Merge branch 'release/0.2.5'

.travis.yml

@@ -2,15 +2,14 @@ language: python
 os: linux
 dist: xenial
 
-matrix:
+jobs:
   include:
     - python: 3.6
       env: PYVERSION=36
     - python: 3.7
       env: PYVERSION=37
     - python: 3.8
       env: PYVERSION=38
-      sudo: true
 
 install:
   - pip install -q pytest pytest-runner pytest-cov coverage

CODE_OF_CONDUCT.md

@@ -1,3 +1,4 @@
 # Code of Conduct
 
-For the project code of conduct, see the [docs page](https://pyrolite.readthedocs.io/en/develop/conduct.html).
+For the project code of conduct, see the
+[docs page](https://pyrolite.readthedocs.io/en/master/dev/conduct.html).

README.md

@@ -20,13 +20,15 @@
 pip install pyrolite
 ```
 
+For more information, see the documentation's [installation page](https://pyrolite.readthedocs.io/en/master/installation.html), and the [Getting Started Guide](https://pyrolite.readthedocs.io/en/master/gettingstarted.html).
+
+
 ### Contributing
 
 The long-term aim of this project is to be designed, built and supported by (and for)
 the geochemistry community. For more information, see the [documentation](https://pyrolite.readthedocs.io/), particularly the [
 Contributing page](https://pyrolite.readthedocs.io/en/latest/contributing.html) and [Code of Conduct](https://pyrolite.readthedocs.io/en/latest/conduct.html).
 
-
 ### Development & Build Status
 
 [![Formatted with Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)

docs/source/api/API.rst

@@ -58,20 +58,16 @@ pyrolite\.mineral
 ---------------------
 
   .. automodule:: pyrolite.mineral
-     :members:
-     :undoc-members:
 
   .. toctree::
-     :maxdepth: 2
+     :maxdepth: 1
 
      mineral
 
 pyrolite\.util
 -------------------------------
 
   .. automodule:: pyrolite.util
-    :members:
-    :undoc-members:
 
   .. toctree::
     :maxdepth: 2

docs/source/api/mineral.rst

@@ -1,7 +1,3 @@
-.. automodule:: pyrolite.mineral
-    :members:
-    :undoc-members:
-
 .. note:: This module is a work in progress and will be gradually updated.
 
 pyrolite\.mineral\.template

docs/source/api/util.rst

@@ -80,8 +80,6 @@ pyrolite\.util\.meta
 pyrolite\.util\.skl
 -------------------------------
   .. automodule:: pyrolite.util.skl
-      :members:
-      :undoc-members:
 
   .. toctree::
      :maxdepth: 2

docs/source/dev/changelog.rst

@@ -1,24 +1,84 @@
 Changelog
 =============
 
-
 All notable changes to this project will be documented here.
 
+Todo
+------
+
+* FEATURE: Updates to include more lithogeochemical plot templates
+  (`#26 <https://github.com/morganjwilliams/pyrolite/issues/26>`__)
+* BUG: Upgrades for :func:`~pyrolite.geochem.transform.convert_chemistry` for performance,
+  reducing data duplication (`#29 <https://github.com/morganjwilliams/pyrolite/issues/29>`__)
+* BUG: Conditional density spider plots should have bins centred on the element indexes
+  (currently this is an edge)
+* BUG: Index memory for :func:`~pyrolite.plot.spider.spider`
+  (`#27 <https://github.com/morganjwilliams/pyrolite/issues/27>`__)
+
+
 `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 <development.html#development-installation>`__.
 
-Todo
-~~~~~~~
+`0.2.5`_
+--------------
 
-* Index memory for :func:`~pyrolite.plot.spider.spider`
-  (`#27 <https://github.com/morganjwilliams/pyrolite/issues/27>`__)
-* Updates to include more lithogeochemical plot templates
-  (`#26 <https://github.com/morganjwilliams/pyrolite/issues/26>`__)
-* Upgrades for :func:`~pyrolite.geochem.transform.convert_chemistry`
+* PR Merged: `@lavender22 <https://github.com/lavender22>`__ updated the spider
+  diagram example to add a link to the normalisation example (which lists
+  different reservoirs you can normalise to).
+* Added an 'Importing Data' section to the docs
+  `Getting Started page <../gettingstarted.html#importing-data>`__.
+* Disabled automatic extension loading (e.g. for :mod:`pyrolite_meltsutil`) to
+  avoid bugs during version mismatches.
+
+:mod:`pyrolite.comp`
+~~~~~~~~~~~~~~~~~~~~~~~
+
+* Updated the :class:`pyrolite.comp.pyrocomp` dataframe accessor API to include
+  reference to compositional data log transform functions within
+  :mod:`pyrolite.comp.codata`
+
+:mod:`pyrolite.plot`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Added support for spider plot index ordering added with the keyword
+  :code:`index_order` (`#30 <https://github.com/morganjwilliams/pyrolite/issues/30>`__)
+* Added support for color indexing in :mod:`~pyrolite.plot.color` using
+  :class:`pandas.Series`, and also for list-like arrays of categories
+* Added a workaround for referring to axes positions where the projection is changed
+  to a ternary projection (displacing the original axis), but the reference to the
+  original axes object (now booted from :code:`fig.axes`/:code:`fig.orderedaxes`) is
+  subsequently used.
+* Updated :func:`~pyrolite.plot.color.process_color` processing of auxillary
+  color keyword arguments (fixing a bug for color arguments in
+  :func:`~pyrolite.plot.stem`)
+* Added support for a :code:`color_mappings` keyword argument for mapping
+  categorical variables to specific colors.
+* Updated the effect of :code:`relim` keyword argument of
+  :func:`~pyrolite.plot.density.density` to remove the scaling (it will no longer
+  log-scale the axes, just the grid/histogram bins).
+* Updated :class:`~pyrolite.plot.ternary.grid.Grid` to accept an x-y tuple to specify
+  numbers of bins in each direction within a grid (e.g. :code:`bins=(20, 40)`)
+* Updated the grids used in some of the :func:`~pyrolite.plot.density.density`
+  methods to be edges, lining up the arrays such that shading parameters
+  will work as expected (e.g. :code:`shading='gouraud'`)
+
+:mod:`pyrolite.geochem`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+* Added sorting function :code:`~pyrolite.geochem.ind.by_imcompatibility`
+  for incompatible element sorting (based on BCC/PM relative abundances).
+
+:mod:`pyrolite.mineral`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+* Minor bugfix for :func:`~pyrolite.mineral.mindb.update_database`
+
+:mod:`pyrolite.util`
+~~~~~~~~~~~~~~~~~~~~~~~
+* Moved :func:`~pyrolite.util.general.check_perl` out of :mod:`pyrolite` into
+  :mod:`pyrolite_meltsutil`
 
 `0.2.4`_
 --------------
@@ -756,6 +816,7 @@ Todo
     but were :code:`alpha` versions which were never considered stable.
 
 .. _Development: https://github.com/morganjwilliams/pyrolite/compare/0.2.4...develop
+.. _0.2.5: https://github.com/morganjwilliams/pyrolite/compare/0.2.4...0.2.5
 .. _0.2.4: https://github.com/morganjwilliams/pyrolite/compare/0.2.3...0.2.4
 .. _0.2.3: https://github.com/morganjwilliams/pyrolite/compare/0.2.2...0.2.3
 .. _0.2.2: https://github.com/morganjwilliams/pyrolite/compare/0.2.1...0.2.2

docs/source/dev/contributing.rst

@@ -31,7 +31,7 @@ Bug Reports
 -------------------------
 
 If you've tried to do something with :code:`pyrolite`, but it didn't work, and googling
-erro messages didn't help (or, if the error messages are full of
+error messages didn't help (or, if the error messages are full of
 :code:`pyrolite.XX.xx`), you can submit a
 `Bug Report <https://github.com/morganjwilliams/pyrolite/issues/new?assignees=morganjwilliams&labels=bug&template=bug-report.md>`__ .
 Perhaps also check the