Code quality improvements: fix mutable defaults, add type hints, explicit imports

pypact/__init__.py

@@ -62,7 +62,3 @@
 # utilities
 from pypact.util.exceptions import PypactException
 from pypact.util.loglevels import *
-
-
-# This makes importing slow, keep it seperate
-#import pypact.analysis

pypact/input/filesfile.py

@@ -2,9 +2,21 @@
 
 from pypact.util.decorators import freeze_it
 from pypact.util.jsonserializable import JSONSerializable
-from pypact.util.exceptions import PypactDeserializeException
+from pypact.util.exceptions import PypactDeserializeException, PypactException
 from pypact.util.file import file_exists, dir_exists
-from pypact.library.projectiles import *
+from pypact.library.projectiles import (
+    PROJECTILE_NEUTRON,
+    PROJECTILE_DEUTERON,
+    PROJECTILE_PROTON,
+    PROJECTILE_ALPHA,
+    PROJECTILE_GAMMA,
+    VALID_PROJECTILES,
+    VALID_PROJECTILE_NAMES,
+    VALID_PROJECTILE_SYMBOLS,
+    get_projectile_name,
+    get_projectile_symbol,
+    get_projectile_value
+)
 
 # represents a null entry string
 NULL_ENTRY = "null"

pypact/input/inputdata.py

@@ -4,8 +4,16 @@
 from pypact.util.exceptions import PypactOutOfRangeException
 from pypact.util.exceptions import PypactInvalidOptionException
 from pypact.util.exceptions import PypactIncompatibleOptionException
+from pypact.util.exceptions import PypactUnphysicalValueException
 from pypact.util.jsonserializable import JSONSerializable
-from pypact.util.loglevels import *
+from pypact.util.loglevels import (
+    LOG_SEVERITY_FATAL,
+    LOG_SEVERITY_ERROR,
+    LOG_SEVERITY_WARNING,
+    LOG_SEVERITY_INFO,
+    LOG_SEVERITY_DEBUG,
+    LOG_SEVERITY_TRACE
+)
 from pypact.library.projectiles import PROJECTILE_NEUTRON, VALID_PROJECTILES
 from pypact.input.keywords import CONTROL_KEYWORDS, INIT_KEYWORDS, INVENTORY_KEYWORDS
 

pypact/library/reactionlib.py

@@ -1,4 +1,4 @@
-from .projectiles import *
+from .projectiles import PROJECTILE_NEUTRON, get_projectile_symbol
 
 REACTION_DICTIONARY = {
       1: 'total', 

pypact/output/nuclide.py

@@ -5,6 +5,10 @@
 
 NUCLIDE_IGNORES = ['\n', '|', '>', '&', '?', '#']
 
+# Constants for parsing nuclide identifiers
+ELEMENT_SYMBOL_LENGTH = 2
+ISOTOPE_NUMBER_LENGTH = 3
+
 
 @freeze_it
 class Nuclide(JSONSerializable):
@@ -30,10 +34,12 @@ def __init__(self):
 
     @property
     def name(self):
+        """Returns the nuclide name as a string (e.g., 'Fe56', 'Co60m')."""
         return f"{self.element}{self.isotope}{self.state}" 
 
     @property
     def zai(self):
+        """Returns the ZAI (Z*10000 + A*10 + I) identifier for this nuclide."""
         return get_zai(self.name) 
 
     def fispact_deserialize(self, linedump, column_headers):
@@ -49,11 +55,11 @@ def fispact_deserialize(self, linedump, column_headers):
         # turn the line into a list
         strings = line.split()
 
-        # first 2 characters are the symbol
-        # next 3 characters are the symbol
-        # last character is the symbol
-        symbollength = 2
-        isotopelength = 3
+        # first 2 characters are the element symbol
+        # next 3 characters are the isotope number
+        # last character (if alpha) is the state
+        symbollength = ELEMENT_SYMBOL_LENGTH
+        isotopelength = ISOTOPE_NUMBER_LENGTH
         if len(strings[0]) > symbollength:
             isotope = strings[0][symbollength:]
             strings[0] = strings[0][:symbollength]
@@ -98,6 +104,13 @@ def get_entry(header_name):
 
 
 def index_containing_substring(the_list, substring):
+    """
+    Find the index of the first list element containing a substring.
+
+    :param the_list: List of strings to search
+    :param substring: Substring to find
+    :return: Index of first matching element, or -1 if not found
+    """
     for i, s in enumerate(the_list):
         if substring in s:
             return i

pypact/util/file.py

@@ -1,52 +1,60 @@
 import os.path
+from typing import List
 
 
-# Returns the content of the file as a string
-def content_as_str(filename):
+def content_as_str(filename: str) -> List[str]:
+    """Returns the content of the file as a list of strings (one per line)."""
     with open(filename, 'r') as file:
         data = file.readlines()
 
     return data
 
 
-# Returns the content of the file as a string, and removes new lines.
-def content_as_str_noreturn(filename):
+def content_as_str_noreturn(filename: str) -> str:
+    """Returns the content of the file as a string, and removes new lines."""
     with open(filename, 'r') as file:
         data = file.read().replace('\n', '')
 
     return data
 
 
-# checks if file exists
-def file_exists(filename):
+def file_exists(filename: str) -> bool:
+    """Checks if file exists."""
     return os.path.isfile(filename)
 
 
-# checks if directory exists
-def dir_exists(filename):
+def dir_exists(filename: str) -> bool:
+    """Checks if directory exists."""
     return os.path.isdir(filename)
 
 
-def file_remove(filename):
+def file_remove(filename: str) -> None:
+    """Removes file if it exists."""
     if file_exists(filename):
         os.remove(filename)
 
 
-def get_filename_ext(filename):
+def get_filename_ext(filename: str) -> str:
+    """Gets the file extension from filename."""
     return os.path.basename(os.path.splitext(filename)[-1])
 
 
-def str_in_file(filename, string):
+def str_in_file(filename: str, string: str) -> bool:
+    """Checks if a string exists in the file."""
     if file_exists(filename):
         with open(filename) as file:
             return string in file.read()
 
     return False
 
 
-# note that regardless of the flag 'ignore_empty_lines' value,
-# the last line is always ignored
-def nr_of_lines(filename, ignore_empty_lines=False):
+def nr_of_lines(filename: str, ignore_empty_lines: bool = False) -> int:
+    """
+    Returns the number of lines in a file.
+
+    Note that regardless of the flag 'ignore_empty_lines' value,
+    the last line is always ignored.
+    """
     with open(filename) as file:
         if ignore_empty_lines:
             return len([i for i in file if i[:-1]])

pypact/util/lines.py

@@ -1,7 +1,8 @@
+from typing import List, Tuple, Optional
 from pypact.util.numerical import is_float, get_float
 
 
-def line_indices(lines, tag):
+def line_indices(lines: List[str], tag: str) -> List[int]:
     """
 
     :param lines: Must be a list of strings representing each line
@@ -12,7 +13,7 @@ def line_indices(lines, tag):
     return [l for l in range(len(lines)) if tag in lines[l]]
 
 
-def strings_from_line(line, linetag, ignoretags=[], endtag=''):
+def strings_from_line(line: str, linetag: str, ignoretags: Optional[List[str]] = None, endtag: str = '') -> List[str]:
     """
 
     :param line: The string representing a line
@@ -22,6 +23,9 @@ def strings_from_line(line, linetag, ignoretags=[], endtag=''):
     :return: A list of strings, without spaces or carriage returns, of string after the linetag
 
     """
+    if ignoretags is None:
+        ignoretags = []
+
     startindex = line.find(linetag)
     if startindex < 0:
         return []
@@ -42,7 +46,7 @@ def strings_from_line(line, linetag, ignoretags=[], endtag=''):
     return strings
 
 
-def join_strings_from_line(line, linetag, ignoretags=[], endtag=''):
+def join_strings_from_line(line: str, linetag: str, ignoretags: Optional[List[str]] = None, endtag: str = '') -> str:
     """
 
     :param line: The string representing a line
@@ -57,13 +61,13 @@ def join_strings_from_line(line, linetag, ignoretags=[], endtag=''):
     return ' '.join(strings)
 
 
-def first_value_from_line(line, linetag, ignoretags=[]):
+def first_value_from_line(line: str, linetag: str, ignoretags: Optional[List[str]] = None) -> float:
     """
 
     :param line: The string representing a line
     :param linetag: The tag to find in the line
     :param ignoretags: The list of strings to ignore
-    :return: The first value, float, after the tag. Returns NaN if no value found.
+    :return: The first value, float, after the tag. Returns 0.0 if no value found.
 
     """
     strings = strings_from_line(line, linetag, ignoretags)
@@ -81,7 +85,7 @@ def first_value_from_line(line, linetag, ignoretags=[]):
     return nan
 
 
-def first_occurrence(lines, tag):
+def first_occurrence(lines: List[str], tag: str) -> Tuple[int, str]:
     """
 
     :param lines: A list of strings representing each line
@@ -92,7 +96,7 @@ def first_occurrence(lines, tag):
     return next_occurrence(lines, tag, 0)
 
 
-def last_occurrence(lines, tag):
+def last_occurrence(lines: List[str], tag: str) -> Tuple[int, str]:
     """
 
     :param lines: A list of strings representing each line
@@ -109,7 +113,7 @@ def last_occurrence(lines, tag):
         return -1, ''
 
 
-def next_occurrence(lines, tag, startindex=0):
+def next_occurrence(lines: List[str], tag: str, startindex: int = 0) -> Tuple[int, str]:
     """
 
     :param lines: A list of strings representing each line

pypact/util/numerical.py

@@ -1,6 +1,8 @@
+from typing import Union, Callable
+
 nan = float('NaN')
 
-def are_values_the_same(value1, value2, rel_tol, abs_tol=0.0):
+def are_values_the_same(value1: float, value2: float, rel_tol: float, abs_tol: float = 0.0) -> bool:
     """
         Use math.isclose algorithm, it is better than numpy.isclose method.
         See https://github.com/numpy/numpy/issues/10161 for more on the discussion
@@ -9,7 +11,7 @@ def are_values_the_same(value1, value2, rel_tol, abs_tol=0.0):
     return abs(value1 - value2) <= max(rel_tol * max(abs(value1), abs(value2)), abs_tol)
 
 
-def get_float(value):
+def get_float(value: Union[str, int, float]) -> Union[float, str]:
     """
         Gets the floating point value from a string
         Will allow for fortran style floats, i.e -2.34321-308
@@ -21,7 +23,7 @@ def get_float(value):
     return _getfortranfloat(value)
 
 
-def _istradiationalfloat(value):
+def _istradiationalfloat(value: Union[str, int, float]) -> bool:
     """
         Checks if the string can be converted to a floating point value
         Does not allow for fortran style floats, i.e -2.34321-308
@@ -33,7 +35,7 @@ def _istradiationalfloat(value):
     except ValueError:
         return False
 
-def is_float(value):
+def is_float(value: Union[str, int, float]) -> bool:
     """
         Checks if the string can be converted to a floating point value
         Will allow for fortran style floats, i.e -2.34321-308
@@ -43,21 +45,21 @@ def is_float(value):
         return _istradiationalfloat(value) or _isfortranfloat(value)
     return False
 
-def _isfortranfloat(value):
+def _isfortranfloat(value: Union[str, int, float]) -> bool:
     passfunc = lambda sign, esign, parts: True
     failfunc = lambda: False
 
     return _fortranfloat(value, passfunc, failfunc)
 
 
-def _getfortranfloat(value):
+def _getfortranfloat(value: Union[str, int, float]) -> Union[float, str]:
     passfunc = lambda sign, esign, parts: float(sign + parts[0] + 'E' + esign + parts[1])
     failfunc = lambda: "nan"
 
     return _fortranfloat(value, passfunc, failfunc)
 
 
-def _fortranfloat(value, passfunc, failfunc):
+def _fortranfloat(value: Union[str, int, float], passfunc: Callable, failfunc: Callable) -> Union[bool, float, str]:
     # could be 2.3
     #          2.3e+10
     #          -2.3e+10

pypact/util/propertyfinder.py

@@ -1,4 +1,9 @@
-from pypact.util.lines import *
+from pypact.util.lines import (
+    first_occurrence,
+    last_occurrence,
+    join_strings_from_line,
+    first_value_from_line
+)
 
 
 def get(datadump, headertag, starttag, endtag='', findfirst=True, ignores=[], asstring=True):