Merge pull request #230 from bjodah/bump-dev-version-to-0.9.x

Bump dev version to 0.9.x

.github/workflows/lint_python.yml

@@ -14,10 +14,10 @@ jobs:
       - run: bandit --recursive --skip B101,B102,B110,B112,B307,B404,B603,B607 .
       - run: black --check . || true
       - run: codespell --ignore-words-list="ans,claus,fith,nam,nd,ond,serie,te"
-      - run: flake8 . --count --max-complexity=66 --max-line-length=118
+      - run: flake8 . --count --max-complexity=66 --max-line-length=129
                       --show-source --statistics
       - run: pip install flake8-bugbear flake8-comprehensions flake8-return flake8-simplify
-      - run: flake8 . --count --exit-zero --max-complexity=66 --max-line-length=118
+      - run: flake8 . --count --exit-zero --max-complexity=66 --max-line-length=129
                       --show-source --statistics
       - run: isort --check-only --profile black . || true
       - run: pip install setuptools

.woodpecker.yaml

@@ -27,6 +27,7 @@ steps:
       - export CPATH=$SUNDBASE/include:$CPATH
       - export LIBRARY_PATH=$SUNDBASE/lib
       - export LD_LIBRARY_PATH=$SUNDBASE/lib
+      - python3 -m pip install --cache-dir $CACHE_ROOT/pip_cache --user --upgrade-strategy=eager --upgrade cython
       - python3 -m pip install --cache-dir $CACHE_ROOT/pip_cache --user -e .[all]
       - python3 -c "import pycvodes; import pyodesys; import pygslodeiv2"  # debug this CI config
       - git fetch -tq

README.rst

@@ -385,7 +385,7 @@ If you make use of ChemPy in e.g. academic work you may cite the following peer-
 Depending on what underlying solver you are using you should also cite the appropriate paper
 (you can look at the list of references in the JOSS article). If you need to reference,
 in addition to the paper, a specific point version of ChemPy (for e.g. reproducibility)
-you can get per-version DOIs from the zendodo archive:
+you can get per-version DOIs from the zenodo archive:
 
 .. image:: https://zenodo.org/badge/8840/bjodah/chempy.svg
    :target: https://zenodo.org/badge/latestdoi/8840/bjodah/chempy

chempy/_release.py

@@ -1 +1 @@
-__version__ = "0.8.1.dev0+git"
+__version__ = "0.9.0.dev0+git"

chempy/util/parsing.py

@@ -95,7 +95,7 @@ def _get_formula_parser():
                  | '{' formula '}'
                  | '[' formula ']' ) count prime charge?
         formula :: term+
-        hydrate :: '.' count? formula
+        hydrate :: ( '..' | '\u00B7' ) count? formula
         state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
         compound :: count formula hydrate? state?
 
@@ -114,7 +114,7 @@ def _get_formula_parser():
                  | '{' formula '}'
                  | '[' formula ']' ) count prime charge?
         formula :: term+
-        hydrate :: '..' count? formula
+        hydrate :: ( '..' | '\u00B7' ) count? formula
         state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
         compound :: count formula hydrate? state?
     """
@@ -334,7 +334,7 @@ def _parse_stoich(stoich):
 
 _unicode_mapping = {k + "-": v + "-" for k, v in zip(_greek_letters, _greek_u)}
 _unicode_mapping["."] = "⋅"
-_unicode_infix_mapping = {"..": "·"}
+_unicode_infix_mapping = {"..": "\u00b7"}  # 0x00b7: '·'
 
 _html_mapping = {k + "-": "&" + k + ";-" for k in _greek_letters}
 _html_mapping["."] = "⋅"
@@ -379,14 +379,19 @@ def formula_to_composition(
     True
     >>> formula_to_composition('Na2CO3..7H2O') == {11: 2, 6: 1, 8: 10, 1: 14}
     True
+    >>> formula_to_composition('UO2.3') == {92: 1, 8: 2.3}
+    True
 
     """
     if prefixes is None:
         prefixes = _latex_mapping.keys()
 
     stoich_tok, chg_tok = _formula_to_parts(formula, prefixes, suffixes)[:2]
     tot_comp = {}
-    parts = stoich_tok.split("..")
+    if '\u00b7' in stoich_tok:
+        parts = stoich_tok.split('\u00b7')
+    else:
+        parts = stoich_tok.split("..")
 
     for idx, stoich in enumerate(parts):
         if idx == 0:
@@ -532,7 +537,10 @@ def _formula_to_format(
     suffixes=("(s)", "(l)", "(g)", "(aq)"),
 ):
     parts = _formula_to_parts(formula, prefixes.keys(), suffixes)
-    stoichs = parts[0].split("..")
+    if '\u00b7' in parts[0]:
+        stoichs = parts[0].split('\u00b7')
+    else:
+        stoichs = parts[0].split("..")
     string = ""
     for idx, stoich in enumerate(stoichs):
         if idx == 0:
@@ -600,9 +608,11 @@ def formula_to_latex(formula, prefixes=None, infixes=None, **kwargs):
     )
 
 
-_unicode_sub = {}
+_unicode_sub = {
+    ".": ".",
+}
 
-for k, v in enumerate("₀₁₂₃₄₅₆₇₈₉"):
+for k, v in enumerate("₀₁₂₃₄₅₆₇₈₉."):
     _unicode_sub[str(k)] = v
 
 _unicode_sup = {

chempy/util/tests/test_parsing.py

@@ -11,6 +11,7 @@
     parsing_library,
     to_reaction,
 )
+
 from ..testing import requires
 
 
@@ -625,6 +626,22 @@ def test_formula_to_latex_caged(species, latex):
         ("[Fe(H2O)6][Fe(CN)6]..19H2O(aq)", r"[Fe(H₂O)₆][Fe(CN)₆]·19H₂O(aq)"),
         ("[Fe(CN)6]-3", r"[Fe(CN)₆]³⁻"),
         ("[Fe(CN)6]-3(aq)", r"[Fe(CN)₆]³⁻(aq)"),
+        (
+            "Ca2.832Fe0.6285Mg5.395(CO3)6",
+            r"Ca₂.₈₃₂Fe₀.₆₂₈₅Mg₅.₃₉₅(CO₃)₆",
+        ),
+        (
+            "Ca2.832Fe0.6285Mg5.395(CO3)6(s)",
+            r"Ca₂.₈₃₂Fe₀.₆₂₈₅Mg₅.₃₉₅(CO₃)₆(s)",
+        ),
+        (
+            "Ca2.832Fe0.6285Mg5.395(CO3)6..8H2O(s)",
+            r"Ca₂.₈₃₂Fe₀.₆₂₈₅Mg₅.₃₉₅(CO₃)₆·8H₂O(s)",
+        ),
+        (
+            "Zn(NO3)2..6H2O",
+            r"Zn(NO₃)₂·6H₂O",
+        ),
     ],
 )
 @requires(parsing_library)
@@ -692,6 +709,26 @@ def test_formula_to_unicode_caged(species, unicode):
         ),
         ("[Fe(CN)6]-3", r"[Fe(CN)<sub>6</sub>]<sup>3-</sup>"),
         ("[Fe(CN)6]-3(aq)", r"[Fe(CN)<sub>6</sub>]<sup>3-</sup>(aq)"),
+        (
+            "Ca2.832Fe0.6285Mg5.395(CO3)6",
+            r"Ca<sub>2.832</sub>Fe<sub>0.6285</sub>Mg<sub>5.395</sub>(CO<sub>3</sub>)<sub>6</sub>",
+        ),
+        (
+            "Ca2.832Fe0.6285Mg5.395(CO3)6(s)",
+            r"Ca<sub>2.832</sub>Fe<sub>0.6285</sub>Mg<sub>5.395</sub>(CO<sub>3</sub>)<sub>6</sub>(s)",
+        ),
+        (
+            "Ca2.832Fe0.6285Mg5.395(CO3)6..8H2O(s)",
+            r"Ca<sub>2.832</sub>Fe<sub>0.6285</sub>Mg<sub>5.395</sub>(CO<sub>3</sub>)<sub>6</sub>&sdot;8H<sub>2</sub>O(s)",
+        ),
+        (
+            "Ca2.832Fe0.6285Mg5.395(CO3)6..8H2O(s)",
+            r"Ca<sub>2.832</sub>Fe<sub>0.6285</sub>Mg<sub>5.395</sub>(CO<sub>3</sub>)<sub>6</sub>&sdot;8H<sub>2</sub>O(s)",
+        ),
+        (
+            "Zn(NO3)2..6H2O",
+            r"Zn(NO<sub>3</sub>)<sub>2</sub>&sdot;6H<sub>2</sub>O",
+        ),
     ],
 )
 @requires(parsing_library)
@@ -712,3 +749,9 @@ def test_formula_to_html(species, html):
 def test_formula_to_html_caged(species, html):
     """Should produce HTML for cage species."""
     assert formula_to_html(species) == html
+
+
+def test_composition_dot_as_crystal_water_chempy08x():
+    ref = {30: 1, 7: 2, 8: 12, 1: 12}
+    assert formula_to_composition('Zn(NO3)2{}6H2O'.format('\u00B7')) == ref
+    assert formula_to_composition('Zn(NO3)2..6H2O') == ref