Fix bug with proton equality while continuing Particle.__init__ ref…

…actoring (PlasmaPy#1366)

* Add failing test for proton equality bug

* Add failing test for Particle("H", Z=1, mass_numb=1)

* Add a hack to fix proton equality bug

* A hack to try to fix

This bug suggests that Particle.__init__ could use some friendly
refactoring.

* Add changelog entry

* More extract method pattern from Particle.__init__

* Create inputs dict in Particle

* Use Particle._inputs instead of arguments to methods

* More extract method

* Move method around

* Minor reorganizing

* More re-organizing

* Rename variable

* Use _inputs instead of arguments

* Finally proton equality bug

* Renaming and reorganization

* Simplify naming

* Simplify naming

* Use _inputs

* Minor changes

* Minor changes

* Minor changes

* Minor changes

* Minor changes

* Renaming variables and some minor reorganization

* Renaming variables and reorganization

* Slight change to test

* Slight change to test

* Slight changes to tests

* Add second changelog entry

* Update docstrings

* Remove Particle.__name__

* Remove unnecessary .keys() for dicts

* Remove unnecessary .keys() for dicts

* Change Particle._inputs to Particle.__inputs

* Rename dict containing data about special particles

* Remove delattr of Particle.__inputs

* Remove unnecessary .keys() for dicts

* Remove unnecessary use of .keys() in tests

* Remove unnecessary import

* Add docstring back for Particle.__init__

Adding this line back because it might be responsible for some
documentation test failures that started happening soon after.

* Add back Particle.__name__

* Remove docstring for Particle.__init__

* Revert Particle.__name__ line to pre-PR form

* Add comment about Particle.__name__

* Updates following code review

* Add comment about why protons are being treated specially

changelog/1366.bugfix.rst

@@ -0,0 +1,2 @@
+Fixed a bug with |Particle| where ``Particle("p+") == Particle("H", Z=1,
+mass_numb=1)`` led to a |ParticleError|.

changelog/1366.trivial.rst

@@ -0,0 +1,2 @@
+Used the extract method refactoring pattern on the initialization of
+|Particle| objects.

plasmapy/particles/atomic.py

@@ -28,14 +28,14 @@
 from typing import Any, List, Optional, Union
 
 from plasmapy.particles.decorators import particle_input
-from plasmapy.particles.elements import _elements
+from plasmapy.particles.elements import _data_about_elements
 from plasmapy.particles.exceptions import (
     InvalidElementError,
     InvalidIsotopeError,
     InvalidParticleError,
     MissingParticleDataError,
 )
-from plasmapy.particles.isotopes import _isotopes
+from plasmapy.particles.isotopes import _data_about_isotopes
 from plasmapy.particles.particle_class import Particle
 from plasmapy.particles.symbols import atomic_symbol
 from plasmapy.utils.decorators.deprecation import deprecated
@@ -590,7 +590,7 @@ def known_isotopes(argument: Union[str, Integral] = None) -> List[str]:
     def known_isotopes_for_element(argument):
         element = atomic_symbol(argument)
         isotopes = []
-        for isotope in _isotopes.keys():
+        for isotope in _data_about_isotopes:
             if element + "-" in isotope and isotope[0 : len(element)] == element:
                 isotopes.append(isotope)
         if element == "H":
@@ -616,7 +616,7 @@ def known_isotopes_for_element(argument):
             raise InvalidParticleError("Invalid particle in known_isotopes.")
     elif argument is None:
         isotopes_list = []
-        for atomic_numb in range(1, len(_elements.keys()) + 1):
+        for atomic_numb in range(1, len(_data_about_elements) + 1):
             isotopes_list += known_isotopes_for_element(atomic_numb)
 
     return isotopes_list
@@ -700,11 +700,13 @@ def common_isotopes_for_element(
         isotopes = known_isotopes(argument)
 
         CommonIsotopes = [
-            isotope for isotope in isotopes if "abundance" in _isotopes[isotope].keys()
+            isotope
+            for isotope in isotopes
+            if "abundance" in _data_about_isotopes[isotope]
         ]
 
         isotopic_abundances = [
-            _isotopes[isotope]["abundance"] for isotope in CommonIsotopes
+            _data_about_isotopes[isotope]["abundance"] for isotope in CommonIsotopes
         ]
 
         sorted_isotopes = [
@@ -818,7 +820,7 @@ def stable_isotopes_for_element(
         StableIsotopes = [
             isotope
             for isotope in KnownIsotopes
-            if _isotopes[isotope]["stable"] == stable_only
+            if _data_about_isotopes[isotope]["stable"] == stable_only
         ]
         return StableIsotopes
 
@@ -962,7 +964,7 @@ def periodic_table_period(argument: Union[str, Integral]) -> Integral:
             "integer representing its atomic number."
         )
     symbol = atomic_symbol(argument)
-    period = _elements[symbol]["period"]
+    period = _data_about_elements[symbol]["period"]
     return period
 
 
@@ -1016,7 +1018,7 @@ def periodic_table_group(argument: Union[str, Integral]) -> Integral:
             "symbol, or an integer representing its atomic number."
         )
     symbol = atomic_symbol(argument)
-    group = _elements[symbol]["group"]
+    group = _data_about_elements[symbol]["group"]
     return group
 
 
@@ -1070,7 +1072,7 @@ def periodic_table_block(argument: Union[str, Integral]) -> str:
             "symbol, or an integer representing its atomic number."
         )
     symbol = atomic_symbol(argument)
-    block = _elements[symbol]["block"]
+    block = _data_about_elements[symbol]["block"]
     return block
 
 
@@ -1122,7 +1124,7 @@ def periodic_table_category(argument: Union[str, Integral]) -> str:
             "symbol, or an integer representing its atomic number."
         )
     symbol = atomic_symbol(argument)
-    category = _elements[symbol]["category"]
+    category = _data_about_elements[symbol]["category"]
     return category
 
 

plasmapy/particles/elements.py

@@ -45,16 +45,16 @@ def _element_obj_hook(obj):
 #    json.dump(_Elements, f, default=plasma_default, indent=2)
 
 
-_elements = json.loads(
+_data_about_elements = json.loads(
     pkgutil.get_data("plasmapy", "particles/data/elements.json"),
     object_hook=_element_obj_hook,
 )
 
 
 _atomic_numbers_to_symbols = {
-    elemdict["atomic number"]: symb for (symb, elemdict) in _elements.items()
+    elemdict["atomic number"]: symb for (symb, elemdict) in _data_about_elements.items()
 }
 
 _element_names_to_symbols = {
-    elemdict["element name"]: symb for (symb, elemdict) in _elements.items()
+    elemdict["element name"]: symb for (symb, elemdict) in _data_about_elements.items()
 }

plasmapy/particles/isotopes.py

@@ -32,7 +32,7 @@ def _isotope_obj_hook(obj):
 
 
 #: Dictionary of isotope data.
-_isotopes = json.loads(
+_data_about_isotopes = json.loads(
     pkgutil.get_data("plasmapy", "particles/data/isotopes.json"),
     object_hook=_isotope_obj_hook,
 )

plasmapy/particles/parsing.py

@@ -16,20 +16,23 @@
 
 from plasmapy.particles.elements import (
     _atomic_numbers_to_symbols,
+    _data_about_elements,
     _element_names_to_symbols,
-    _elements,
 )
 from plasmapy.particles.exceptions import (
     InvalidElementError,
     InvalidParticleError,
     ParticleWarning,
 )
-from plasmapy.particles.isotopes import _isotopes
-from plasmapy.particles.special_particles import _Particles, ParticleZoo
+from plasmapy.particles.isotopes import _data_about_isotopes
+from plasmapy.particles.special_particles import (
+    _data_about_special_particles,
+    ParticleZoo,
+)
 from plasmapy.utils import roman
 
 
-def _create_alias_dicts(Particles: dict) -> (Dict[str, str], Dict[str, str]):
+def _create_alias_dicts(particles: dict) -> (Dict[str, str], Dict[str, str]):
     """
     Create dictionaries for case sensitive aliases and case
     insensitive aliases of special particles and antiparticles.
@@ -42,8 +45,8 @@ def _create_alias_dicts(Particles: dict) -> (Dict[str, str], Dict[str, str]):
     case_sensitive_aliases = {}
     case_insensitive_aliases = {}
 
-    for symbol in Particles.keys():
-        name = Particles[symbol]["name"]
+    for symbol in particles:
+        name = particles[symbol]["name"]
         case_insensitive_aliases[name.lower()] = symbol
 
     case_sensitive_aliases_for_a_symbol = [
@@ -111,7 +114,9 @@ def _create_alias_dicts(Particles: dict) -> (Dict[str, str], Dict[str, str]):
     return case_sensitive_aliases, case_insensitive_aliases
 
 
-_case_sensitive_aliases, _case_insensitive_aliases = _create_alias_dicts(_Particles)
+_case_sensitive_aliases, _case_insensitive_aliases = _create_alias_dicts(
+    _data_about_special_particles
+)
 
 
 def _dealias_particle_aliases(alias: Union[str, Integral]) -> str:
@@ -129,9 +134,9 @@ def _dealias_particle_aliases(alias: Union[str, Integral]) -> str:
         or alias in _case_insensitive_aliases.values()
     ):
         symbol = alias
-    elif alias in _case_sensitive_aliases.keys():
+    elif alias in _case_sensitive_aliases:
         symbol = _case_sensitive_aliases[alias]
-    elif alias.lower() in _case_insensitive_aliases.keys():
+    elif alias.lower() in _case_insensitive_aliases:
         symbol = _case_insensitive_aliases[alias.lower()]
     else:
         symbol = alias
@@ -269,7 +274,7 @@ def _atomic_number_to_symbol(atomic_numb: Integral):
         `~plasmapy.particles.exceptions.InvalidParticleError` if the atomic number does
         not represent a known element.
         """
-        if atomic_numb in _atomic_numbers_to_symbols.keys():
+        if atomic_numb in _atomic_numbers_to_symbols:
             return _atomic_numbers_to_symbols[atomic_numb]
         else:
             raise InvalidParticleError(f"{atomic_numb} is not a valid atomic number.")
@@ -311,7 +316,7 @@ def _get_element(element_info: str) -> str:
         Receive a `str` representing an element's symbol or
         name, and returns a `str` representing the atomic symbol.
         """
-        if element_info.lower() in _element_names_to_symbols.keys():
+        if element_info.lower() in _element_names_to_symbols:
             element = _element_names_to_symbols[element_info.lower()]
         elif element_info in _atomic_numbers_to_symbols.values():
             element = element_info
@@ -339,7 +344,7 @@ def _reconstruct_isotope_symbol(element: str, mass_numb: Integral) -> str:
             elif isotope == "H-3":
                 isotope = "T"
 
-            if isotope not in _isotopes.keys():
+            if isotope not in _data_about_isotopes:
                 raise InvalidParticleError(
                     f"The string '{isotope}' does not correspond to "
                     f"a valid isotope."
@@ -440,10 +445,10 @@ def _reconstruct_ion_symbol(
         Z = Z_from_arg
 
     if isinstance(Z, Integral):
-        if Z > _elements[element]["atomic number"]:
+        if Z > _data_about_elements[element]["atomic number"]:
             raise InvalidParticleError(
                 f"The charge number Z = {Z} cannot exceed the atomic number "
-                f"of {element}, which is {_elements[element]['atomic number']}."
+                f"of {element}, which is {_data_about_elements[element]['atomic number']}."
             )
         elif Z <= -3:
             warnings.warn(
@@ -463,7 +468,7 @@ def _reconstruct_ion_symbol(
     else:
         symbol = element
 
-    nomenclature_dict = {
+    return {
         "symbol": symbol,
         "element": element,
         "isotope": isotope,
@@ -472,8 +477,6 @@ def _reconstruct_ion_symbol(
         "charge number": Z,
     }
 
-    return nomenclature_dict
-
 
 def _parse_and_check_molecule_input(argument: str, Z: Integral = None):
     """