Merge pull request #72 from SMTG-Bham/bug-fix

update from JOSS review 1

README.rst

@@ -1,6 +1,6 @@
 .. image:: figures/tp-logo-header.png
     :alt: The ThermoParser logo, which looks like "TP"
-    :target: https://smtg-ucl.github.io/ThermoParser/
+    :target: https://smtg-bham.github.io/ThermoParser/
     :align: center
 
 .. code-block::
@@ -17,9 +17,9 @@
     |____________________________________:_______________________/____________:_____/
 
 
-.. image:: https://app.travis-ci.com/SMTG-UCL/ThermoParser.svg?branch=master
+.. image:: https://travis-ci.com/smtg-bham/ThermoParser.svg?branch=master
     :alt: The travis-ci badge
-    :target: https://app.travis-ci.com/SMTG-UCL/ThermoParser
+    :target: https://travis-ci.com/smtg-bham/ThermoParser
 
 ThermoParser is a toolkit used to simplify the analysis of data
 produced by specialist materials science codes, centred around
@@ -35,9 +35,9 @@ Click on the image to go to the `gallery`_!
 
 .. image:: figures/wideband.png
    :alt: A phonon dispersion where widened bands show phonon scattering
-   :target: https://smtg-ucl.github.io/ThermoParser/gallery.html
+   :target: https://smtg-bham.github.io/ThermoParser/gallery.html
 
-.. _gallery: https://smtg-ucl.github.io/ThermoParser/gallery.html
+.. _gallery: https://smtg-bham.github.io/ThermoParser/gallery.html
 
 Installation
 ------------
@@ -46,7 +46,7 @@ ThermoParser can easily be installed with git and pip:
 
 .. code-block:: bash
 
-    git clone https://github.com/SMTG-UCL/ThermoParser.git
+    git clone https://github.com/smtg-bham/ThermoParser.git
     cd ThermoParser
     pip install .
 
@@ -66,7 +66,7 @@ longer process is required:
 2. ``python3 -m pip install cython numpy``
 3. ``brew info hdf5`` to retrieve the path to your hdf5 install
 4. ``HDF5_DIR=YOUR_HDF5_PATH --no-build-isolation h5py``
-5. ``git clone https://github.com/SMTG-UCL/ThermoParser.git``
+5. ``git clone https://github.com/smtg-bham/ThermoParser.git``
 6. ``cd ThermoParser``
 7. ``pip install --user -e .``
 
@@ -107,8 +107,8 @@ The best way to get a feel for ThermoParser is to see it in action:
 Take a look at our  `examples`_ and `tutorials`_. Currently supported
 codes are:
 
-.. _examples: https://github.com/smtg-ucl/ThermoParser/tree/master/examples
-.. _tutorials: https://smtg-ucl.github.io/ThermoParser/tutorials.html
+.. _examples: https://github.com/smtg-bham/ThermoParser/tree/master/examples
+.. _tutorials: https://smtg-bham.github.io/ThermoParser/tutorials.html
 
 * Phononic properties:
 
@@ -156,10 +156,10 @@ 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/ .``.
 
-.. _issue tracker: https://github.com/smtg-ucl/ThermoParser/issues
+.. _issue tracker: https://github.com/smtg-bham/ThermoParser/issues
 .. _fork and pull: https://guides.github.com/activities/forking
-.. _documentation: https://smtg-ucl.github.io/ThermoParser/
-.. _tests: https://github.com/smtg-ucl/ThermoParser/tree/master/tests
+.. _documentation: https://smtg-bham.github.io/ThermoParser/
+.. _tests: https://github.com/smtg-bham/ThermoParser/tree/master/tests
 
 Testing
 -------

citation.cff

@@ -16,4 +16,4 @@ authors:
 title: "ThermoParser: Streamlined Analysis of Thermoelectric Properties"
 version: 3.0.0
 date-released: 2023-08-16
-url: "https://github.com/SMTG-UCL/ThermoParser"
+url: "https://github.com/smtg-bham/ThermoParser"

examples/01-python-foundations/README.rst

@@ -88,10 +88,10 @@ ThermoParser has extensive docs. Docstrings are available throughout
 the code itself, if you are using IPython or Jupyter and you can access
 them by typing the command name followed by two question marks, and
 IDEs normally have options too. If you are on the master branch,
-they can also be found `here <https://smtg-ucl.github.io/ThermoParser/>`_.
+they can also be found `here <https://smtg-bham.github.io/ThermoParser/>`_.
 
-.. _Tutorial-03: https://smtg-ucl.github.io/ThermoParser/tutorial-03.html
-.. _Tutorial-05: https://smtg-ucl.github.io/ThermoParser/tutorial-05.html
-.. _Axes: https://smtg-ucl.github.io/ThermoParser/tp.axes.html
-.. _Load: https://smtg-ucl.github.io/ThermoParser/tp.data.html#module-tp.data.load
-.. _Plot: https://smtg-ucl.github.io/ThermoParser/tp.plot.html
+.. _Tutorial-03: https://smtg-bham.github.io/ThermoParser/tutorial-03.html
+.. _Tutorial-05: https://smtg-bham.github.io/ThermoParser/tutorial-05.html
+.. _Axes: https://smtg-bham.github.io/ThermoParser/tp.axes.html
+.. _Load: https://smtg-bham.github.io/ThermoParser/tp.data.html#module-tp.data.load
+.. _Plot: https://smtg-bham.github.io/ThermoParser/tp.plot.html

examples/02-individual-customisation/README.rst

@@ -77,5 +77,5 @@ midpoint you specify, and ``uniform`` calculates the midpoint position
 based on the relative compositions of the colours, which is used for
 heatmaps.
 
-.. _Tutorial-01: https://smtg-ucl.github.io/ThermoParser/tutorial-01.html
-.. _colourmap generators: https://smtg-ucl.github.io/ThermoParser/tp.plot.html#module-tp.plot.colour
+.. _Tutorial-01: https://smtg-bham.github.io/ThermoParser/tutorial-01.html
+.. _colourmap generators: https://smtg-bham.github.io/ThermoParser/tp.plot.html#module-tp.plot.colour

examples/02-individual-customisation/tutorial-02.py

@@ -13,7 +13,7 @@
 # You can ignore down to line 20!
 from os import path
 if not path.isfile(kfile) or (path.getsize(kfile) < 1024*1024*100):
-    raise Exception('File not found, please use get-data.sh')
+    raise Exception('File not found, please use get-data.sh in the folder above.')
 # Stop ignoring!
 
 # Axes

examples/03-compound-axes/README.rst

@@ -65,4 +65,4 @@ and ``labels`` arguments, so in order to specify your own, you must set
 ``tp.axes.legend.consolidate`` may also be useful for non-ThermoParser
 endaevors, as will be discussed in `Tutorial-05`_.
 
-.. _Tutorial-05: https://smtg-ucl.github.io/ThermoParser/tutorial-05.html
+.. _Tutorial-05: https://smtg-bham.github.io/ThermoParser/tutorial-05.html

examples/04-layered-plots/README.rst

@@ -70,4 +70,4 @@ which removes the ticks and tick labels and the y axis label, while all
 the default labels can be accessed with ``settings.labels``. These will
 be covered more in `Tutorial-05`_.
 
-.. _Tutorial-05: https://smtg-ucl.github.io/ThermoParser/tutorial-05.html
+.. _Tutorial-05: https://smtg-bham.github.io/ThermoParser/tutorial-05.html

examples/04-layered-plots/tutorial-04.py

@@ -1,55 +1,55 @@
-#!/usr/bin/env python3
-
-import tp
-
-scs = '222 333 444 555'.split()
-pfiles = ['../data/basno3/band-{}.yaml'.format(s) for s in scs]
-kfile = '../data/basno3/kappa-m363636.hdf5'
-dfile = '../data/basno3/projected_dos.dat'
-poscar = '../data/basno3/POSCAR'
-
-direction = 'avg'
-temperature = 300
-waterfall = 'mean_free_path'
-quantities = ['waterfall', waterfall]
-
-colour = 'winter_r'
-colours = {'Ba': '#ffcf06',
-           'Sn': '#59c605',
-           'O':  '#00b1f7'}
-cmap = 'viridis'
-
-# You can ignore down to line 23!
-from os import path
-if not path.isfile(kfile) or (path.getsize(kfile) < 1024*1024*100):
-    raise Exception('File not found, please use get-data.sh')
-# Stop ignoring!
-
-# Axes
-fig, ax, add_legend = tp.axes.small.two_h()
-
-# Load
-dispersions = [tp.data.load.phonopy_dispersion(f) for f in pfiles]
-kappa = tp.data.load.phono3py(kfile, quantities=quantities)
-dos = tp.data.load.phonopy_dos(dfile, poscar=poscar)
-
-# Plot
-tp.plot.phonons.add_multi(ax[0], dispersions, colour=colour, label=scs)
-tp.plot.frequency.format_waterfall(ax[1], kappa, waterfall, direction=direction,
-                                   temperature=temperature, invert=True)
-tp.plot.frequency.add_dos(ax[1], dos, colour=colours, scale=True, main=False,
-                          alpha=0.6, line=False, invert=True)
-tp.plot.frequency.add_waterfall(ax[1], kappa, waterfall, colour=cmap,
-                                direction=direction, temperature=temperature,
-                                invert=True)
-
-# Formatting
-
-tp.plot.utilities.set_locators(ax[1], x='log', y='linear')
-axlabels = tp.settings.labels()
-ax[1].set_xlabel(axlabels['mean_free_path'])
-ax[1].set_ylabel(axlabels['frequency'])
-add_legend()
-
-# Save
-fig.savefig('tutorial-04.png')
+#!/usr/bin/env python3
+
+import tp
+
+scs = '222 333 444 555'.split()
+pfiles = ['../data/basno3/band-{}.yaml'.format(s) for s in scs]
+kfile = '../data/basno3/kappa-m363636.hdf5'
+dfile = '../data/basno3/projected_dos.dat'
+poscar = '../data/basno3/POSCAR'
+
+direction = 'avg'
+temperature = 300
+waterfall = 'mean_free_path'
+quantities = ['waterfall', waterfall]
+
+colour = 'winter_r'
+colours = {'Ba': '#ffcf06',
+           'Sn': '#59c605',
+           'O':  '#00b1f7'}
+cmap = 'viridis'
+
+# You can ignore down to line 23!
+from os import path
+if not path.isfile(kfile) or (path.getsize(kfile) < 1024*1024*100):
+    raise Exception('File not found, please use get-data.sh in the folder above.')
+# Stop ignoring!
+
+# Axes
+fig, ax, add_legend = tp.axes.small.two_h()
+
+# Load
+dispersions = [tp.data.load.phonopy_dispersion(f) for f in pfiles]
+kappa = tp.data.load.phono3py(kfile, quantities=quantities)
+dos = tp.data.load.phonopy_dos(dfile, poscar=poscar)
+
+# Plot
+tp.plot.phonons.add_multi(ax[0], dispersions, colour=colour, label=scs)
+tp.plot.frequency.format_waterfall(ax[1], kappa, waterfall, direction=direction,
+                                   temperature=temperature, invert=True)
+tp.plot.frequency.add_dos(ax[1], dos, colour=colours, scale=True, main=False,
+                          alpha=0.6, line=False, invert=True)
+tp.plot.frequency.add_waterfall(ax[1], kappa, waterfall, colour=cmap,
+                                direction=direction, temperature=temperature,
+                                invert=True)
+
+# Formatting
+
+tp.plot.utilities.set_locators(ax[1], x='log', y='linear')
+axlabels = tp.settings.labels()
+ax[1].set_xlabel(axlabels['mean_free_path'])
+ax[1].set_ylabel(axlabels['frequency'])
+add_legend()
+
+# Save
+fig.savefig('tutorial-04.png')

examples/05-helper-functions/tutorial-05.py

@@ -1,57 +1,57 @@
-#!/usr/bin/env python3
-
-import tp
-from matplotlib.gridspec import GridSpec
-import matplotlib.pyplot as plt
-
-afile = '../data/basno3/transport_75x75x75.json'
-kfile = '../data/basno3/kappa-m363636.hdf5'
-
-doping = [-1e18, -1e19, -1e20, -1e21]
-direction = 'avg'
-quantities = ['conductivity', 'seebeck']
-scale = ['log', 'linear', 'linear']
-
-from os import path
-if not path.isfile(kfile) or (path.getsize(kfile) < 1024*1024*100):
-    raise Exception('File not found, please use get-data.sh')
-
-# Axes
-plt.style.use('tp')
-fig = plt.figure(figsize=(27/2.54, 8.3/2.54))
-grid = GridSpec(1, 14)
-ax = [fig.add_subplot(grid[0, :4]),
-      fig.add_subplot(grid[0, 5:9]),
-      fig.add_subplot(grid[0, 10:])]
-plt.subplots_adjust(left=0.06, right=0.98,
-                    bottom=0.12, top=0.95)
-
-# Load
-adata = tp.data.load.amset(afile)
-kdata = tp.data.load.phono3py(kfile)
-
-# Plot
-for i, q in enumerate(quantities):
-    for d in doping:
-        data = tp.data.utilities.resolve(adata, q, direction=direction, doping=d)
-        ax[i].plot(data['temperature'], data[q],
-                   label="{:.2e}".format(data['meta']['doping']))
-
-q = 'lattice_thermal_conductivity'
-data = tp.data.utilities.resolve(kdata, q, direction=direction)
-ax[2].plot(data['temperature'], data[q])
-
-# Formatting
-axlabels = tp.settings.labels()
-for i, q in enumerate([*quantities, q]):
-    ax[i].set_xlabel(axlabels['temperature'])
-    ax[i].set_ylabel(axlabels[q])
-    tp.plot.utilities.set_locators(ax[i], x='linear', y=scale[i])
-
-handles, labels = tp.axes.legend.consolidate(ax)
-ax[2].legend(loc='best', title=axlabels['doping'], handles=handles,
-             labels=labels)
-tp.axes.legend.alphabetise(ax, preset='roman', suffix=')', x=-0.12)
-
-# Save
-fig.savefig('tutorial-05.png')
+#!/usr/bin/env python3
+
+import tp
+from matplotlib.gridspec import GridSpec
+import matplotlib.pyplot as plt
+
+afile = '../data/basno3/transport_75x75x75.json'
+kfile = '../data/basno3/kappa-m363636.hdf5'
+
+doping = [-1e18, -1e19, -1e20, -1e21]
+direction = 'avg'
+quantities = ['conductivity', 'seebeck']
+scale = ['log', 'linear', 'linear']
+
+from os import path
+if not path.isfile(kfile) or (path.getsize(kfile) < 1024*1024*100):
+    raise Exception('File not found, please use get-data.sh in the folder above.')
+
+# Axes
+plt.style.use('tp')
+fig = plt.figure(figsize=(27/2.54, 8.3/2.54))
+grid = GridSpec(1, 14)
+ax = [fig.add_subplot(grid[0, :4]),
+      fig.add_subplot(grid[0, 5:9]),
+      fig.add_subplot(grid[0, 10:])]
+plt.subplots_adjust(left=0.06, right=0.98,
+                    bottom=0.12, top=0.95)
+
+# Load
+adata = tp.data.load.amset(afile)
+kdata = tp.data.load.phono3py(kfile)
+
+# Plot
+for i, q in enumerate(quantities):
+    for d in doping:
+        data = tp.data.utilities.resolve(adata, q, direction=direction, doping=d)
+        ax[i].plot(data['temperature'], data[q],
+                   label="{:.2e}".format(data['meta']['doping']))
+
+q = 'lattice_thermal_conductivity'
+data = tp.data.utilities.resolve(kdata, q, direction=direction)
+ax[2].plot(data['temperature'], data[q])
+
+# Formatting
+axlabels = tp.settings.labels()
+for i, q in enumerate([*quantities, q]):
+    ax[i].set_xlabel(axlabels['temperature'])
+    ax[i].set_ylabel(axlabels[q])
+    tp.plot.utilities.set_locators(ax[i], x='linear', y=scale[i])
+
+handles, labels = tp.axes.legend.consolidate(ax)
+ax[2].legend(loc='best', title=axlabels['doping'], handles=handles,
+             labels=labels)
+tp.axes.legend.alphabetise(ax, preset='roman', suffix=')', x=-0.12)
+
+# Save
+fig.savefig('tutorial-05.png')

examples/06-package-customisation/README.rst

@@ -33,7 +33,7 @@ dictionaries like the locators. The aliases are listed as:
 
 If you add unit conversions, remember to update the units and labels
 too! An example has been provided for converting from
-S m\ :sup:`-1` to S cm\ :sup:`-1` `here <https://github.com/SMTG-UCL/ThermoParser/blob/master/examples/06-package-customisation/tprc.yaml>`_.
+S m\ :sup:`-1` to S cm\ :sup:`-1` `here <https://github.com/smtg-bham/ThermoParser/blob/master/examples/06-package-customisation/tprc.yaml>`_.
 There are six labels dictionaries. ``long_``, ``medium_`` and
 ``short_labels`` contain the actual labels of those lengths, while
 ``labels``, ``inverted_labels`` and ``large_labels`` point to which of