Merge branch 'release/0.1.21'

morganjwilliams · Sep 19, 2019 · 63ac7a0 · 63ac7a0
2 parents 29d0c3a + 41fa5c6
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diff --git a/CHANGELOG b/CHANGELOG
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -0,0 +1,126 @@
+Changelog
+==============
+
+All notable changes to this project will be documented here.
+
+`Development`_
+--------------
+
+.. 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 <installation.html#development-installation>`__.
+
+
+`0.1.21`_
+--------------
+
+* Parallel coordinate plots
+* Updated :func:`~pyrolite.plot.pyroplot.scatter` and
+  :func:`~pyrolite.plot.tern.ternary` to better deal with colormaps
+* Updated alphaMELTS interface
+  * Docs
+  * Updated to default to tables with percentages (Wt%, Vol%)
+  * Updated plot templates y-labels
+  * Fixed automation grid bug
+
+`0.1.20`_
+--------------
+
+New
+~~~~~~~~
+
+* Stub for DataFrame.pyrochem accessor (yet to be developed)
+* Added :func:`pyrolite.util.skl.vis.plot_mapping` for manifold dimensional reduction
+* Added :func:`pyrolite.util.skl.vis.alphas_from_multiclass_prob` for visualising
+  multi-class classification probabilities in scatter plots
+
+Updates
+~~~~~~~~
+
+* Convert reference compositions and normalisation to use a JSON database
+* Updated default y-aspect for ternary plots and axes patches
+* Updated :mod:`pyrolite.ext.alphamelts.automation`,
+  :mod:`pyrolite.ext.alphamelts.meltsfile`, :mod:`pyrolite.ext.alphamelts.tables`
+* Updated docs to use :class:`pyrolite.ext.alphamelts.automation.MeltsBatch` with a parameter grid
+* Added :mod:`pyrolite.plot.biplot` to API docs
+
+`0.1.19`_
+--------------
+
+`0.1.18`_
+--------------
+
+`0.1.17`_
+--------------
+
+`0.1.16`_
+--------------
+
+`0.1.15`_
+--------------
+
+`0.1.14`_
+--------------
+
+`0.1.13`_
+--------------
+
+`0.1.12`_
+--------------
+
+`0.1.11`_
+--------------
+
+`0.1.10`_
+--------------
+
+`0.1.9`_
+--------------
+
+`0.1.8`_
+--------------
+
+`0.1.7`_
+--------------
+
+`0.1.6`_
+--------------
+
+`0.1.5`_
+--------------
+
+`0.1.4`_
+--------------
+
+`0.1.2`_
+--------------
+
+`0.1.1`_
+--------------
+
+`0.1.0`_
+--------------
+
+
+.. _Development: https://github.com/morganjwilliams/pyrolite/compare/0.1.21...develop
+.. _0.1.21: https://github.com/morganjwilliams/pyrolite/compare/0.1.20...0.1.21
+.. _0.1.20: https://github.com/morganjwilliams/pyrolite/compare/0.1.19...0.1.20
+.. _0.1.19: https://github.com/morganjwilliams/pyrolite/compare/0.1.18...0.1.19
+.. _0.1.18: https://github.com/morganjwilliams/pyrolite/compare/0.1.17...0.1.18
+.. _0.1.17: https://github.com/morganjwilliams/pyrolite/compare/0.1.16...0.1.17
+.. _0.1.16: https://github.com/morganjwilliams/pyrolite/compare/0.1.15...0.1.16
+.. _0.1.15: https://github.com/morganjwilliams/pyrolite/compare/0.1.14...0.1.15
+.. _0.1.14: https://github.com/morganjwilliams/pyrolite/compare/0.1.13...0.1.14
+.. _0.1.13: https://github.com/morganjwilliams/pyrolite/compare/0.1.12...0.1.13
+.. _0.1.12: https://github.com/morganjwilliams/pyrolite/compare/0.1.11...0.1.12
+.. _0.1.11: https://github.com/morganjwilliams/pyrolite/compare/0.1.10...0.1.11
+.. _0.1.10: https://github.com/morganjwilliams/pyrolite/compare/0.1.9...0.1.10
+.. _0.1.9: https://github.com/morganjwilliams/pyrolite/compare/0.1.8...0.1.9
+.. _0.1.8: https://github.com/morganjwilliams/pyrolite/compare/0.1.7...0.1.8
+.. _0.1.7: https://github.com/morganjwilliams/pyrolite/compare/0.1.6...0.1.7
+.. _0.1.6: https://github.com/morganjwilliams/pyrolite/compare/0.1.5...0.1.6
+.. _0.1.5: https://github.com/morganjwilliams/pyrolite/compare/0.1.4...0.1.5
+.. _0.1.4: https://github.com/morganjwilliams/pyrolite/compare/0.1.2...0.1.4
+.. _0.1.2: https://github.com/morganjwilliams/pyrolite/compare/0.1.1...0.1.2
+.. _0.1.1: https://github.com/morganjwilliams/pyrolite/compare/0.1.0...0.1.1
+.. _0.1.0: https://github.com/morganjwilliams/pyrolite/compare/0.0.17...0.1.0
diff --git a/docs/examples/alphamelts/montecarlo.py b/docs/examples/alphamelts/montecarlo.py
@@ -47,7 +47,7 @@ def blur_compositions(df, noise=0.05, scale=100):
 df[compositional] = df[compositional].astype(float).renormalise()
 df[compositional] = blur_compositions(df[compositional])
 
-df.Title = df.Title + " " + df.index.map(str) # differentiate titles
+df.Title = df.Title + " " + df.index.map(str)  # differentiate titles
 df.Title = df.Title.apply(slugify)
 # %% setup an environment for isobaric fractional crystallisation
 from pyrolite.ext.alphamelts.env import MELTS_Env
@@ -79,24 +79,29 @@ def blur_compositions(df, noise=0.05, scale=100):
         "modes": ["isobaric"],
     },
     grid={
-        #"Initial Pressure": [3000, 7000],
+        # "Initial Pressure": [3000, 7000],
         "Log fO2 Path": [None, "FMQ"],
-        #"modifychem": [None, {"H2O": 0.5}],
+        # "modifychem": [None, {"H2O": 0.5}],
     },
     env=env,
     logger=logger,
     fromdir=tempdir,
 )
 
+batch.grid  # [{}, {'Log fO2 Path': 'FMQ'}]
+
 batch.run(
     overwrite=True
 )  # overwrite=False if you don't want to update existing exp folders
 
 # %% aggregate the results over the same gridded space
+from pathlib import Path
 from pyrolite.ext.alphamelts.tables import get_experiments_summary
 from pyrolite.ext.alphamelts.plottemplates import table_by_phase
 
-summary = get_experiments_summary(tempdir / "isobar5kbar", kelvin=False)
-fig = table_by_phase(summary, plotswide=2, figsize=(10, 5))
+tempdir = Path("./") / "montecarlo"
+
+summary = get_experiments_summary(tempdir / "isobar5kbar1300-800C", kelvin=False)
+fig = table_by_phase(summary, table="phasemass", plotswide=2, figsize=(10, 8))
 # %% save figure
 save_figure(fig, save_at="../../source/_static", name="melts_montecarlo")
diff --git a/docs/examples/plotting/logo.py b/docs/examples/plotting/logo.py
@@ -22,10 +22,13 @@
 
 np.random.seed(82)
 # %% colors ----------------------------------------------------------------------------
-t10b3 = [  # tableau 10 colorblind safe colors, a selection of 3
-    (r / 255.0, g / 255.0, b / 255.0)
-    for r, g, b in [(0, 107, 164), (171, 171, 171), (89, 89, 89), (95, 158, 209)]
+t10b3 = [  # tableau 10 colorblind safe colors, a selection of 4
+    (0, 107, 164),
+    (171, 171, 171),
+    (89, 89, 89),
+    (95, 158, 209)
 ]
+t10b3 = [(r / 255.0, g / 255.0, b / 255.0) for r, g, b in t10b3]
 # %% data and transforms ---------------------------------------------------------------
 d = 1.0  # distance from centre
 sig = 0.1  # scale for variance
@@ -45,7 +48,7 @@
 )
 
 means = ILRTransform().inverse_transform(means)  # compositional means (D=3)
-size = 2000 # logo @ 10000
+size = 2000  # logo @ 10000
 pts = [random_composition(mean=M, cov=C, size=size) for M, C in zip(means, covs)]
 
 T = ILRTransform()
@@ -110,6 +113,9 @@
 fmts = ["png", "jpg"]
 save_axes(ax[1], name="icon", save_at=save_at, save_fmts=fmts, dpi=dpi)
 save_axes(ax[1], name="icon_small", save_at=save_at, save_fmts=fmts, dpi=60)
+
+save_axes(ax[1], name="sticker", save_at=save_at, save_fmts=["pdf"], dpi=dpi)
+
 ax[0].set_title("Synthetic Data")
 ax[1].set_title("Covariance Ellipses and PCA Vectors")
 ax[-2].set_title("Individual Density, with Contours")

diff --git a/docs/examples/plotting/parallel.py b/docs/examples/plotting/parallel.py
@@ -0,0 +1,44 @@
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import matplotlib.axes
+import pyrolite.plot
+import pyrolite.data.Aitchison
+
+# %% Data
+# let's load up an example dataset from Aitchison
+df = pyrolite.data.Aitchison.load_coxite()
+comp = [
+    i for i in df.columns if i not in ["Depth", "Porosity"]
+]  # compositional data variables
+# %% Default
+ax = df.pyroplot.parallel()
+# %% save
+from pyrolite.util.plot import save_figure
+
+save_figure(ax.figure, save_at="../../source/_static", name="parallel_default")
+# %% Default Rescale
+ax = df.pyroplot.parallel(rescale=True)
+# %% save
+save_figure(ax.figure, save_at="../../source/_static", name="parallel_rescale")
+# %% CLR
+from pyrolite.util.skl.transform import CLRTransform
+
+cmap = "inferno"
+compdata = df.copy()
+compdata[comp] = CLRTransform().transform(compdata[comp])
+ax = compdata.loc[:, comp].pyroplot.parallel(color_by=compdata.Depth.values, cmap=cmap)
+
+# we can add a meaningful colorbar to indicate one variable also, here Depth
+sm = plt.cm.ScalarMappable(cmap=cmap)
+sm.set_array(df.Depth)
+plt.colorbar(sm)
+# %% save
+save_figure(ax.figure, save_at="../../source/_static", name="parallel_CLR")
+# %% CLR Rescale
+ax = compdata.loc[:, comp].pyroplot.parallel(
+    rescale=True, color_by=compdata.Depth.values, cmap=cmap
+)
+plt.colorbar(sm)
+# %% save
+save_figure(ax.figure, save_at="../../source/_static", name="parallel_CLR_rescale")
diff --git a/docs/source/_static/logo_eg_all.jpg b/docs/source/_static/logo_eg_all.jpg
diff --git a/docs/source/_static/logo_eg_all.png b/docs/source/_static/logo_eg_all.png
diff --git a/docs/source/_static/logo_eg_contours.jpg b/docs/source/_static/logo_eg_contours.jpg
diff --git a/docs/source/_static/logo_eg_contours.png b/docs/source/_static/logo_eg_contours.png
diff --git a/docs/source/_static/logo_eg_density.jpg b/docs/source/_static/logo_eg_density.jpg
diff --git a/docs/source/_static/logo_eg_density.png b/docs/source/_static/logo_eg_density.png
diff --git a/docs/source/_static/logo_eg_ellipses.jpg b/docs/source/_static/logo_eg_ellipses.jpg
diff --git a/docs/source/_static/logo_eg_ellipses.png b/docs/source/_static/logo_eg_ellipses.png
diff --git a/docs/source/_static/logo_eg_points.jpg b/docs/source/_static/logo_eg_points.jpg
diff --git a/docs/source/_static/logo_eg_points.png b/docs/source/_static/logo_eg_points.png
diff --git a/docs/source/_static/melts_montecarlo.png b/docs/source/_static/melts_montecarlo.png
diff --git a/docs/source/_static/parallel_CLR.png b/docs/source/_static/parallel_CLR.png
diff --git a/docs/source/_static/parallel_CLR_rescale.png b/docs/source/_static/parallel_CLR_rescale.png
diff --git a/docs/source/_static/parallel_default.png b/docs/source/_static/parallel_default.png
diff --git a/docs/source/_static/parallel_rescale.png b/docs/source/_static/parallel_rescale.png
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -0,0 +1,5 @@
+Changelog
+=============
+
+.. include:: ../../CHANGELOG.rst
+  :start-line: 3
diff --git a/docs/source/contributors.rst b/docs/source/contributors.rst
@@ -4,8 +4,9 @@ Contributors
 This list includes people who have contributed to the project in the form of code,
 comments, testing, bug reports, feature requests.
 
-* Morgan Williams
+* `Morgan Williams <https://github.com/morganjwilliams>`__`
 * Hayden Dalton
-* Louise Schoneveld
+* `Louise Schoneveld <https://github.com/lavender22>`__
 * Adam Bath
 * Yajing Mao
+* `Justin Gosses <https://github.com/JustinGOSSES>`__.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -46,6 +46,7 @@ make use of your geochemical data to build and test geological models.
    installation
    usage/examples
    submodules
+   changelog
    future
    tests
    contributing

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -22,6 +22,18 @@ on `PyPi <https://pypi.org/project/pyrolite/>`_ using the :code:`--upgrade` flag
    pip install --upgrade pyrolite
 
 
+Development Installation
+----------------------------
+
+To access and use the development version, you can either
+`clone the repository <https://github.com/morganjwilliams/pyrolite>`__ or install
+via pip directly from GitHub:
+
+.. code-block:: bash
+
+  pip install git+git://github.com//morganjwilliams/pyrolite.git@develop#egg=pyrolite
+
+
 Optional Dependencies and Local Development
 -------------------------------------------
 
@@ -33,10 +45,3 @@ For example:
    pip install pyrolite[dev]
 
    pip install pyrolite[dev,skl,spatial,db]
-
-
-To download the development version, you can install via pip directly from GitHub:
-
-.. code-block:: bash
-
-   pip install git+git://github.com//morganjwilliams/pyrolite.git@develop#egg=pyrolite
diff --git a/docs/source/submoddoc/plot.rst b/docs/source/submoddoc/plot.rst
@@ -29,6 +29,12 @@ pyrolite\.plot\.stem
       :members:
       :undoc-members:
 
+pyrolite\.plot\.parallel
+-------------------------------
+  .. automodule:: pyrolite.plot.parallel
+      :members:
+      :undoc-members:
+
 pyrolite\.plot\.biplot
 -------------------------------
   .. automodule:: pyrolite.plot.biplot