Minor bugfixes, styling, test import cleaning

pyrolite/geochem/alteration.py

@@ -1,6 +1,7 @@
 """
 Functions for calcuating indexes of chemical alteration.
 """
+
 import pandas as pd
 
 from ..util.log import Handle

pyrolite/geochem/ind.py

@@ -6,6 +6,7 @@
 ------
 * Incompatibility indexes for spider plot ordering.
 """
+
 import re
 
 import numpy as np
@@ -254,9 +255,11 @@ def simple_oxides(cation, output="string"):
 
     # for 3.6+, could use f'{cation}{1}O{c//2}',  f'{cation}{2}O{c}'
     oxides = [
-        str(cation) + str(1) + "O" + str(c // 2)
-        if not c % 2
-        else str(cation) + str(2) + "O" + str(c)
+        (
+            str(cation) + str(1) + "O" + str(c // 2)
+            if not c % 2
+            else str(cation) + str(2) + "O" + str(c)
+        )
         for c in ions
     ]
     oxides = [pt.formula(ox) for ox in oxides]
@@ -291,7 +294,7 @@ def get_cations(component: str, exclude=[], total_suffix="T"):
 
     exclude += ["O"]
     atms = pt.formula(component).atoms
-    cations = [el for el in atms.keys() if not el.__str__() in exclude]
+    cations = [el for el in atms.keys() if el.__str__() not in exclude]
     return cations
 
 
@@ -398,7 +401,7 @@ def get_ionic_radii(
     variant=[],
     source="shannon",
     pauling=True,
-    **kwargs
+    **kwargs,
 ):
     """
     Function to obtain ionic radii for a given ion and coordination [#ref_1]_
@@ -464,7 +467,7 @@ def get_ionic_radii(
                 variant=variant,
                 source=source,
                 pauling=pauling,
-                **kwargs
+                **kwargs,
             )
             for e in element
         ]

pyrolite/geochem/norm.py

@@ -1,6 +1,7 @@
 """
 Reference compostitions and compositional normalisation.
 """
+
 import json
 from pathlib import Path
 

pyrolite/geochem/transform.py

@@ -2,6 +2,8 @@
 Functions for converting, transforming and parameterizing geochemical data.
 """
 
+from collections import Counter
+
 import numpy as np
 import pandas as pd
 import periodictable as pt
@@ -12,13 +14,7 @@
 from ..util.meta import update_docstring_references
 from ..util.text import remove_suffix, titlecase
 from ..util.types import iscollection
-from .ind import (
-    _common_elements,
-    _common_oxides,
-    get_cations,
-    get_ionic_radii,
-    simple_oxides,
-)
+from .ind import _common_elements, _common_oxides, get_cations, simple_oxides
 from .norm import Composition, get_reference_composition
 
 logger = Handle(__name__)
@@ -102,7 +98,7 @@ def devolatilise(
     :class:`pandas.DataFrame`
         Transformed dataframe.
     """
-    keep = [i for i in df.columns if not i in exclude]
+    keep = [i for i in df.columns if i not in exclude]
     if renorm:
         return renormalise(df.loc[:, keep])
     else:
@@ -141,7 +137,7 @@ def oxide_conversion(oxin, oxout, molecular=False):
         # Assertion of simple oxide
         assert (len(in_els) == len(out_els)) & (len(in_els) == 1)
         assert in_els == out_els  # Need to be dealing with the same element!
-    except:
+    except AssertionError:
         raise ValueError("Incompatible compounds: {} --> {}".format(in_els, out_els))
     # Moles of product vs. moles of reactant
     cation_coefficient = list(inatoms.values())[0] / list(outatoms.values())[0]
@@ -342,7 +338,7 @@ def aggregate_element(
 
     for t in targetnames:
         if t not in _df:
-            _df[t] = 0.  # avoid missing column errors
+            _df[t] = 0.0  # avoid missing column errors
 
     coeff = np.array(coeff)
     if coeff.ndim == 2:
@@ -603,7 +599,7 @@ def lambda_lnREE(
     norm_df.loc[(norm_df <= 0.0).any(axis=1), :] = np.nan  # remove zero or below
     norm_df.loc[:, ree] = np.log(norm_df.loc[:, ree])
 
-    if not (sigmas is None):
+    if sigmas is not None:
         if isinstance(sigmas, pd.Series):  # convert this to an array
             sigmas = sigmas[ree].values
 
@@ -707,7 +703,7 @@ def convert_chemistry(
     # and speciated components
     ####################################################################################
     output_compositional = [
-        i for i in to if i not in coupled_sets + noncomp + new_ratios
+        i for i in to if i not in (coupled_sets + noncomp + new_ratios)
     ]
     # check that these are all unique components
     assert len(set(output_compositional)) == len(
@@ -753,6 +749,16 @@ def convert_chemistry(
             **kwargs,
         )
 
+    # TODO: warning for duplication should also be crossed over into speciated components above.. 
+    _duplicated_cations = [
+        str(k)
+        for k, v in Counter(  # get the first cation in each component, and count duplicates
+            [get_cations(t, total_suffix=total_suffix)[0] for t in output_compositional]
+        ).items()
+        if v > 1
+    ]
+    if _duplicated_cations:
+        logger.warning("Cations duplicated in compositional components: {}. The output retains this duplication!".format(','.join(_duplicated_cations)))
     # Aggregate the singular compositional items, then get new columns
     for item in output_compositional:
         df = aggregate_element(df, to=item, logdata=logdata, molecular=molecular)
@@ -788,3 +794,5 @@ def convert_chemistry(
     else:
         logger.debug("Recalculation Done. Data not renormalised.")
         return df.loc[:, output_columns]
+        logger.debug("Recalculation Done. Data not renormalised.")
+        return df.loc[:, output_columns]

pyrolite/mineral/lattice.py

@@ -27,6 +27,7 @@
             doi: {hazen1979}
 
 """
+
 import numpy as np
 
 from ..util.log import Handle

pyrolite/mineral/mindb.py

@@ -6,6 +6,7 @@
 Accessing and modifying the database across multiple with multiple threads/processes
 *could* result in database corruption (e.g. through repeated truncation etc).
 """
+
 import functools
 from pathlib import Path
 

pyrolite/mineral/normative.py

@@ -7,6 +7,7 @@
 
 from ..comp.codata import close, renormalise
 from ..geochem.transform import convert_chemistry, to_molecular
+from ..util.classification import TAS
 from ..util.log import Handle
 from ..util.pd import to_frame
 from ..util.units import scale
@@ -201,8 +202,6 @@ def endmember_decompose(
 # CIPW Norm and Related functions
 ################################################################################
 
-from ..util.classification import TAS
-
 # fuctions which map <TAS field, [SiO2, Na2O + K2O]> to Fe2O3/FeO ratios.
 _MiddlemostTASRatios = dict(
     F=lambda t, x: 0.4 if x[1] > 10 else 0.3,

pyrolite/mineral/sites.py

@@ -85,7 +85,7 @@ def __init__(
         affinities={"Si{4+}": 0, "Al{3+}": 1, "Fe{3+}": 2},
         *args,
         mode="cation",
-        **kwargs
+        **kwargs,
     ):
         super().__init__(name, coordination, *args, affinities=affinities, **kwargs)
 

pyrolite/util/math.py

@@ -424,7 +424,8 @@ def signify_digit(n, unc=None, leeway=0, low_filter=True):
             if round_to <= 0:
                 fmt = int
             else:
-                fmt = lambda x: x
+                def fmt(x):
+                    return x
             sig_n = round(n, round_to)
             if low_filter and sig_n == 0.0:
                 return np.nan
@@ -604,12 +605,12 @@ def solve_ratios(*eqs, evaluate=True):
     Solve a ternary system (top-left-right) given two constraints on
     two ratios, which together describe intersecting lines/a point.
     """
-    t, l, r = sympy.symbols("t l r")
+    t, L, r = sympy.symbols("t l r")
 
     def to_sympy(t):  # rearrange to have =0 equvalent expressions
         return sympy.sympify("-".join(t.split("=")))
 
     result = sympy.solve(
-        [to_sympy(e) for e in eqs] + [to_sympy("t + l + r = 1")], (t, l, r)
+        [to_sympy(e) for e in eqs] + [to_sympy("t + l + r = 1")], (t, L, r)
     )
     return list(result.values())

pyrolite/util/resampling.py

@@ -403,7 +403,7 @@ def _metric_name(metric):
                 msg = "Gaussian Process boostrapping not yet implemented."
                 raise NotImplementedError(msg)
             else:
-                msg = "Bootstrap method {} not recognised.".format(boostrap_method)
+                msg = "Bootstrap method {} not recognised.".format(bootstrap_method)
                 raise NotImplementedError(msg)
 
         # whether to independently estimate metric values for individual categories?

test/comp/comp_aggregate.py

@@ -1,9 +1,18 @@
-import logging
 import unittest
 
 import numpy as np
-
-from pyrolite.comp.aggregate import *
+import pandas as pd
+
+from pyrolite.comp.aggregate import (
+    compositional_mean,
+    cross_ratios,
+    get_full_column,
+    nan_weighted_compositional_mean,
+    nan_weighted_mean,
+    np_cross_ratios,
+    standardise_aggregate,
+    weights_from_array,
+)
 from pyrolite.util.synthetic import normal_frame
 
 

test/comp/comp_codata.py

@@ -1,8 +1,23 @@
 import unittest
 
 import numpy as np
-
-from pyrolite.comp.codata import *
+import pandas as pd
+
+from pyrolite.comp.codata import (
+    ALR,
+    CLR,
+    ILR,
+    boxcox,
+    close,
+    get_ILR_labels,
+    inverse_ALR,
+    inverse_boxcox,
+    inverse_CLR,
+    inverse_ILR,
+    inverse_sphere,
+    renormalise,
+    sphere,
+)
 from pyrolite.util.synthetic import normal_frame
 
 

test/comp/comp_impute.py

@@ -1,17 +1,10 @@
 import unittest
 
 import numpy as np
-import pandas as pd
 
-from pyrolite.comp.aggregate import np_cross_ratios
-from pyrolite.comp.impute import EMCOMP, _little_sweep, _multisweep, _reg_sweep
+from pyrolite.comp.impute import EMCOMP, _little_sweep, _multisweep
 from pyrolite.util.math import augmented_covariance_matrix
-from pyrolite.util.synthetic import (
-    normal_frame,
-    normal_series,
-    random_composition,
-    random_cov_matrix,
-)
+from pyrolite.util.synthetic import random_composition, random_cov_matrix
 
 
 class TestRegSweep(unittest.TestCase):

test/geochem/geochem_alteration.py

@@ -1,8 +1,18 @@
 import unittest
 
 import numpy as np
+import pandas as pd
 
-from pyrolite.geochem.alteration import *
+from pyrolite.geochem.alteration import (
+    CCPI,
+    CIA,
+    CIW,
+    PIA,
+    SAR,
+    WIP,
+    IshikawaAltIndex,
+    SiTiIndex,
+)
 
 
 class TestAlterationIndicies(unittest.TestCase):
@@ -56,4 +66,4 @@ def test_CCPI_default(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    unittest.main()

test/geochem/geochem_ind.py

@@ -1,6 +1,18 @@
 import unittest
 
-from pyrolite.geochem.ind import *
+import periodictable as pt
+
+from pyrolite.geochem.ind import (
+    REE,
+    REY,
+    by_incompatibility,
+    by_number,
+    common_elements,
+    common_oxides,
+    get_cations,
+    get_ionic_radii,
+    simple_oxides,
+)
 
 
 class TestGetCations(unittest.TestCase):

test/geochem/geochem_isotope.py

@@ -5,5 +5,4 @@
 
 class TestDeadtimeCorrection(unittest.TestCase):
     def test_default(self):
-        pass
         deadtime_correction(10000, 20)

test/geochem/geochem_norm.py

@@ -1,8 +1,5 @@
 import unittest
 
-import numpy as np
-
-import pyrolite
 from pyrolite.geochem.norm import (
     Composition,
     all_reference_compositions,
@@ -11,8 +8,6 @@
     update_database,
 )
 from pyrolite.util.general import remove_tempdir, temp_path
-from pyrolite.util.meta import pyrolite_datafolder
-from pyrolite.util.synthetic import normal_frame
 
 
 class TestComposition(unittest.TestCase):

test/geochem/geochem_parse.py

@@ -4,7 +4,12 @@
 import pandas as pd
 
 from pyrolite.geochem.ind import REE
-from pyrolite.geochem.parse import *
+from pyrolite.geochem.parse import (
+    check_multiple_cation_inclusion,
+    ischem,
+    repr_isotope_ratio,
+    tochem,
+)
 
 
 class TestIsChem(unittest.TestCase):

test/geochem/geochem_pyrochem.py

@@ -6,9 +6,7 @@
 import pyrolite.geochem
 from pyrolite.comp.codata import renormalise
 from pyrolite.geochem.norm import get_reference_composition
-from pyrolite.util.synthetic import normal_frame, normal_series
-
-# [print("# " + i) for i in dir(df.pyrochem) if "__" not in i and not i.startswith("_")]
+from pyrolite.util.synthetic import normal_frame
 
 
 class TestPyrochem(unittest.TestCase):