Merge pull request #45 from SMTG-UCL/master

update to current version
SMTG-Bham · Oct 25, 2022 · 791133e · 791133e
2 parents e11fe73 + aa304e8
commit 791133e
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diff --git a/.travis.yml b/.travis.yml
@@ -1,15 +1,15 @@
-language: python
-
-python:
-  - "3.6"
-
-install:
-  - pip install --upgrade pip
-  -  python -m pip install -r requirements.txt .
-
-branches:
-  only:
-  - /.*/
-
-script: 
+language: python
+
+python:
+  - "3.6"
+
+install:
+  - pip install --upgrade pip
+  -  python -m pip install -r requirements.txt .
+
+branches:
+  only:
+  - /.*/
+
+script: 
   - cd tests/ && python -m unittest
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,5 +1,4 @@
 {
-    "restructuredtext.confPath": "${workspaceFolder}\\docs\\src",
     "restructuredtext.languageServer.disabled": true,
     "python.testing.unittestArgs": [
         "-v",
@@ -9,5 +8,8 @@
         "test_*.py"
     ],
     "python.testing.pytestEnabled": false,
-    "python.testing.unittestEnabled": true
+    "python.testing.unittestEnabled": true,
+    "esbonio.sphinx.confDir": "${workspaceFolder}\\docs\\src",
+    "esbonio.server.enabled": false,
+    "restructuredtext.confPath": "${workspaceFolder}\\docs\\src"
 }
diff --git a/LICENSE b/LICENSE
diff --git a/README.rst b/README.rst
@@ -13,7 +13,7 @@
     | |   |__   __  |___  |_____   __ :|___/ |    ___  __|__ __|__  __  |__  \
     | |   |  | /  \ |   \ |  |  | /  \:|     |   /   \   |     |   /  \ |  \ /
     | |   |  | |__/ |     |  |  | |  |:|     |   |   |   |     |   |__/ |    \_____
-    | |   |  | \__  |     |  |  | \__/:|     \__ \___/   \__   \__ \__  |    :2.0.0\
+    | |   |  | \__  |     |  |  | \__/:|     \__ \___/   \__   \__ \__  |    :2.3.0\
     |_________________________________:______________________________________:_____/
 
 
@@ -48,7 +48,7 @@ ThermoPlotter can easily be installed with git and pip:
 
     git clone https://github.com/SMTG-UCL/ThermoPlotter.git
     cd ThermoPlotter
-    pip install --user .
+    pip install .
 
 After installing, you may want to copy ``ThermoPlotter/tprc.yaml`` to
 ``~/.config/tprc.yaml``, if you want to set your own default axis
@@ -72,6 +72,12 @@ longer process is required:
 
 Using conda may circumvent this process.
 
+Command Line Usage
+------------------
+
+ThermoPlotter uses `click`_, which has an easily navigable structure
+from the command-line, detailed in the `tutorials`_.
+
 Python Usage
 ------------
 
@@ -90,13 +96,15 @@ As ThermoPlotter is dependent on matplotlib, each stage can be
 substituted with bespoke code, e.g. using ``matplotlib.pyplot.subplots``
 or ``matplotlib.axes.Axes.scatter``. These can still be supplemented
 with ThermoPlotter helper functions, such as default labels which the
-user can set in ``tp.settings`` or colourmap generators in
-``tp.plot.colour``.
+user can set in ``tp.settings``, colourmap generators in
+``tp.plot.colour`` or legend helpers such as ``tp.axes.legend.alphabetise``.
 
 The best way to get a feel for ThermoPlotter is to see it in action:
-Take a look at our  `examples <https://github.com/smtg-ucl/ThermoPlotter/tree/master/examples>`_ scripts.
+Take a look at our  `examples`_ and `tutorials`_. Currently supported
+codes are:
 
-Currently supported codes are:
+.. _examples: https://github.com/smtg-ucl/ThermoPlotter/tree/master/examples
+.. _tutorials: https://smtg-ucl.github.io/ThermoPlotter/tutorials.html
 
 * Phononic properties:
 
@@ -126,8 +134,8 @@ Current plotting modes are split into four areas.
   concentration; and one which plots the lattice thermal conductivity
   required to reach a target ZT, again against temperature and doping.
 
-A set of example scripts is provided in the ``tp/examples`` folder, and
-there is `documentation`_.
+A set of example scripts is provided in the ``tp/examples`` folder and
+in our online `examples`_, and there is `documentation`_.
 
 Contributing
 ------------
@@ -142,11 +150,10 @@ while contributions can be made using the `fork and pull`_ approach.
 Contributions should include comprehensive docstrings, and where
 appropriate `examples`_, further `documentation`_ and `tests`_ are greatly
 appreciated. Documentation uses the `sphinx`_ package, and can be built from
-the docs directory with ``sphinx-build -b html src/ .``.
+the ``docs`` directory with ``sphinx-build -b html src/ .``.
 
 .. _issue tracker: https://github.com/smtg-ucl/ThermoPlotter/issues
 .. _fork and pull: https://guides.github.com/activities/forking
-.. _examples: https://github.com/smtg-ucl/ThermoPlotter/tree/master/examples
 .. _documentation: https://smtg-ucl.github.io/ThermoPlotter/
 .. _tests: https://github.com/smtg-ucl/ThermoPlotter/tree/master/tests
 
@@ -172,6 +179,7 @@ Roughly chronologically, they are so far:
 * Sean R. Kavanagh
 * Warda Rahim
 * Katarina Brlec
+* Joe Willis
 
 License
 -------
@@ -193,4 +201,3 @@ ThermoPlotter uses the following open-source packages:
 * `scipy <https://www.scipy.org>`_
 * `sphinx <https://www.sphinx-doc.org>`_
 * `yaml <https://pyyaml.org/>`_
-
diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 3490feed2dd8ec192e4d1c58a848b976
+config: 8763cfb3d8fdbb00210c4d226bd71e51
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/contents.doctree b/docs/.doctrees/contents.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/gallery.doctree b/docs/.doctrees/gallery.doctree
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/tp.axes.doctree b/docs/.doctrees/tp.axes.doctree
diff --git a/docs/.doctrees/tp.cli.doctree b/docs/.doctrees/tp.cli.doctree
diff --git a/docs/.doctrees/tp.data.doctree b/docs/.doctrees/tp.data.doctree
diff --git a/docs/.doctrees/tp.doctree b/docs/.doctrees/tp.doctree
diff --git a/docs/.doctrees/tp.plot.doctree b/docs/.doctrees/tp.plot.doctree
diff --git a/docs/.doctrees/tp.setup.doctree b/docs/.doctrees/tp.setup.doctree
diff --git a/docs/.doctrees/tutorial-00.doctree b/docs/.doctrees/tutorial-00.doctree
diff --git a/docs/.doctrees/tutorial-01.doctree b/docs/.doctrees/tutorial-01.doctree
diff --git a/docs/.doctrees/tutorial-02.doctree b/docs/.doctrees/tutorial-02.doctree
diff --git a/docs/.doctrees/tutorial-03.doctree b/docs/.doctrees/tutorial-03.doctree
diff --git a/docs/.doctrees/tutorial-04.doctree b/docs/.doctrees/tutorial-04.doctree
diff --git a/docs/.doctrees/tutorial-05.doctree b/docs/.doctrees/tutorial-05.doctree
diff --git a/docs/.doctrees/tutorial-06.doctree b/docs/.doctrees/tutorial-06.doctree
diff --git a/docs/.doctrees/tutorial-0X.doctree b/docs/.doctrees/tutorial-0X.doctree
diff --git a/docs/.doctrees/tutorials.doctree b/docs/.doctrees/tutorials.doctree
diff --git a/docs/.nojekyll b/docs/.nojekyll
@@ -1 +1 @@
-
+
diff --git a/docs/_images/cumkappa.png b/docs/_images/cumkappa.png
diff --git a/docs/_images/dos.png b/docs/_images/dos.png
diff --git a/docs/_images/kappa-target.png b/docs/_images/kappa-target.png
diff --git a/docs/_images/multiphon.png b/docs/_images/multiphon.png
diff --git a/docs/_images/phonons.png b/docs/_images/phonons.png
diff --git a/docs/_images/prophon.png b/docs/_images/prophon.png
diff --git a/docs/_images/tutorial-01.png b/docs/_images/tutorial-01.png
diff --git a/.../02-individual-customisation/wideband.png → docs/_images/tutorial-02.png b/.../02-individual-customisation/wideband.png → docs/_images/tutorial-02.png
diff --git a/docs/_images/tutorial-03.png b/docs/_images/tutorial-03.png
diff --git a/examples/04-layered-plots/phonons.png → docs/_images/tutorial-04.png b/examples/04-layered-plots/phonons.png → docs/_images/tutorial-04.png
diff --git a/docs/_images/tutorial-05.png b/docs/_images/tutorial-05.png
diff --git a/docs/_images/wideband.png b/docs/_images/wideband.png
diff --git a/docs/_images/ztdiff.png b/docs/_images/ztdiff.png
diff --git a/docs/_images/ztmap.png b/docs/_images/ztmap.png
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; ThermoPlotter 1.0.0 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <title>Overview: module code &mdash; ThermoPlotter 2.0.0 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
@@ -35,7 +35,9 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../gallery.html">Gallery</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#command-line-usage">Command Line Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#python-usage">Python Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#contributing">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#testing">Testing</a></li>
@@ -69,22 +71,24 @@
            <div itemprop="articleBody">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="tp/axes/four.html">tp.axes.four</a></li>
-<li><a href="tp/axes/one.html">tp.axes.one</a></li>
-<li><a href="tp/axes/three.html">tp.axes.three</a></li>
-<li><a href="tp/axes/two.html">tp.axes.two</a></li>
+<ul><li><a href="tp/axes/large.html">tp.axes.large</a></li>
+<li><a href="tp/axes/legend.html">tp.axes.legend</a></li>
+<li><a href="tp/axes/small.html">tp.axes.small</a></li>
 <li><a href="tp/calculate.html">tp.calculate</a></li>
+<li><a href="tp/cli/options.html">tp.cli.options</a></li>
 <li><a href="tp/data/load.html">tp.data.load</a></li>
 <li><a href="tp/data/resolve.html">tp.data.resolve</a></li>
 <li><a href="tp/data/run.html">tp.data.run</a></li>
 <li><a href="tp/data/save.html">tp.data.save</a></li>
+<li><a href="tp/data/utilities.html">tp.data.utilities</a></li>
 <li><a href="tp/plot/colour.html">tp.plot.colour</a></li>
 <li><a href="tp/plot/frequency.html">tp.plot.frequency</a></li>
 <li><a href="tp/plot/heatmap.html">tp.plot.heatmap</a></li>
 <li><a href="tp/plot/mfp.html">tp.plot.mfp</a></li>
 <li><a href="tp/plot/phonons.html">tp.plot.phonons</a></li>
 <li><a href="tp/plot/utilities.html">tp.plot.utilities</a></li>
 <li><a href="tp/settings.html">tp.settings</a></li>
+<li><a href="tp/setup/vasp.html">tp.setup.vasp</a></li>
 </ul>
 
            </div>

diff --git a/docs/_modules/tp/axes/four.html b/docs/_modules/tp/axes/four.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>tp.axes.four &mdash; ThermoPlotter 1.0.0 documentation</title><link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
+  <title>tp.axes.four &mdash; ThermoPlotter 2.0.0 documentation</title><link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../../../_static/js/html5shiv.min.js"></script>