From f095c78cd3dc65d2fef941a4a7babc0fea006ba5 Mon Sep 17 00:00:00 2001
From: SUENO Omozawa <39725660+Augus1999@users.noreply.github.com>
Date: Fri, 15 Jul 2022 12:18:43 +0100
Subject: [PATCH] update

---
 mol2chemfigPy3/atom.py             | 12 ++++++------
 mol2chemfigPy3/bond.py             | 20 ++++++++++----------
 mol2chemfigPy3/chemfig_mappings.py | 20 ++++++++++----------
 mol2chemfigPy3/common.py           |  2 +-
 mol2chemfigPy3/molecule.py         | 24 ++++++++++++------------
 mol2chemfigPy3/optionparser.py     | 28 ++++++++++++++--------------
 mol2chemfigPy3/processor.py        |  8 ++++----
 7 files changed, 57 insertions(+), 57 deletions(-)

diff --git a/mol2chemfigPy3/atom.py b/mol2chemfigPy3/atom.py
index 72b5d15..1999867 100644
--- a/mol2chemfigPy3/atom.py
+++ b/mol2chemfigPy3/atom.py
@@ -3,7 +3,7 @@
 define Atom object
 """
 import string
-from typing import Optional, Union
+from typing import Optional, Union, Dict, List, Tuple
 from . import chemfig_mappings as cfm
 
 # some atoms should carry their hydrogen to the left, rather than
@@ -43,7 +43,7 @@ class Atom:
 
     def __init__(
         self,
-        options: dict,
+        options: Dict,
         idx: int,
         x: Union[int, float],
         y: Union[int, float],
@@ -51,7 +51,7 @@ def __init__(
         hydrogens: Optional[int],
         charge: int,
         radical: int,
-        neighbors: list[int],
+        neighbors: List[int],
     ):
         self.options = options
         self.idx = idx
@@ -91,7 +91,7 @@ def _score_angle(a: int, b: int, turf: int) -> int:
         angle = min(diff, 360 - diff)
         return (max(0, turf - angle)) ** 2
 
-    def _score_angles(self, choices: list[list[int, int, str]], turf: int) -> list[str]:
+    def _score_angles(self, choices: List[List], turf: int) -> List[str]:
         """
         backend for score_angles
 
@@ -143,7 +143,7 @@ def score_angles(self) -> None:
             0
         ]
 
-    def render_phantom(self) -> tuple[Optional[str], str]:
+    def render_phantom(self) -> Tuple[Optional[str], str]:
         """
         render a bond that closes a ring or loop, or for
         late-rendered cross bonds. The target atom
@@ -162,7 +162,7 @@ def render_phantom(self) -> tuple[Optional[str], str]:
         )
         return atom_code, comment_code
 
-    def render(self) -> tuple[str, str]:
+    def render(self) -> Tuple[str, str]:
         """
         render the atom and a comment
 
diff --git a/mol2chemfigPy3/bond.py b/mol2chemfigPy3/bond.py
index 465907f..ff0f6e7 100644
--- a/mol2chemfigPy3/bond.py
+++ b/mol2chemfigPy3/bond.py
@@ -2,7 +2,7 @@
 """
 My name is Bond. JAMES Bond.
 """
-from typing import Optional, Union
+from typing import Optional, Union, Tuple, Dict
 from copy import deepcopy, copy
 from math import atan, tan, pi
 from indigo import Indigo
@@ -32,7 +32,7 @@
 
 def compare_positions(
     x1: float, y1: float, x2: float, y2: float
-) -> tuple[float, float]:
+) -> Tuple[float, float]:
     """
     calculate distance and angle between the
     coordinates of two atoms.
@@ -98,7 +98,7 @@ class Bond:
 
     def __init__(
         self,
-        options: dict,
+        options: Dict,
         start_atom: Atom,
         end_atom: Atom,
         bond_type: Optional[str] = None,
@@ -145,7 +145,7 @@ def __init__(
         else:
             self.marker = ""
 
-    def bond_dimensions(self) -> tuple[float, float]:
+    def bond_dimensions(self) -> Tuple[float, float]:
         """
         determine bond angle and distance between two atoms
 
@@ -266,7 +266,7 @@ def _adjoining_angles(
 
         return int(round(angles[0])), int(round(angles[-1]))
 
-    def upstream_angles(self) -> dict:
+    def upstream_angles(self) -> Dict:
         """
         determine the narrowest upstream left and upstream right angle.
 
@@ -280,7 +280,7 @@ def upstream_angles(self) -> dict:
 
         return dict(left=first, right=last)
 
-    def downstream_angles(self) -> dict:
+    def downstream_angles(self) -> Dict:
         """
         determine the narrowest downstream left and downstream right angle.
 
@@ -345,7 +345,7 @@ def shorten_stroke(
 
         return self.cotan100(angle)
 
-    def fancy_double(self) -> Optional[tuple[str, int, int]]:
+    def fancy_double(self) -> Optional[Tuple[str, int, int]]:
         """
         work out the parameters for rendering a fancy double bond.
 
@@ -427,7 +427,7 @@ def fancy_double(self) -> Optional[tuple[str, int, int]]:
 
         return side, start, end
 
-    def fancy_triple(self) -> tuple[int, int]:
+    def fancy_triple(self) -> Tuple[int, int]:
         """
         work out parameters for fancy triple bond. We don't
         need to choose sides here, just calculate the required
@@ -545,7 +545,7 @@ def render(self, level: int) -> str:
         return self.indent(level, bond_code, atom_code, comment_code)
 
 
-class DummyFirstBond:
+class DummyFirstBond(Bond):
     """
     semi-dummy class that only takes an end-atom, which is the
     first atom in the molecule, and just renders that.
@@ -581,7 +581,7 @@ class AromaticRingBond(Bond):
 
     def __init__(
         self,
-        options: dict,
+        options: Dict,
         parent: Optional[Bond],
         angle: Union[int, float],
         length: Union[int, float],
diff --git a/mol2chemfigPy3/chemfig_mappings.py b/mol2chemfigPy3/chemfig_mappings.py
index 69e3059..91083cd 100644
--- a/mol2chemfigPy3/chemfig_mappings.py
+++ b/mol2chemfigPy3/chemfig_mappings.py
@@ -6,7 +6,7 @@
 the TeX syntax defined by the chemfig package.
 """
 import textwrap
-from typing import Union, Optional
+from typing import Union, Optional, List, Tuple, Dict
 
 BOND_CODE_WIDTH = 50  # space for bonds - generous upfront, will be trimmed at the end
 TERSE_LINE_WIDTH = 75  # in terse code format, force linebreaks
@@ -137,7 +137,7 @@ def num_round(num: Union[int, float], sig: Union[int, float]) -> Union[int, floa
 
 
 def format_angle(
-    options: dict, angle: Union[int, float], parent_angle: Union[int, float, None]
+    options: Dict, angle: Union[int, float], parent_angle: Union[int, float, None]
 ) -> str:
     """
     format prefix and number for bond angle
@@ -175,7 +175,7 @@ def specifier_default(val: any, default: any) -> str:
 
 
 def format_bond(
-    options: dict,
+    options: Dict,
     angle: Union[int, float, None],
     parent_angle: Union[int, float, None],
     bond_type: str,
@@ -184,8 +184,8 @@ def format_bond(
     length: Union[int, float],
     departure: str,
     arrival: str,
-    tikz_styles: Union[set, dict],
-    tikz_values: Union[set, dict],
+    tikz_styles: Union[set, Dict],
+    tikz_values: Union[set, Dict],
     marker: str,
 ) -> str:
     """
@@ -262,7 +262,7 @@ def format_bond(
     return bond_code + modifier + specifiers
 
 
-def fill_atom(keys: tuple, data: dict, phantom: str, phantom_pos: int = 0) -> tuple:
+def fill_atom(keys: Tuple, data: Dict, phantom: str, phantom_pos: int = 0) -> tuple:
     """
     helper for finalizing atom code. phantom_pos is the
     target position of a bond attaching to a phantom;
@@ -298,7 +298,7 @@ def format_marker(marker: Optional[str]) -> Optional[str]:
 
 
 def format_atom(
-    options: dict,
+    options: Dict,
     idx: int,
     element: str,
     hydrogens: Optional[int],
@@ -307,7 +307,7 @@ def format_atom(
     first_quadrant: str,
     second_quadrant: str,
     charge_angle: Optional[str],
-) -> tuple:
+) -> Tuple:
     """
     render an atom with hydrogens and charges. Return
     - the chemfig code of the rendered atom
@@ -417,7 +417,7 @@ def format_atom(
     return fill_atom(keys, data, element_phantom)
 
 
-def format_atom_comment(options: dict, idx: int) -> str:
+def format_atom_comment(options: Dict, idx: int) -> str:
     """
     render an optional end-of-line comment after a regular atom
 
@@ -449,7 +449,7 @@ def format_aromatic_ring(
     parent_angle: Union[int, float, None],
     length: Union[int, float],
     radius: Union[int, float],
-) -> tuple[str, str, str]:
+) -> (str, str, str):
     """
     :param options: option dict
     :param angle: angle
diff --git a/mol2chemfigPy3/common.py b/mol2chemfigPy3/common.py
index ac913c3..b6e3a8b 100644
--- a/mol2chemfigPy3/common.py
+++ b/mol2chemfigPy3/common.py
@@ -4,7 +4,7 @@
 """
 from .options import getParser
 
-program_version = "1.5.5"
+program_version = "1.5.6"
 
 # pubchem url for retrieving sdf for numerical IDs
 pubchem_url = (
diff --git a/mol2chemfigPy3/molecule.py b/mol2chemfigPy3/molecule.py
index 7099888..d34b803 100644
--- a/mol2chemfigPy3/molecule.py
+++ b/mol2chemfigPy3/molecule.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # parse a molfile molecule and render to chemfig code
 import math
-from typing import Optional, Union
+from typing import Optional, Union, Tuple, List, Dict
 from indigo import IndigoException, IndigoObject
 from . import chemfig_mappings as cfm
 from .common import MCFError, Counter
@@ -13,7 +13,7 @@ class Molecule:
     bond_scale = 1.0  # can be overridden by user option
     exit_bond = None  # the first bond in the tree that connects to the exit atom
 
-    def __init__(self, options: dict, tkmol: IndigoObject):
+    def __init__(self, options: Dict, tkmol: IndigoObject):
         self.options = options
         self.tkmol = tkmol
 
@@ -138,7 +138,7 @@ def connect_fragments(self) -> None:
             for atom in un_bonded:
                 self.link_atoms(anchor, atom)
 
-    def molecule_fragments(self) -> list:
+    def molecule_fragments(self) -> List:
         """
         identify unconnected fragments in the molecule.
         used by connect_fragments
@@ -146,7 +146,7 @@ def molecule_fragments(self) -> list:
         :return: fragments
         """
 
-        def split_pairs(pair_list: list) -> tuple[list, list]:
+        def split_pairs(pair_list: List) -> Tuple[List, List]:
             """
             break up pair_list into one list that contains all pairs
             that are connected, directly or indirectly, to the first
@@ -194,7 +194,7 @@ def split_pairs(pair_list: list) -> tuple[list, list]:
             else:
                 atom_pairs = rest
 
-    def treebonds(self, root: bool = False) -> list:
+    def treebonds(self, root: bool = False) -> List:
         """
         return a list with all bonds in the molecule tree
 
@@ -307,7 +307,7 @@ def default_exit_bond(self) -> Bond:
         bond_out = bonds[scored[-1]]
         return bond_out
 
-    def pickFirstLastAtoms(self) -> tuple[Optional[Atom], Optional[Atom]]:
+    def pickFirstLastAtoms(self) -> Tuple[Optional[Atom], Optional[Atom]]:
         """
         If the first atom is not given, we try to pick one
         that has only one bond to the rest of the molecule,
@@ -334,7 +334,7 @@ def pickFirstLastAtoms(self) -> tuple[Optional[Atom], Optional[Atom]]:
 
         return entry_atom, exit_atom
 
-    def parseAtoms(self) -> dict:
+    def parseAtoms(self) -> Dict:
         """
         Read some attributes from the toolkit atom object
 
@@ -375,7 +375,7 @@ def parseAtoms(self) -> dict:
 
         return wrapped_atoms
 
-    def parseBonds(self) -> tuple[dict, list]:
+    def parseBonds(self) -> Tuple[Dict, List]:
         """
         read some bond attributes
 
@@ -622,7 +622,7 @@ def scaleBonds(self) -> None:
         for bond in self.treebonds():
             bond.length = self.bond_scale * bond.length
 
-    def render(self) -> list:
+    def render(self) -> List:
         """
         render molecule to chemfig
 
@@ -655,7 +655,7 @@ def render_server(self) -> str:
 
         return cfm.format_output(params, self._rendered)
 
-    def _renderBranches(self, output: list, level: int, bonds: list) -> None:
+    def _renderBranches(self, output: List, level: int, bonds: List) -> None:
         """
         render a list of branching bonds indented and inside enclosing brackets.
 
@@ -673,7 +673,7 @@ def _renderBranches(self, output: list, level: int, bonds: list) -> None:
 
     def _render(
         self,
-        output: list,
+        output: List,
         bond: Union[Bond, DummyFirstBond, AromaticRingBond],
         level: int,
     ) -> None:
@@ -702,7 +702,7 @@ def _render(
             self._renderBranches(output, level + 1, branches)
             self._render(output, first, level)
 
-    def dimensions(self) -> tuple[float, float]:
+    def dimensions(self) -> Tuple[float, float]:
         r"""
         this calculates the approximate width and height
         of the rendered molecule, in units of chemfig
diff --git a/mol2chemfigPy3/optionparser.py b/mol2chemfigPy3/optionparser.py
index e4e1192..16f128e 100644
--- a/mol2chemfigPy3/optionparser.py
+++ b/mol2chemfigPy3/optionparser.py
@@ -15,7 +15,7 @@ class attributes and more subclassing than
 import getopt
 import re
 import textwrap
-from typing import Union, Optional
+from typing import Union, Optional, List, Tuple, Dict
 
 
 class OptionError(Exception):
@@ -36,7 +36,7 @@ def __init__(
         form_text: Optional[str] = None,
         key: Optional[str] = None,
         default: Union[bool, int, float, str, None] = None,
-        valid_range: Union[list, tuple, None] = None,
+        valid_range: Union[List, Tuple, None] = None,
         help_text: str = """
                  Our engineers deemed it self-explanatory
                  """,
@@ -97,7 +97,7 @@ def validate_form_value(self, value: any) -> bool:
         """
         return self.validate(value)
 
-    def _validate(self, value: any) -> tuple[bool, any]:
+    def _validate(self, value: any) -> Tuple[bool, any]:
         """
         no-op default
 
@@ -157,7 +157,7 @@ def format_tag_value(self, value: any) -> str:
             return ""
         return str(value)
 
-    def format_tag(self, value: any = None) -> tuple[str, str, str, str]:
+    def format_tag(self, value: any = None) -> Tuple[str, str, str, str]:
         """
         render a html form tag
 
@@ -250,7 +250,7 @@ def _default(self) -> None:
         except (TypeError, IndexError):
             raise OptionError("valid_range does not supply default")
 
-    def _validate(self, value: str) -> tuple[bool, str]:
+    def _validate(self, value: str) -> Tuple[bool, str]:
         """
         we enforce conversion to lowercase
 
@@ -259,7 +259,7 @@ def _validate(self, value: str) -> tuple[bool, str]:
         """
         return True, value.lower()
 
-    def format_tag(self, value: any = None) -> tuple[str, str, str, str]:
+    def format_tag(self, value: any = None) -> Tuple[str, str, str, str]:
         """
         :param value: value
         :return: (key, tag, form text, help text)
@@ -295,7 +295,7 @@ class TypeOption(Option):
         r"""<input type="text" name="%(key)s" value="%(value)s" size="8"/>"""
     )
 
-    def _validate(self, value: any) -> tuple[bool, any]:
+    def _validate(self, value: any) -> Tuple[bool, any]:
         """
         :param value: any value
         :return: (bool, value)
@@ -332,7 +332,7 @@ class RangeOption(Option):
         r"""<input type="text" name="%(key)s" value="%(value)s" size="8"/>"""
     )
 
-    def _validate(self, raw_value: str) -> tuple[bool, Union[list, str]]:
+    def _validate(self, raw_value: str) -> Tuple[bool, Union[List, str]]:
         """
         :param raw_value: string value
         :return: (bool, range)
@@ -380,7 +380,7 @@ def append(self, option: any) -> None:
         # also maintain options ordered in a list
         self._options.append(option)
 
-    def validKeys(self) -> list:
+    def validKeys(self) -> List:
         """
         required by the web form front end
 
@@ -388,7 +388,7 @@ def validKeys(self) -> list:
         """
         return list(self._options_by_key.keys())
 
-    def option_values(self) -> dict:
+    def option_values(self) -> Dict:
         """
         read current option values
 
@@ -401,7 +401,7 @@ def option_values(self) -> dict:
 
         return option_dict
 
-    def process_form_fields(self, fields: any) -> tuple[dict, list]:
+    def process_form_fields(self, fields: any) -> Tuple[Dict, List]:
         """
         process options received through the web form.
         we don't look at the cargo data here at all.
@@ -422,7 +422,7 @@ def process_form_fields(self, fields: any) -> tuple[dict, list]:
 
         return self.option_values(), warnings
 
-    def process_cli(self, raw_input: Union[list, str]) -> tuple[dict, list]:
+    def process_cli(self, raw_input: Union[List, str]) -> Tuple[Dict, List]:
         """
         process input from the command line interface
         - assemble template strings for getopt and run getopt
@@ -452,7 +452,7 @@ def process_cli(self, raw_input: Union[list, str]) -> tuple[dict, list]:
 
         return self.option_values(), args
 
-    def format_for_getopt(self) -> tuple[str, list]:
+    def format_for_getopt(self) -> Tuple[str, List]:
         """
         :return: (shorts, [long_1, long_2,...])
         """
@@ -494,7 +494,7 @@ def format_help(
 
         return "\n".join(output)
 
-    def form_tags(self) -> list:
+    def form_tags(self) -> List:
         """
         collect the html for each option
 
diff --git a/mol2chemfigPy3/processor.py b/mol2chemfigPy3/processor.py
index a6b2836..37cc648 100644
--- a/mol2chemfigPy3/processor.py
+++ b/mol2chemfigPy3/processor.py
@@ -6,7 +6,7 @@
 import os.path
 import traceback
 from urllib import request
-from typing import Union
+from typing import Union, List, Tuple
 from indigo import Indigo, IndigoException, IndigoObject
 from . import common, options, molecule
 
@@ -26,7 +26,7 @@ class Processor:
 
     def __init__(
         self,
-        raw_args: Union[list, str, None],
+        raw_args: Union[List, str, None],
         data: str,
         form_fields: any,
         program_name: str,
@@ -206,14 +206,14 @@ def parseMolecule(self) -> IndigoObject:
 
 
 def process(
-    raw_args: Union[list, str, None] = None,
+    raw_args: Union[List, str, None] = None,
     data: any = None,
     form_fields: any = None,
     program_name: str = "mol2chemfigPy3",
     web_form: bool = False,
     rpc: bool = False,
     inline: bool = False,
-) -> tuple[bool, Union[str, molecule.Molecule]]:
+) -> Tuple[bool, Union[str, molecule.Molecule]]:
     """
     process is a convenience wrapper for external callers