Add plumbing files to pass tests

python/mrchem/input_parser/plumbing/pyparsing/__init__.py

@@ -56,7 +56,7 @@
 :class:`'|'<MatchFirst>`, :class:`'^'<Or>` and :class:`'&'<Each>` operators.
 
 The :class:`ParseResults` object returned from
-:class:`ParserElement.parseString` can be
+:class:`ParserElement.parse_string` can be
 accessed as a nested list, a dictionary, or an object with named
 attributes.
 
@@ -85,11 +85,11 @@
    and :class:`'&'<Each>` operators to combine simple expressions into
    more complex ones
  - associate names with your parsed results using
-   :class:`ParserElement.setResultsName`
+   :class:`ParserElement.set_results_name`
  - access the parsed data, which is returned as a :class:`ParseResults`
    object
- - find some helpful expression short-cuts like :class:`delimitedList`
-   and :class:`oneOf`
+ - find some helpful expression short-cuts like :class:`DelimitedList`
+   and :class:`one_of`
  - find more useful common expressions in the :class:`pyparsing_common`
    namespace class
 """
@@ -106,30 +106,22 @@ class version_info(NamedTuple):
     @property
     def __version__(self):
         return (
-            "{}.{}.{}".format(self.major, self.minor, self.micro)
+            f"{self.major}.{self.minor}.{self.micro}"
             + (
-                "{}{}{}".format(
-                    "r" if self.releaselevel[0] == "c" else "",
-                    self.releaselevel[0],
-                    self.serial,
-                ),
+                f"{'r' if self.releaselevel[0] == 'c' else ''}{self.releaselevel[0]}{self.serial}",
                 "",
             )[self.releaselevel == "final"]
         )
 
     def __str__(self):
-        return "{} {} / {}".format(__name__, self.__version__, __version_time__)
+        return f"{__name__} {self.__version__} / {__version_time__}"
 
     def __repr__(self):
-        return "{}.{}({})".format(
-            __name__,
-            type(self).__name__,
-            ", ".join("{}={!r}".format(*nv) for nv in zip(self._fields, self)),
-        )
+        return f"{__name__}.{type(self).__name__}({', '.join('{}={!r}'.format(*nv) for nv in zip(self._fields, self))})"
 
 
-__version_info__ = version_info(3, 0, 9, "final", 0)
-__version_time__ = "05 May 2022 07:02 UTC"
+__version_info__ = version_info(3, 1, 1, "final", 1)
+__version_time__ = "29 Jul 2023 22:27 UTC"
 __version__ = __version_info__.__version__
 __versionTime__ = __version_time__
 __author__ = "Paul McGuire <[email protected]>"
@@ -139,9 +131,9 @@ def __repr__(self):
 from .actions import *
 from .core import __diag__, __compat__
 from .results import *
-from .core import *
+from .core import *  # type: ignore[misc, assignment]
 from .core import _builtin_exprs as core_builtin_exprs
-from .helpers import *
+from .helpers import *  # type: ignore[misc, assignment]
 from .helpers import _builtin_exprs as helper_builtin_exprs
 
 from .unicode import unicode_set, UnicodeRangeList, pyparsing_unicode as unicode
@@ -153,11 +145,11 @@ def __repr__(self):
 
 # define backward compat synonyms
 if "pyparsing_unicode" not in globals():
-    pyparsing_unicode = unicode
+    pyparsing_unicode = unicode  # type: ignore[misc]
 if "pyparsing_common" not in globals():
-    pyparsing_common = common
+    pyparsing_common = common  # type: ignore[misc]
 if "pyparsing_test" not in globals():
-    pyparsing_test = testing
+    pyparsing_test = testing  # type: ignore[misc]
 
 core_builtin_exprs += common_builtin_exprs + helper_builtin_exprs
 
@@ -174,7 +166,9 @@ def __repr__(self):
     "CaselessKeyword",
     "CaselessLiteral",
     "CharsNotIn",
+    "CloseMatch",
     "Combine",
+    "DelimitedList",
     "Dict",
     "Each",
     "Empty",
@@ -227,9 +221,11 @@ def __repr__(self):
     "alphas8bit",
     "any_close_tag",
     "any_open_tag",
+    "autoname_elements",
     "c_style_comment",
     "col",
     "common_html_entity",
+    "condition_as_parse_action",
     "counted_array",
     "cpp_style_comment",
     "dbl_quoted_string",
@@ -241,6 +237,7 @@ def __repr__(self):
     "html_comment",
     "identchars",
     "identbodychars",
+    "infix_notation",
     "java_style_comment",
     "line",
     "line_end",
@@ -255,8 +252,12 @@ def __repr__(self):
     "null_debug_action",
     "nums",
     "one_of",
+    "original_text_for",
     "printables",
     "punc8bit",
+    "pyparsing_common",
+    "pyparsing_test",
+    "pyparsing_unicode",
     "python_style_comment",
     "quoted_string",
     "remove_quotes",
@@ -267,38 +268,33 @@ def __repr__(self):
     "srange",
     "string_end",
     "string_start",
+    "token_map",
     "trace_parse_action",
+    "ungroup",
+    "unicode_set",
     "unicode_string",
     "with_attribute",
-    "indentedBlock",
-    "original_text_for",
-    "ungroup",
-    "infix_notation",
-    "locatedExpr",
     "with_class",
-    "CloseMatch",
-    "token_map",
-    "pyparsing_common",
-    "pyparsing_unicode",
-    "unicode_set",
-    "condition_as_parse_action",
-    "pyparsing_test",
     # pre-PEP8 compatibility names
     "__versionTime__",
     "anyCloseTag",
     "anyOpenTag",
     "cStyleComment",
     "commonHTMLEntity",
+    "conditionAsParseAction",
     "countedArray",
     "cppStyleComment",
     "dblQuotedString",
     "dblSlashComment",
     "delimitedList",
     "dictOf",
     "htmlComment",
+    "indentedBlock",
+    "infixNotation",
     "javaStyleComment",
     "lineEnd",
     "lineStart",
+    "locatedExpr",
     "makeHTMLTags",
     "makeXMLTags",
     "matchOnlyAtCol",
@@ -308,6 +304,7 @@ def __repr__(self):
     "nullDebugAction",
     "oneOf",
     "opAssoc",
+    "originalTextFor",
     "pythonStyleComment",
     "quotedString",
     "removeQuotes",
@@ -317,15 +314,12 @@ def __repr__(self):
     "sglQuotedString",
     "stringEnd",
     "stringStart",
+    "tokenMap",
     "traceParseAction",
     "unicodeString",
     "withAttribute",
-    "indentedBlock",
-    "originalTextFor",
-    "infixNotation",
-    "locatedExpr",
     "withClass",
-    "tokenMap",
-    "conditionAsParseAction",
-    "autoname_elements",
+    "common",
+    "unicode",
+    "testing",
 ]

python/mrchem/input_parser/plumbing/pyparsing/actions.py

@@ -1,7 +1,7 @@
 # actions.py
 
 from .exceptions import ParseException
-from .util import col
+from .util import col, replaced_by_pep8
 
 
 class OnlyOnce:
@@ -38,7 +38,7 @@ def match_only_at_col(n):
 
     def verify_col(strg, locn, toks):
         if col(locn, strg) != n:
-            raise ParseException(strg, locn, "matched token not at column {}".format(n))
+            raise ParseException(strg, locn, f"matched token not at column {n}")
 
     return verify_col
 
@@ -148,15 +148,13 @@ def pa(s, l, tokens):
                 raise ParseException(
                     s,
                     l,
-                    "attribute {!r} has value {!r}, must be {!r}".format(
-                        attrName, tokens[attrName], attrValue
-                    ),
+                    f"attribute {attrName!r} has value {tokens[attrName]!r}, must be {attrValue!r}",
                 )
 
     return pa
 
 
-with_attribute.ANY_VALUE = object()
+with_attribute.ANY_VALUE = object()  # type: ignore [attr-defined]
 
 
 def with_class(classname, namespace=""):
@@ -195,13 +193,25 @@ def with_class(classname, namespace=""):
         1 4 0 1 0
         1,3 2,3 1,1
     """
-    classattr = "{}:class".format(namespace) if namespace else "class"
+    classattr = f"{namespace}:class" if namespace else "class"
     return with_attribute(**{classattr: classname})
 
 
 # pre-PEP8 compatibility symbols
-replaceWith = replace_with
-removeQuotes = remove_quotes
-withAttribute = with_attribute
-withClass = with_class
-matchOnlyAtCol = match_only_at_col
+# fmt: off
+@replaced_by_pep8(replace_with)
+def replaceWith(): ...
+
+@replaced_by_pep8(remove_quotes)
+def removeQuotes(): ...
+
+@replaced_by_pep8(with_attribute)
+def withAttribute(): ...
+
+@replaced_by_pep8(with_class)
+def withClass(): ...
+
+@replaced_by_pep8(match_only_at_col)
+def matchOnlyAtCol(): ...
+
+# fmt: on