Merge branch 'release/0.2.8'

Author: morganjwilliams

.codacy.yml

@@ -9,3 +9,4 @@ exclude_paths:
   - '.github/**'
   - 'CODE_OF_CONDUCT.md'
   - 'CHANGELOG.md'
+  - 'CONTRIBUTING.md'

.gitattributes

@@ -1,6 +1,5 @@
 pyrolite/_version.py export-subst
 
-*.ipynb filter=nbstripout
 *.ipynb diff=jupyternotebook
 
 *.svg binary

.gitignore

@@ -108,8 +108,5 @@ venv.bak/
 
 doc/examples/scratch\.py
 
-# GEOROC Contents - this is automatically updated
-pyrolite/data/georoc/contents\.json
-
 # local alphamelts install folder
 pyrolite/data/alphamelts/localinstall/*

.travis.yml

@@ -1,23 +1,15 @@
 language: python
-os: linux
 dist: bionic
-
-jobs:
-  include:
-    - python: 3.6
-      env: PYVERSION=36
-    - python: 3.7
-      env: PYVERSION=37
-    - python: 3.8
-      env: PYVERSION=38
+os: linux
+cache: pip
 
 before_install:
   - sudo apt-get install jq curl
 
 install:
   - pip install -q pytest pytest-runner pytest-cov coverage codacy-coverage
   - pip install coveralls
-  - pip install -e .[skl,stats] # install skl, statsmodels
+  - pip install .[skl,stats] # install skl, statsmodels
 
 script:
   - xvfb-run python setup.py test
@@ -26,3 +18,38 @@ after_success:
   - "ls -lr htmlcov"
   - coveralls # coverage to coveralls.io
   - python-codacy-coverage -r coverage.xml
+
+jobs:
+  allow_failures:
+    - os: osx
+
+  include:
+    - python: 3.6
+      env: PYVERSION=36
+    - python: 3.7
+      env: PYVERSION=37
+    - python: 3.8
+      env: PYVERSION=38
+    - os: osx
+      language: sh
+      env:
+        - HOMEBREW_NO_INSTALL_CLEANUP=1
+        - HOMEBREW_NO_ANALYTICS=1
+        - PYVERSION=36
+      before_cache:
+        # - brew cleanup
+        - rm -f "$HOME/Library/Caches/pip/log/debug.log"
+      cache:
+        directories:
+          # - "$HOME/Library/Caches/Homebrew"
+          - "$HOME/Library/Caches/pip"
+      addons:
+        homebrew:
+          # update: true
+          packages: python3
+      before_install:
+        - python3 -m pip install --upgrade virtualenv
+        - virtualenv -p python3 --system-site-packages "$HOME/venv"
+        - source "$HOME/venv/bin/activate"
+      script:
+        - python3 setup.py test

CONTRIBUTING.md

@@ -1,6 +1,5 @@
 # Contributing
 
-
 The long-term aim of this project is to be designed, built and supported by (and for) the geochemistry community. In the present, the majority of the work involves
 incorporating geological knowledge and frameworks into a practically useful core set of tools which can be later be expanded. As such, requests for features and bug reports are particularly valuable contributions, in addition to code and expanding the documentation. All individuals contributing to the project are expected to follow the [Code of Conduct](https://pyrolite.readthedocs.io/en/develop/dev/conduct.html), which outlines community expectations and
 responsibilities.
@@ -10,35 +9,32 @@ Also, be sure to add your name or GitHub username to the
 
 **Note**: This project is currently in `beta`, and as such there's much work to be done.
 
-Feature Requests
--------------------------
+## Feature Requests
 
 If you're new to Python, and want to implement a specific process, plot or framework as part of `pyrolite`, you can submit a [Feature Request](https://github.com/morganjwilliams/pyrolite/issues/new?assignees=morganjwilliams&labels=enhancement&template=feature-request.md).
 Perhaps also check the [Issues Board](https://github.com/morganjwilliams/pyrolite/issues) first to see if someone else has suggested something similar (or if something is in development), and comment there.
 
-Bug Reports
--------------------------
+## Bug Reports
 
 If you've tried to do something with `pyrolite`, but it didn't work, and googling
 error messages didn't help (or, if the error messages are full of
 `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 [Issues Board](https://github.com/morganjwilliams/pyrolite/issues) first to see if someone else is having the same issue, and comment there.
 
-Contributing to Documentation
-------------------------------
+## Contributing to Documentation
 
 The [documentation and examples](https://pyrolite.readthedocs.io) for `pyrolite`
 are gradually being developed, and any contributions or corrections would be greatly appreciated. Currently the examples are patchy, and any 'getting started' guides would be a helpful addition.
 
 These pages serve multiple purposes:
-  * A human-readable reference of the source code (compiled from docstrings).
-  * A set of simple examples to demonstrate use and utility.
-  * A place for developing extended examples
 
-    * Note: these examples could easily be distributed as educational resources showcasing the utility of programmatic approaches to geochemistry
+* A human-readable reference of the source code (compiled from docstrings).
+* A set of simple examples to demonstrate use and utility.
+* A place for developing extended examples
+
+  * Note: these examples could easily be distributed as educational resources showcasing the utility of programmatic approaches to geochemistry
 
-Contributing Code
--------------------------
+## Contributing Code
 
 Code contributions are always welcome, whether it be small modifications or entire
 features. As the project gains momentum, check the [Issues Board](https://github.com/morganjwilliams/pyrolite/issues) for outstanding issues, features under development. If you'd like to contribute, but you're not so
@@ -51,16 +47,16 @@ changes back to into the project, push your changes to your remote fork, and the
 
 Notes:
 
-  * See the [Installation page](https://pyrolite.readthedocs.io/en/develop/installation.html) for directions for installing extra dependencies for development, and the [Development page](https://pyrolite.readthedocs.io/en/develop/dev/development.html) for information on development environments and tests.
+* See the [Installation page](https://pyrolite.readthedocs.io/en/develop/installation.html) for directions for installing extra dependencies for development, and the [Development page](https://pyrolite.readthedocs.io/en/develop/dev/development.html) for information on development environments and tests.
 
-  * `pyrolite` development roughly follows a [`gitflow` workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow).
-    `pyrolite/master` is only used for releases, and large separable features
-    should be build on `feature` branches off `develop`.
+* `pyrolite` development roughly follows a [`gitflow` workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow).
+  `pyrolite/master` is only used for releases, and large separable features
+  should be build on `feature` branches off `develop`.
 
-  * Contributions introducing new functions, classes or entire features should
-    also include appropriate tests where possible (see [Writing Tests](#writing-tests), below).
+* Contributions introducing new functions, classes or entire features should
+  also include appropriate tests where possible (see [Writing Tests](#writing-tests), below).
 
-  * `pyrolite` uses [Black](https://github.com/python/black/) for code formatting, and submissions which have passed through `Black` are appreciated, although not critical.
+* `pyrolite` uses [Black](https://github.com/python/black/) for code formatting, and submissions which have passed through `Black` are appreciated, although not critical.
 
 
 Writing Tests

MANIFEST.in

@@ -2,11 +2,10 @@ include versioneer.py
 include pyrolite/_version.py
 include LICENSE
 recursive-include pyrolite/data/Aitchison *
-include pyrolite/data/alphamelts/env.py
 recursive-include pyrolite/data/geochem *
+recursive-include pyrolite/data/mineral *
 recursive-include pyrolite/data/models *
 recursive-include pyrolite/data/radii *
 recursive-include pyrolite/data/timescale *
-recursive-include pyrolite/data/mineral *
-# recursive-exclude pyrolite/data/alphamelts/localinstall *
+recursive-include pyrolite/data/_config *
 # global-exclude __pycache__

README.md

@@ -16,7 +16,7 @@ geochemical variables (e.g. elements to oxides), functions for common plotting
 tasks (e.g. spiderplots, ternary diagrams, bivariate and ternary density diagrams),
 and numerous auxiliary utilities.
 
-pyrolite's is principally developed for use use in geochemical research, but is also
+pyrolite's is principally developed for use in geochemical research, but is also
 well suited to being incorporated into university-level geochemistry and petrology
 classes which wish to include a little Python. The documentation is continually
 evolving, and more examples and tutorials will gradually be added (feel free to

docs/source/_templates/layout.html

@@ -0,0 +1,6 @@
+{% extends "!layout.html" %}
+
+{% block menu %}
+{{ super() }}
+<a href="{{pathto('genindex.html', 1)}}">Index</a>
+{% endblock %}

docs/source/api/API.rst

@@ -42,7 +42,7 @@ pyrolite\.geochem
 
 
 pyrolite\.comp
----------------------
+-----------------
 
   .. automodule:: pyrolite.comp
 
@@ -56,7 +56,7 @@ pyrolite\.comp
     comp/impute
 
 pyrolite\.mineral
----------------------
+-------------------
 
   .. automodule:: pyrolite.mineral
 
@@ -66,14 +66,30 @@ pyrolite\.mineral
      mineral
 
 pyrolite\.util
--------------------------------
+----------------
 
   .. automodule:: pyrolite.util
 
   .. toctree::
     :maxdepth: 2
 
-    util
+    util/general
+    util/pd
+    util/plot
+    util/text
+    util/web
+    util/time
+    util/math
+    util/lambdas
+    util/distributions
+    util/synthetic
+    util/missing
+    util/units
+    util/types
+    util/meta
+    util/skl
+    util/classification
+    util/log
 
 
 .. seealso:: `Extensions <../ext/extensions.html>`__