Updated documentation

Numpydoc seems to fail if references are being used. Removed now, but we need to fix this in the future. Consider to not use LaTeX and render html maths and make a pdf instead as this is really sensitive to get to work.

docs/conf.py

@@ -150,7 +150,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = []
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

src/t4me/bandstructure.py

@@ -904,13 +904,12 @@ def fetch_velocities_along_line(self,
  The :func:`interpolate` is used to perform the interpolation
  of the data along the line.
 
+ .. warning:: The factor :math:`\\hbar^{-1}` is not returned and need to be included externally.
+
  See Also
  --------
  interpolate
 
- .. warning:: The factor : math: `\\hbar^{-1}` is not returned
- and need to be included externally.
-
  """
  # set logger
  logger = logging.getLogger(sys._getframe().f_code.co_name) # pylint: disable=protected-access
@@ -976,13 +975,12 @@ def fetch_velocities_at_kpoints(self,
  -----
  The :func:`interpolate` is used to perform the interpolation.
 
+ .. warning:: The factor :math:`\\hbar^{-1}` is not returned and need to be included externally.
+
  See Also
  --------
  interpolate
 
- .. warning:: The factor : math: `\\hbar^{-1}` is not returned
- and need to be included externally.
-
  """
  # set logger
  logger = logging.getLogger(sys._getframe().f_code.co_name) # pylint: disable=protected-access
@@ -1408,15 +1406,18 @@ def interpolate( # pylint: disable=too-many-locals # noqa: MC0001
  if `velocities` is not supplied or `gen_velocities` is
  set to False.
 
+
+ Notes
+ -----
+ .. todo:: DOCUMENT THE DIFFERENT INTERPOLATION SCHEMES,
+ OR AT LEAST ADD PROPER REFERENCES.
+
  See Also
  --------
  linearnd
  interpn
  rbf
 
- .. todo:: DOCUMENT THE DIFFERENT INTERPOLATION SCHEMES,
- OR AT LEAST ADD PROPER REFERENCES.
-
  """
 
  # set logger
@@ -3039,8 +3040,7 @@ def non_parabolic_velocity_2(k, effmass, a):
  -----
  Consult comments in :func:`non_parabolic_energy_1`
 
- .. warning:: The factor :math:`\\hbar^{-1}` is not returned
- and need to be included externally.
+ .. warning:: The factor :math:`\\hbar^{-1}` is not returned and need to be included externally.
 
  """
 

src/t4me/lattice.py

@@ -825,14 +825,7 @@ def create_kmesh( # pylint: disable=too-many-locals # noqa: MC0001
 
  Notes
  -----
- This routines use spglib, an excellent tool written by A. Togo
- : cite: `spglib`
-
- .. rubric: : References
-
- .. bibliography: : references.bib
- : style: unsrt
- : filter: docname in docnames
+ This routines use spglib, an excellent tool written by A. Togo.
 
  """
 

src/t4me/lbtecoeff.py

@@ -96,7 +96,7 @@ def parabolice(tr, eta, temperature, bs, tau0, method):
 
 def parabolic_closed(tr, eta, bs, tau0_t, temperature): # pylint: disable=too-many-locals
  r"""
- Calculates the parabolic and parabolic Fermi integrals for the transport coefficients.
+ Calculates the parabolic Fermi integrals for the transport coefficients.
 
  Parameters
  ----------
@@ -176,9 +176,9 @@ def parabolic_closed(tr, eta, bs, tau0_t, temperature): # pylint: disable=too-m
 
  See Also
  --------
- setup_scattering()
- find_r_from_tau0()
- parabolic_numeric()
+ setup_scattering
+ find_r_from_tau0
+ parabolic_numeric
 
  """
 
@@ -427,12 +427,6 @@ def parabolic_numeric(tr, eta, bs, tau0_t, temperature): # pylint: disable=too-
  .. todo:: ADD POSIBILITY TO USE DIFFERENT EFFECTIVE MASSES ALONG
  DIFFERENT DIRECTIONS
 
- .. rubric:: References
-
- .. bibliography:: references.bib
- :style: unsrt
- :filter: docname in docnames
-
  """
  # set logger
  logger = logging.getLogger(sys._getframe().f_code.co_name) # pylint: disable=protected-access

src/t4me/scattering.py

@@ -109,10 +109,7 @@ def scattering_dos(tr, dos, energies, select_scattering): # pylint: disable=too
 
  Only the acoustic phonon scattering has been tested.
 
- Please consult the book of C. Jacoboni :cite:`jacoboni_2010_toetis` and the
- publication concerning this software by
- E. Flage-Larsen :cite:`t4me` for additional details
- on the involved parameters. Also consult the bandstructure
+ Consult the bandstructure
  configuration file for the respective constants that have to
  be set besides `select_scattering` and their units.
 
@@ -477,22 +474,13 @@ def scattering_parabolic(tr, energies, select_scattering, use_eonk=False): # py
  12 Constant (energy and k-point independent)
  ========================= ====================
 
- Please consult the book of C. Jacoboni :cite:`jacoboni_2010_toetis` and the
- publication concerning this software by
- E. Flage-Larsen :cite:`t4me` for additional details
- on the involved parameters. Also consult the bandstructure
+ Also consult the bandstructure
  configuration file for the respective constants that have to
  be set besides `select_scattering` and their units.
 
  .. todo:: Add more extensive documentation for the different scattering
  mechanisms.
 
- .. rubric:: References
-
- .. bibliography:: references.bib
- :style: unsrt
- :filter: docname in docnames
-
  """
  # set logger
  logger = logging.getLogger(sys._getframe().f_code.co_name) # pylint: disable=protected-access

tests/fixtures.py

@@ -50,8 +50,9 @@ def may_data():
  data : ndarray
  | Dimension: (11,5)
 
- Contains the data from Table 11.1 in
- Ref.:cite:`rowe_2012_mpacit_may`. With 11 entries
+ Contains the data from Table 11.1 in Andrew F. May and G. Jeffrey Snyder, 
+ Introduction to Modelling Thermoelectric Transport at High Temperature, 
+ Taylor \& Francis Inc, 2012, Chapter 11. With 11 entries
  of different unitless chemical potentials (first index
  of the second axis). The remaining 4 indexes of the
  second axis contains the Seebeck coefficient, Lorenz
@@ -68,7 +69,7 @@ def may_data():
  Fermi-Dirac integrals. The data given by may is converted to
  a conduction band and thus the Seebeck should be
  negative. Otherwise the values entered should be precicely the
- same as in Ref.:cite:`rowe_2012_mpacit_may`.
+ same as in the reference given above.
 
  """
  data = np.zeros((11, 5))