remove superscript 1 from AtomicConfiguration output of singly-occupi…

…ed AOs and remove semicolons from HTML output of StatefulSpecies

README.rst

@@ -140,7 +140,7 @@ As ``Formula``, also ``StatefulSpecies`` have ``html`` and ``latex`` attributes.
     \mathrm{Ne}^{+} \; 1s^{2}2s^{2}2p^{5}; \; {}^{2}P_{1/2}
 
     >>> StatefulSpecies('(52Cr)(1H) 1sigma2.2sigma1.1delta2.1pi2; 6SIGMA+; v=0; J=2').html
-    '<sup>52</sup>Cr<sup>1</sup>H 1σ<sup>2</sup>.2σ<sup>1</sup>.1δ<sup>2</sup>.1π<sup>2</sup>; <sup>6</sup>Σ<sup>+</sup>; v=0; J=2'
+    '<sup>52</sup>Cr<sup>1</sup>H 1σ<sup>2</sup>.2σ<sup>1</sup>.1δ<sup>2</sup>.1π<sup>2</sup> <sup>6</sup>Σ<sup>+</sup> v=0 J=2'
 
 
 Reaction
@@ -155,13 +155,13 @@ separated by ``' -> '``, such as
     >>> from pyvalem.reaction import Reaction
     >>> reaction = Reaction('He+2 + H -> He+ 3p1 + H+ + hv')
     >>> reaction
-    He+2 + H → He+ 3p1 + H+ + hν
+    He+2 + H → He+ 3p + H+ + hν
 
     >>> reaction.html
-    'He<sup>2+</sup> + H → He<sup>+</sup> 3p<sup>1</sup> + H<sup>+</sup> + hν'
+    'He<sup>2+</sup> + H → He<sup>+</sup> 3p + H<sup>+</sup> + hν'
 
     >>> print(reaction.latex)
-    \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p^{1} + \mathrm{H}^{+} + h\nu
+    \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p + \mathrm{H}^{+} + h\nu
 
 The ``Reaction`` class also watches out for charge balance and stoichiometry
 conservation during instantiation.
@@ -216,4 +216,4 @@ Always make sure to format your code before submitting a pull request, by runnin
 
 .. _GitHub: https://github.com/xnx/pyvalem
 .. _PyPI: https://pypi.org/project/pyvalem/
-.. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html
+.. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html

doc/introduction.rst

@@ -126,14 +126,14 @@ As ``Formula``, also ``StatefulSpecies`` have ``html`` and ``latex`` attributes.
     \mathrm{Ne}^{+} \; 1s^{2}2s^{2}2p^{5}; \; {}^{2}P_{1/2}
 
     >>> StatefulSpecies('(52Cr)(1H) 1sigma2.2sigma1.1delta2.1pi2; 6SIGMA+; v=0; J=2').html
-    '<sup>52</sup>Cr<sup>1</sup>H 1σ<sup>2</sup>.2σ<sup>1</sup>.1δ<sup>2</sup>.1π<sup>2</sup>; <sup>6</sup>Σ<sup>+</sup>; v=0; J=2'
+    '<sup>52</sup>Cr<sup>1</sup>H 1σ<sup>2</sup>.2σ<sup>1</sup>.1δ<sup>2</sup>.1π<sup>2</sup> <sup>6</sup>Σ<sup>+</sup> v=0 J=2'
 
 These two examples render as:
 
 .. raw:: html
 
-    Ne<sup>+</sup> 1s<sup>2</sup>2s<sup>2</sup>2p<sup>5</sup>; <sup>2</sup>P<sub>1/2</sub><br>
-    <sup>52</sup>Cr<sup>1</sup>H 1σ<sup>2</sup>.2σ<sup>1</sup>.1δ<sup>2</sup>.1π<sup>2</sup>; <sup>6</sup>Σ<sup>+</sup>; v=0; J=2
+    Ne<sup>+</sup> 1s<sup>2</sup>2s<sup>2</sup>2p<sup>5</sup> <sup>2</sup>P<sub>1/2</sub><br>
+    <sup>52</sup>Cr<sup>1</sup>H 1σ<sup>2</sup>.2σ<sup>1</sup>.1δ<sup>2</sup>.1π<sup>2</sup> <sup>6</sup>Σ<sup>+</sup> v=0 J=2
 
 
 Reaction
@@ -148,13 +148,13 @@ separated by ``' -> '``, such as
     >>> from pyvalem.reaction import Reaction
     >>> reaction = Reaction('He+2 + H -> He+ 3p1 + H+ + hv')
     >>> reaction
-    He+2 + H → He+ 3p1 + H+ + hν
+    He+2 + H → He+ 3p + H+ + hν
 
     >>> reaction.html
-    'He<sup>2+</sup> + H → He<sup>+</sup> 3p<sup>1</sup> + H<sup>+</sup> + hν'
+    'He<sup>2+</sup> + H → He<sup>+</sup> 3p + H<sup>+</sup> + hν'
 
     >>> print(reaction.latex)
-    \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p^{1} + \mathrm{H}^{+} + h\nu
+    \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p + \mathrm{H}^{+} + h\nu
 
 The ``Reaction`` class also watches out for charge balance and stoichiometry
 conservation during instantiation.

doc/reaction.rst

@@ -23,7 +23,7 @@ Examples
 An HTML representation of the reaction is stored as the ``html`` attribute::
 
     >>> print(r2.html)
-    CO v=1 + O<sub>2</sub> J=2; X<sup>3</sup>Σ<sup>-</sup><sub>g</sub> → CO<sub>2</sub> + O
+    CO v=1 + O<sub>2</sub> J=2 X<sup>3</sup>Σ<sup>-</sup><sub>g</sub> → CO<sub>2</sub> + O
     >>> print(r4.html)
     C<sub>6</sub>H<sub>5</sub>OH + 7O<sub>2</sub> → 6CO<sub>2</sub> + 3H<sub>2</sub>O
 

doc/stateful_species.rst

@@ -26,13 +26,13 @@ An HTML representation is accessible through the ``html`` attribute:
 .. code-block:: pycon
 
     >>> print(ss4.html)
-    CrH 1σ<sup>2</sup>.2σ<sup>1</sup>.1π<sup>4</sup>.3σ<sup>1</sup>; <sup>6</sup>Σ<sup>+</sup>
+    CrH 1σ<sup>2</sup>.2σ<sup>1</sup>.1π<sup>4</sup>.3σ<sup>1</sup> <sup>6</sup>Σ<sup>+</sup>
 
 This example renders as:
 
 .. raw:: html
 
-    CrH 1σ<sup>2</sup>.2σ<sup>1</sup>.1π<sup>4</sup>.3σ<sup>1</sup>; <sup>6</sup>Σ<sup>+</sup>
+    CrH 1σ<sup>2</sup>.2σ<sup>1</sup>.1π<sup>4</sup>.3σ<sup>1</sup> <sup>6</sup>Σ<sup>+</sup>
 
 
 The ``Formula`` object and a list of the parse ``State`` objects are returned by the
@@ -70,4 +70,4 @@ This is checked for:
     >>> StatefulSpecies('Li 1s2.2s1; 1s2.2p1')
     Traceback (most recent call last):
       ...
-    pyvalem.stateful_species.StatefulSpeciesError: Multiple states of type AtomicConfiguration specified for Li 1s2.2p1;1s2.2s1
+    pyvalem.stateful_species.StatefulSpeciesError: Multiple states of type AtomicConfiguration specified for Li 1s2.2p;1s2.2s

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="pyvalem",
-    version="2.5.2",
+    version="2.5.3",
     description="A package for managing simple chemical species and states",
     long_description=long_description,
     long_description_content_type="text/x-rst",

src/pyvalem/reaction.py

@@ -120,7 +120,7 @@ class Reaction:
 
     >>> # HTML attribute
     >>> r1.html
-    'CO v=1 + O<sub>2</sub> J=2; X<sup>3</sup>Σ<sup>-</sup><sub>g</sub> → CO<sub>2</sub> + O'
+    'CO v=1 + O<sub>2</sub> J=2 X<sup>3</sup>Σ<sup>-</sup><sub>g</sub> → CO<sub>2</sub> + O'
 
     >>> # Consistency checks
     >>> Reaction('BeH+ + I2 <-> BeI + HI')

src/pyvalem/stateful_species.py

@@ -139,7 +139,7 @@ def verify_multiple_key_value_pairs(self):
     def html(self):
         if not self.states:
             return self.formula.html
-        return "{} {}".format(self.formula.html, "; ".join(s.html for s in self.states))
+        return "{} {}".format(self.formula.html, " ".join(s.html for s in self.states))
 
     @property
     def latex(self):

src/pyvalem/states/atomic_configuration.py

@@ -63,7 +63,7 @@ class AtomicOrbital:
     l : int, optional
         The azimuthal quantum number (0, 1, 2, ..., n-1)
         At least one of {`l`, `lletter`} must be passed.
-    nocc : int, default: 0
+    nocc : int, default: 1
         Number of occupied electrons.
     lletter : str, optional
         The letter corresponding to l: 's', 'p', 'd', ... for l = 0, 1, 2, ...
@@ -115,7 +115,9 @@ def __init__(self, n, l=None, nocc=0, lletter=None):
         self._validate_atomic_orbital()
 
     def __repr__(self):
-        return "{}{}{}".format(self.n, self.lletter, self.nocc)
+        if self.nocc != 1:
+            return "{}{}{}".format(self.n, self.lletter, self.nocc)
+        return "{}{}".format(self.n, self.lletter)
 
     @property
     def html(self):
@@ -125,7 +127,9 @@ def html(self):
         -------
         str
         """
-        return "{}{}<sup>{}</sup>".format(self.n, self.lletter, self.nocc)
+        if self.nocc != 1:
+            return "{}{}<sup>{}</sup>".format(self.n, self.lletter, self.nocc)
+        return "{}{}".format(self.n, self.lletter)
 
     @property
     def latex(self):
@@ -135,7 +139,9 @@ def latex(self):
         -------
         str
         """
-        return "{}{}^{{{}}}".format(self.n, self.lletter, self.nocc)
+        if self.nocc != 1:
+            return "{}{}^{{{}}}".format(self.n, self.lletter, self.nocc)
+        return "{}{}".format(self.n, self.lletter)
 
     def _validate_atomic_orbital(self):
         """Validator method for the atomic orbital class.
@@ -209,11 +215,11 @@ class AtomicConfiguration(State):
     (3, 1, 1)
 
     >>> repr(ac1)
-    '1s2.2s2.2p6.3p1'
+    '1s2.2s2.2p6.3p'
 
     >>> ac2 = AtomicConfiguration("[Ne].3p")
     >>> repr(ac2)
-    '1s2.2s2.2p6.3p1'
+    '1s2.2s2.2p6.3p'
     """
 
     def __init__(self, state_str):

tests/test_atomic_configurations.py

@@ -18,7 +18,7 @@ def test_atomic_configuration(self):
         c2 = AtomicConfiguration("1s2.2s2.2p6")
         c3 = AtomicConfiguration("1s2.2s2.2p6.3s2.3d10")
         c4 = AtomicConfiguration("[He].2s1")
-        c5 = AtomicConfiguration("2s2.2p1.3s1")
+        c5 = AtomicConfiguration("2s2.2p1.3s")
 
         self.assertRaises(AtomicConfigurationError, AtomicConfiguration, "s4.w2")
         self.assertRaises(AtomicConfigurationError, AtomicConfiguration, "1s 2.2s2")
@@ -71,8 +71,8 @@ def test_excited_atomic_configuration(self):
     def test_atomic_configuration_repr(self):
         c1 = AtomicConfiguration("1s2.2s2.2p6.3s2.3p6.4s2.3d")
         c2 = AtomicConfiguration("[Ar].4s2.3d1")
-        self.assertEqual(repr(c1), "1s2.2s2.2p6.3s2.3p6.4s2.3d1")
-        self.assertEqual(repr(c2), "1s2.2s2.2p6.3s2.3p6.4s2.3d1")
+        self.assertEqual(repr(c1), "1s2.2s2.2p6.3s2.3p6.4s2.3d")
+        self.assertEqual(repr(c2), "1s2.2s2.2p6.3s2.3p6.4s2.3d")
 
     def test_atomic_configuration_default_nocc(self):
         c1 = AtomicConfiguration("1s")

tests/test_reaction.py

@@ -68,7 +68,7 @@ def test_reaction_parsing(self):
         self.assertEqual(r2.reactants[1][1].states[1].__repr__(), "X(3Σ-g)")
         self.assertEqual(
             r2.html,
-            "CO v=1 + O<sub>2</sub> J=2; "
+            "CO v=1 + O<sub>2</sub> J=2 "
             "X<sup>3</sup>Σ<sup>-</sup><sub>g</sub> → "
             "CO<sub>2</sub> + O",
         )

tests/test_stateful_species.py

@@ -68,7 +68,7 @@ def test_atomic_configuration_verification(self):
         self.assertTrue(ss1.verify_atomic_configuration())
         ss2 = StatefulSpecies("Ar+ 1s2.2s2.2p6.3s2.3p6")
         ss3 = StatefulSpecies("Ar+ [Ne].3s2.3p6")
-        ss4 = StatefulSpecies("Ar+ [Ne].3s2.3p6.4s1")
+        ss4 = StatefulSpecies("Ar+ [Ne].3s2.3p6.4s")
         for ss in (ss2, ss3, ss4):
             self.assertRaises(StatefulSpeciesError, ss.verify_atomic_configuration)
 
@@ -97,10 +97,10 @@ def test_stateful_species_repr(self):
         self.assertEqual(repr(ss2), "(235U) 3*;l=0;n=1")
 
         for ss_text in ["C+ 4P;2s2.2p1", "C+ 2s2.2p1;4P"]:
-            self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p1;4P")
+            self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p;4P")
 
         for ss_text in ["C+ 2P;2s2.2p1", "C+ 2s2.2p1;2P"]:
-            self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p1;2P")
+            self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p;2P")
 
 
 if __name__ == "__main__":