Merge pull request #70 from SMTG-Bham/develop

Develop

README.rst

@@ -17,9 +17,9 @@
     |____________________________________:_______________________/____________:_____/
 
 
-.. image:: https://app.travis-ci.com/SMTG-UCL/ThermoParser.svg?branch=master
+.. image:: https://app.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://app.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
@@ -37,7 +37,7 @@ Click on the image to go to the `gallery`_!
    :alt: A phonon dispersion where widened bands show phonon scattering
    :target: https://smtg-ucl.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
 -------

tests/test_data/test_load.py

@@ -132,6 +132,8 @@ def test_spin(self):
             f['ir_kpoints']                       = [[1, 2, 3]]
             f['scattering_rates_up'][0,0,1,0,0]   = 1
             f['scattering_rates_down'][0,0,1,0,0] = 3
+            f['energies_up']                      = np.zeros((1, 2, 2, 3, 1))
+            f['energies_down']                    = np.zeros((1, 2, 2, 3, 1))
 
         data = load.amset_mesh('test.hdf5', 'scattering_rates', spin='avg')
         for q2 in ['scattering_rates', 'temperature', 'doping', 'meta']:
@@ -378,4 +380,4 @@ def test_default(self, mock_load, mock_poscar):
 
         data2 = load.phonopy_dos('mock')
         mock_load.assert_called_once()
-        mock_poscar.assert_called_once()
+        mock_poscar.assert_called_once()

tp/cli/cli.py

@@ -159,7 +159,7 @@ def get():
               show_default=True)
 @click.option('-s', '--scattering',
               help='Scattering mechanism.',
-              type=click.Choice(['ADP', 'IMP', 'PIE', 'POP', 'total'],
+              type=click.Choice(['ADP', 'IMP', 'PIE', 'POP', 'Total'],
                                 case_sensitive=False),
               default='total',
               show_default=True)
@@ -272,7 +272,7 @@ def get_amset(amset_file, quantity, dtype, doping, direction, temperature, spin,
 @get.command('occupation')
 @inputs_function('amset_mesh_file', nargs=1)
 @doping_type_option
-@doping_option
+@doping_function()
 @temperature_option
 @click.option('--spin',
               help='Spin direction.',

tp/data/load.py

@@ -326,6 +326,8 @@ def resolve_spin(data, q, spin):
                 spin2 = 'up'
             elif 'energies_down' in f:
                 spin2 = 'down'
+        else:
+            spin2 = spin
 
         data = {'meta': {'doping_type':       doping,
                          'electronic_source': 'amset',