderer import ChromSeqRendered
+from hgvs.pretty.console.chrom_seq_reverse_renderer import ChromReverseSeqRendered
+from hgvs.pretty.console.pos_info import ChrPositionInfo
+from hgvs.pretty.console.prot_mapping_renderer import ProtMappingRenderer
+from hgvs.pretty.console.prot_ruler_renderer import ProtRulerRenderer
+from hgvs.pretty.console.prot_seq_renderer import ProtSeqRenderer
+from hgvs.pretty.console.ruler import ChrRuler
+from hgvs.pretty.console.shuffled_variant import ShuffledVariant
+from hgvs.pretty.console.tx_alig_renderer import TxAligRenderer
+from hgvs.pretty.console.tx_mapping_renderer import TxMappingRenderer
+from hgvs.pretty.console.tx_pos import TxRulerRenderer
+from hgvs.pretty.console.tx_ref_disagree_renderer import TxRefDisagreeRenderer
 from hgvs.repeats import RepeatAnalyser
 from hgvs.sequencevariant import SequenceVariant
 
-TGREEN = "\033[32m"  # Green Text
-TGREENBG = "\033[30;42m"
-TRED = "\033[31m"  # Red Text
-TREDBG = "\033[30;41m"
-TBLUE = "\033[34m"  # Blue Text
-TBLUEBG = "\033[30;44m"
-TPURPLE = "\033[35m"  # Purple Text
-TPURPLEBG = "\033[30;45m"
-TYELLOW = "\033[33m"  # Yellow Text
-TYELLOWBG = "\033[30;43m"
 
-ENDC = "\033[m"  # reset to the defaults
 
 
 class PrettyPrint:
@@ -117,20 +107,6 @@ def _map_to_chrom(self, sv: SequenceVariant) -> SequenceVariant:
         elif sv.type == "t":
             return am.t_to_g(sv)
 
-    def _colorize_hgvs(self, hgvs_str: str) -> str:
-        if not self.config.useColor:
-            return hgvs_str
-
-        spl = hgvs_str.split(":")
-        var_str = TPURPLE + spl[0] + ENDC
-        var_str += ":"
-
-        sec = spl[1].split(".")
-        var_str += TYELLOW + sec[0] + ENDC
-        var_str += "."
-        var_str += sec[1]
-
-        return var_str
 
     def get_hgvs_names(
         self, sv: SequenceVariant, tx_ac: str = None
@@ -210,14 +186,14 @@ def create_repre(
             head = head_c = head_p = refa = ""
 
         if self.config.useColor:
-            var_g_print = self._colorize_hgvs(str(var_g))
+            var_g_print = colorize_hgvs(str(var_g))
         else:
             var_g_print = str(var_g)
 
         var_str = head + var_g_print + "\n"
         if data.var_c_or_n:
             if self.config.useColor:
-                var_c_print = self._colorize_hgvs(str(var_c_or_n))
+                var_c_print = colorize_hgvs(str(var_c_or_n))
             else:
                 var_c_print = str(var_c_or_n)
             if data.var_c_or_n.type == "c":
@@ -228,7 +204,7 @@ def create_repre(
 
         if data.var_p:
             if self.config.useColor:
-                var_p_print = self._colorize_hgvs(str(data.var_p))
+                var_p_print = colorize_hgvs(str(data.var_p))
             else:
                 var_p_print = str(data.var_p)
             var_str += head_p + var_p_print + "\n"

tests/test_pretty_print.py

@@ -1,12 +1,10 @@
 # -*- coding: utf-8 -*-
-import os
 import unittest
 
 import pytest
-from support import CACHE
 
 import hgvs
-from hgvs.pretty_print import PrettyPrint
+from hgvs.pretty.pretty_print import PrettyPrint
 
 
 @pytest.mark.quick