Merge branch 'release/0.3.2' into main

.github/workflows/unittest.yml

@@ -14,6 +14,7 @@ jobs:
     name: Unit Tests
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.7, 3.8, 3.9]

MANIFEST.in

@@ -7,5 +7,6 @@ recursive-include pyrolite/data/mineral *
 recursive-include pyrolite/data/models *
 recursive-include pyrolite/data/radii *
 recursive-include pyrolite/data/timescale *
+recursive-include pyrolite/data/testing *
 recursive-include pyrolite/data/_config *
 # global-exclude __pycache__

binder/environment.yml

@@ -11,4 +11,4 @@ dependencies:
   - scipy>=1.2
   - pandas>=0.23
   - pip:
-      - -e git+git://github.com/morganjwilliams/pyrolite.git@develop#egg=pyrolite[dev,skl]
+      - -e git+https://github.com/morganjwilliams/pyrolite.git@develop#egg=pyrolite[dev,skl]

docs/source/dev/changelog.rst

@@ -8,7 +8,41 @@ All notable changes to this project will be documented here.
 
 .. note:: Changes noted in this subsection are to be released in the next version.
         If you're keen to check something out before its released, you can use a
-        `development install <development.html#development-installation>`__.
+        `development install <development.html#development-installation>`__ .
+
+`0.3.2`_
+--------------
+
+* **New Contributor**: `Angela Rodrigues <https://github.com/AngRodrigues>`__
+* **Bugfix**: Edited docstrings and added ignore-warning for :mod:`numpydoc` warnings.
+* **Bugfix**: Updated installation instructions and Binder configuration to use
+  secure protocols when installing via `git` (i.e. https://)
+* **Bugfix**: Update CI builds so that tests can be run on MacOS.
+
+:mod:`pyrolite.mineral`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* **Feature**: Added a TAS-based iron correction following Middlemost (1989).
+* **Bugfix**: Fixed some errors in mineral formulae and handling leading to
+  inaccurate outputs from CIPW Norm.
+* Split out volcanic from intrusive samples in the CIPW Norm volcanic rock comparison.
+* Added SINCLAS abbreviations to the mineral dictionary associated with the CIPW
+  Norm, so alternate mineral naming systems can be compared.
+
+:mod:`pyrolite.util`
+~~~~~~~~~~~~~~~~~~~~~~~
+* **PR Merged**: `Louise Schoneveld <https://github.com/lavender22>`__ submitted
+  a pull request to add bivariate and ternary classifier models for spinel
+  compositions (:class:`~pyrolite.util.classification.SpinelFeBivariate`,
+  :class:`~pyrolite.util.classification.SpinelTrivalentTernary`).
+* **PR Merged**: `Angela Rodrigues <https://github.com/AngRodrigues>`__ submitted
+  a pull request to add the Jensen ternary cation classifier model for subalkalic
+  volcanic rocks (:class:`~pyrolite.util.classification.JensenPlot`,
+  :class:`~pyrolite.util.classification.JensenPlot`).
+* Updated :func:`pyrolite.util.skl.vis.plot_confusion_matrix` to be able to plot on
+  existing axes, use an explicit class order and use rotation for e.g. long
+  x-axis class label names.
+* Updated references to :func:`scipy.stats.gaussian_kde` after namespace deprecation.
 
 `0.3.1`_
 --------------
@@ -21,7 +55,7 @@ All notable changes to this project will be documented here.
   Python 3.4). This will fix an issue blocking setting up a `conda-forge`
   recipe (`#51 <https://github.com/morganjwilliams/pyrolite/issues/51>`__).
 * Updated instances of redundant :mod:`numpy` types throughout to silence
-  depreciation warnings (using base types :class:`float`, :class:`int` except
+  deprecation warnings (using base types :class:`float`, :class:`int` except
   where specific :mod:`numpy` types are required).
 * Added a minimum :mod:`sympy` version requirement (v1.7) to avoid potential import
   errors.
@@ -192,7 +226,7 @@ All notable changes to this project will be documented here.
   argument.
 * Updated automated pyrolite :mod:`matplotlib` style export to be more reliable.
 * Changed the default shading for :func:`~pyrolite.plot.pyroplot.density` to suppress
-  error about upcoming :mod:`matplotlib` depreciation.
+  error about upcoming :mod:`matplotlib` deprecation.
 * Ordering for contours, contour names and contour styles is now preserved for
   :func:`~pyrolite.plot.density.density` and related functions.
 * Updated :mod:`pyrolite.plot.templates.pearce` to use ratios from
@@ -1255,7 +1289,8 @@ All notable changes to this project will be documented here.
     `GitHub <https://github.com/morganjwilliams/pyrolite/releases>`__ for reference,
     but were :code:`alpha` versions which were never considered stable.
 
-.. _Development: https://github.com/morganjwilliams/pyrolite/compare/0.3.1...develop
+.. _Development: https://github.com/morganjwilliams/pyrolite/compare/0.3.2...develop
+.. _0.3.2: https://github.com/morganjwilliams/pyrolite/compare/0.3.1...0.3.2
 .. _0.3.1: https://github.com/morganjwilliams/pyrolite/compare/0.3.0...0.3.1
 .. _0.3.0: https://github.com/morganjwilliams/pyrolite/compare/0.2.8...0.3.0
 .. _0.2.8: https://github.com/morganjwilliams/pyrolite/compare/0.2.7...0.2.8

docs/source/dev/contributors.rst

@@ -17,3 +17,5 @@ comments, testing, bug reports, or feature requests.
 * `Nicolas Piette-Lauziere <https://github.com/NicolasPietteLauziere>`__
 * `Chetan Nathwani <https://github.com/ChetanNathwani>`__
 * `Martin Bentley <https://github.com/mtb-za>`__
+* `Tom Buckle <https://github.com/bomtuckle>`__
+* `Angela Rodrigues <https://github.com/AngRodrigues>`__

docs/source/dev/development.rst

@@ -25,7 +25,7 @@ via pip directly from GitHub:
 
 .. code-block:: bash
 
-  pip install --user git+git://github.com/morganjwilliams/pyrolite.git@develop#egg=pyrolite
+  pip install --user git+https://github.com/morganjwilliams/pyrolite.git@develop#egg=pyrolite
 
 
 Tests

docs/source/gallery/examples/geochem/CIPW.py

@@ -68,24 +68,32 @@
 # The function accepts a few keyword arguments, all to do with the iron compositions
 # and related adjustment/corrections:
 #
-# :code:`Fe_correction = <callable>`
-#   For specifying the Fe-correction method/function. Currently only Le LeMaitre's
-#   correction method is implemented [LeMaitre1976]_ .
+# :code:`Fe_correction = "LeMaitre" | "Middlemost"`
+#   For specifying the Fe-correction method/function. Currently includes LeMaitre's
+#   correction method [LeMaitre1976]_ (the default) and Middlemost's TAS-based
+#   correction [Middlemost1989]_ .
 #
 # :code:`Fe_correction_mode = 'volcanic'`
-#   For specificying the Fe-correction mode where relevant
+#   For specificying the Fe-correction mode, for LeMaitre's correction.
 #
 # :code:`adjust_all_Fe = False`
 #   Specifying whether you want to adjust all iron compositions, or only those
 #   which are partially specified (i.e. only have a singular value for one of
 #   FeO, Fe2O3, FeOT, Fe2O3T).
 #
+NORM = CIPW_norm(df.pyrochem.compositional, Fe_correction="Middlemost")
+########################################################################################
 # For the purpose of establishing the congruency of our algorithm with Verma's,
-# we'll use :code:`adjust_all_Fe = True`. Notably, this won't make too much
-# difference to the format of the output, but it will adjust the estimates of
-# normative mineralogy depending on oxidation state.
+# we'll use :code:`adjust_all_Fe = True` and LeMaitre's correction. Notably, this
+# won't make too much difference to the format of the output, but it will adjust
+# the estimates of normative mineralogy depending on oxidation state.
 #
-NORM = CIPW_norm(df.pyrochem.compositional, adjust_all_Fe=True)
+NORM = CIPW_norm(
+    df.pyrochem.compositional,
+    adjust_all_Fe=True,
+    Fe_correction="LeMaitre",
+    Fe_correction_mode="volcanic",
+)
 ########################################################################################
 # Now we have the normative mineralogical outputs, we can have a look to see how
 # these compare to some relevant geochemical inputs:
@@ -132,36 +140,70 @@
     k: v for (k, v) in translation.items() if (df[v] > 0).sum() and (NORM[k] > 0).sum()
 }
 ########################################################################################
-import matplotlib.pyplot as plt
+# To compare SINCLAS and the :mod:`pyrolite` NORM outputs, we'll construct a grid
+# of plots which compare the respective mineralogical norms relative to a 1:1 line,
+# and highlight discrepancies. As we'll do it twice below (once for samples labelled as
+# volanic, and once for everything else), we may as well make a function of it.
+#
+# After that, let's take a look at the volcanic samples in isolation, which are the
+# the key samples for which the NORM should be applied:
+#
 from pyrolite.plot.color import process_color
 
-ncols = 4
-nrows = len(minerals.keys()) // ncols + 1 if len(minerals.keys()) % ncols else 0
 
-fig, ax = plt.subplots(
-    nrows,
-    ncols,
-    figsize=(ncols * 2.5, nrows * 2),
-)
-fig.suptitle("Comparing pyrolite's CIPW Norm to SINCLAS/IgRoCS", fontsize=16)
-ax = ax.flat
-
-for ix, (b, a) in enumerate(minerals.items()):
-    ax[ix].set_title("\n".join(b.split()), y=0.9, va="top")
-    if a in df.columns and b in NORM.columns:
-        c = process_color(
-            np.abs((df[a] / NORM[b]) - 1),
-            cmap="RdBu_r",
-            norm=plt.Normalize(vmin=0, vmax=0.1),
-        )["c"]
-        ax[ix].scatter(df[a], NORM[b], c=c)
-    ax[ix].plot([0, df[a].max()], [0, df[a].max()], color="k", ls="--")
-
-for a in ax:
-    a.set(xticks=[], yticks=[])  # turn off the ticks
-    if not a.collections:  # turn off the axis for empty axes
-        a.axis("off")
-plt.tight_layout()
+def compare_NORMs(SINCLAS_outputs, NORM_outputs, name=""):
+    """
+    Create a grid of axes comparing the outputs of SINCLAS and `pyrolite`'s NORM,
+    after translating the column names to the appropriate form.
+    """
+    ncols = 4
+    nrows = len(minerals.keys()) // ncols + 1 if len(minerals.keys()) % ncols else 0
+
+    fig, ax = plt.subplots(nrows, ncols, figsize=(ncols * 2.5, nrows * 2))
+    fig.suptitle(
+        " - ".join(
+            ["Comparing pyrolite's CIPW Norm to SINCLAS/IgRoCS"] + [name]
+            if name
+            else []
+        ),
+        fontsize=16,
+        y=1.01,
+    )
+    ax = ax.flat
+    for ix, (b, a) in enumerate(minerals.items()):
+        ax[ix].set_title("\n".join(b.split()), y=0.9, va="top")
+        if a in SINCLAS_outputs.columns and b in NORM_outputs.columns:
+            # colour by deviation from unity
+            c = process_color(
+                np.abs((SINCLAS_outputs[a] / NORM_outputs[b]) - 1),
+                cmap="RdBu_r",
+                norm=plt.Normalize(vmin=0, vmax=0.1),
+            )["c"]
+            ax[ix].scatter(SINCLAS_outputs[a], NORM_outputs[b], c=c)
+        # add a 1:1 line
+        ax[ix].plot(
+            [0, SINCLAS_outputs[a].max()],
+            [0, SINCLAS_outputs[a].max()],
+            color="k",
+            ls="--",
+        )
+
+    for a in ax:
+        a.set(xticks=[], yticks=[])  # turn off the ticks
+        if not a.collections:  # turn off the axis for empty axes
+            a.axis("off")
+    return fig, ax
+
+
+volcanic_filter = df.loc[:, "ROCK_TYPE"].str.lower().str.startswith("volc")
+fig, ax = compare_NORMs(df.loc[volcanic_filter, :], NORM.loc[volcanic_filter])
+
+
+########################################################################################
+# And everything else:
+#
+fig, ax = compare_NORMs(df.loc[~volcanic_filter, :], NORM.loc[~volcanic_filter])
+plt.show()
 ########################################################################################
 # These normative mineralogical components could be input into mineralogical
 # classifiers, as mentioned above. For example, the IUGS QAP classifier:
@@ -219,3 +261,8 @@
 #     Contributions to Mineralogy and Petrology 56, no. 2 (1 January 1976): 181–89.
 #     `doi: doi.org/10.1007/BF00399603 <https://doi.org/10.1007/BF00399603>`__
 #
+# .. [Middlemost1989] Middlemost, Eric A. K. (1989). Iron Oxidation Ratios,
+#     Norms and the Classification of Volcanic Rocks.
+#     Chemical Geology 77, 1: 19–26.
+#     `doi: doi.org/10.1016/0009-2541(89)90011-9. <https://doi.org/10.1016/0009-2541(89)90011-9.>`__
+#

docs/source/gallery/examples/geochem/convert_chemistry.py

@@ -7,10 +7,11 @@
 :func:`~pyrolite.geochem.transform.convert_chemistry` function. Note that by default
 pyrolite assumes that data are in the same units.
 """
-import pyrolite.geochem
 import pandas as pd
 
-pd.set_option("precision", 3)  # smaller outputs
+import pyrolite.geochem
+
+pd.set_option("display.precision", 3)  # smaller outputs
 ########################################################################################
 # Here we create some synthetic data to work with, which has some variables in Wt% and
 # some in ppm. Notably some elements are present in more than one column (Ca, Na):

docs/source/gallery/examples/geochem/indexes_selectors.py

@@ -3,10 +3,11 @@
 ==================================
 
 """
-import pyrolite.geochem
 import pandas as pd
 
-pd.set_option("precision", 3)  # smaller outputs
+import pyrolite.geochem
+
+pd.set_option("display.precision", 3)  # smaller outputs
 ########################################################################################
 from pyrolite.util.synthetic import normal_frame
 
@@ -73,7 +74,7 @@
 ########################################################################################
 # All elements (up to U):
 #
-from pyrolite.geochem.ind import common_elements, common_oxides, REE, REY
+from pyrolite.geochem.ind import REE, REY, common_elements, common_oxides
 
 common_elements()  # string return
 

docs/source/gallery/examples/geochem/mineral_mindb.py

@@ -6,15 +6,11 @@
 compositions.
 """
 import pandas as pd
-from pyrolite.mineral.mindb import (
-    list_groups,
-    list_minerals,
-    list_formulae,
-    get_mineral,
-    get_mineral_group,
-)
 
-pd.set_option("precision", 3)  # smaller outputs
+from pyrolite.mineral.mindb import (get_mineral, get_mineral_group,
+                                    list_formulae, list_groups, list_minerals)
+
+pd.set_option("display.precision", 3)  # smaller outputs
 ########################################################################################
 # From the database, you can get the list of its contents using a few utility
 # functions:

docs/source/gallery/examples/geochem/scaling.py

@@ -2,14 +2,17 @@
 Unit Scaling
 =============
 """
-import pyrolite.geochem
 import pandas as pd
 
-pd.set_option("precision", 3)  # smaller outputs
+import pyrolite.geochem
+
+pd.set_option("display.precision", 3)  # smaller outputs
 ########################################################################################
 from pyrolite.util.synthetic import normal_frame
 
-df = normal_frame(columns=['CaO', 'MgO', 'SiO2', 'FeO', 'Ni', 'Ti', 'La', 'Lu', 'Mg/Fe'])
+df = normal_frame(
+    columns=["CaO", "MgO", "SiO2", "FeO", "Ni", "Ti", "La", "Lu", "Mg/Fe"]
+)
 ########################################################################################
 cols = ["Ni", "NiO", "La", "La2O3"]
 df.head(2).pyrochem.convert_chemistry(to=cols)[cols]  # these are in ppm!

docs/source/gallery/examples/plotting/templates.py

@@ -14,16 +14,22 @@
 # First let's build a simple total-alkali vs silica (
 # :func:`~pyrolite.plot.templates.TAS`) diagram:
 #
-from pyrolite.plot.templates import TAS
+from pyrolite.plot.templates import TAS, SpinelFeBivariate
 from pyrolite.util.plot.axes import share_axes
 
-# sphinx_gallery_thumbnail_number = 2
+# sphinx_gallery_thumbnail_number = 3
 
 
 ax = TAS(linewidth=0.5, add_labels=True)
 plt.show()
 ########################################################################################
-# The other templates currently included in :mod:`pyrolite` are the
+# For distinguishing Fe-rich variants of spinel phases, the bivariate spinel
+# diagram can be useful:
+#
+ax = SpinelFeBivariate(linewidth=0.5, add_labels=True)
+plt.show()
+########################################################################################
+# The other bivariate templates currently included in :mod:`pyrolite` are the
 # :func:`~pyrolite.plot.templates.pearceThNbYb` and
 # :func:`~pyrolite.plot.templates.pearceTiNbYb` diagrams.
 # We can create some axes and add these templates to them:
@@ -44,7 +50,13 @@
 # the :func:`~pyrolite.plot.templates.QAP` and
 # :func:`~pyrolite.plot.templates.USDASoilTexture` diagrams:
 #
-from pyrolite.plot.templates import QAP, FeldsparTernary, USDASoilTexture
+from pyrolite.plot.templates import (
+    QAP,
+    FeldsparTernary,
+    JensenPlot,
+    SpinelTrivalentTernary,
+    USDASoilTexture,
+)
 
 ax = QAP(linewidth=0.4)
 plt.show()
@@ -63,6 +75,19 @@
 plt.tight_layout()
 plt.show()
 ########################################################################################
+# For general spinel phase discrimination, a ternary classification diagram can
+# be used to give labels based on trivalent cationic content (:math:`\mathrm{Cr^{3+}}`,
+# :math:`\mathrm{Al^{3+}}`, :math:`\mathrm{Fe^{3+}}`):
+#
+SpinelTrivalentTernary(linewidth=0.4, add_labels=True, figsize=(6, 6))
+plt.show()
+########################################################################################
+# The Jensen plot is another cationic ternary discrimination diagram (Jensen, 1976),
+# for subalkaline volcanic rocks:
+#
+JensenPlot(linewidth=0.4, add_labels=True, figsize=(7, 7))
+plt.show()
+########################################################################################
 # References and other notes for diagram templates can be found within the docstrings
 # and within the pyrolite documentation:
 #