Cleanup

abipy/abio/inputs.py

@@ -761,8 +761,8 @@ def set_kptgw(self, kptgw, bdgw):
         Args
             kptgw: List of k-points in reduced coordinates.
             bdgw: Specifies the range of bands for the GW corrections.
-              Accepts iterable that be reshaped to (nkptgw, 2)
-              or a tuple of two integers if the extrema are the same for each k-point.
+                Accepts iterable that be reshaped to (nkptgw, 2)
+                or a tuple of two integers if the extrema are the same for each k-point.
         """
         kptgw = np.reshape(kptgw, (-1,3))
         nkptgw = len(kptgw)
@@ -2704,29 +2704,6 @@ class OpticError(Exception):
 class OpticInput(AbstractInput, MSONable):
     """
     Input file for optic executable
-
-    Example:
-        &FILES
-         ddkfile_1 = 'abo_1WF7',
-         ddkfile_2 = 'abo_1WF8',
-         ddkfile_3 = 'abo_1WF9',
-         wfkfile = 'abo_WFK'
-        /
-        &PARAMETERS
-         broadening = 0.002,
-         domega = 0.0003,
-         maxomega = 0.3,
-         scissor = 0.000,
-         tolerance = 0.002
-        /
-        &COMPUTATIONS
-         num_lin_comp = 1,
-         lin_comp = 11,
-         num_nonlin_comp = 2,
-         nonlin_comp = 123,222,
-         num_linel_comp = 0,
-         num_nonlin2_comp = 0,
-        /
     """
     Error = OpticError
 

abipy/core/mesh3d.py

@@ -316,7 +316,7 @@ def gvecs(self):
 
     @lazy_property
     def gmods(self):
-        """[ng] array with |G|"""
+        """[ng] array with $|G|$"""
         gmet = np.dot(self.inv_vectors.T, self.inv_vectors)
         gmods = np.empty(self.size)
         for i, g in enumerate(self.gvecs):

abipy/core/skw.py

@@ -572,7 +572,7 @@ def plot_dos_vs_kmeshes(self, kmeshes, is_shift=None, method="gaussian", step=0.
             method: String defining the method for the computation of the DOS.
             step: Energy step (eV) of the linear mesh.
             width: Standard deviation (eV) of the gaussian.
-            ax: matplotlib :class:`Axes` or None if a new figure should be created.
+            ax: matplotlib `Axes` or None if a new figure should be created.
 
         Returns:
             matplotlib figure.

abipy/core/structure.py

@@ -429,9 +429,10 @@ def rocksalt(cls, a, species, **kwargs):
             species: Chemical species. See __init__ method of :class:`pymatgen.Structure`
             kwargs: All keyword arguments accepted by :class:`pymatgen.Structure`
 
-        Example::
+        .. Example::
 
             Structure.rocksalt(a, ["Na", "Cl"])
+
         """
         lattice = 0.5 * float(a) * np.array([
             0,  1,  1,
@@ -462,7 +463,7 @@ def from_abivars(cls, *args, **kwargs):
         """
         Build a :class:`Structure` object from a dictionary with ABINIT variables.
 
-        Example::
+        .. Example::
 
             al_structure = Structure.from_abivars(
                 acell=3*[7.5],
@@ -697,10 +698,11 @@ def spget_equivalent_atoms(self, symprec=1e-3, angle_tolerance=5, printout=False
             eqmap: Mapping irred atom position --> list with positions of symmetrical atoms
             spgdata: spglib dataset with additional data reported by spglib.
 
-        Example::
+        .. Example::
 
             for irr_pos in irred_pos:
                 eqmap[irr_pos]   # List of symmetrical positions associated to the irr_pos atom.
+
         """
         spgan = SpacegroupAnalyzer(self, symprec=symprec, angle_tolerance=angle_tolerance)
         spgdata = spgan.get_symmetry_dataset()
@@ -1735,13 +1737,14 @@ def dataframes_from_structures(struct_objects, index=None, with_spglib=True, car
             `coords` the atomic positions.
         The list of structures is available in the `structures` entry.
 
-    Example::
+    .. Example::
 
         dfs = dataframes_from_structures(files)
         dfs.lattice
         dfs.coords
         for structure in dfs.structures:
             print(structure)
+
     """
     structures = [Structure.as_structure(obj) for obj in struct_objects]
     # Build Frame with lattice parameters.

abipy/dfpt/ddb.py

@@ -503,7 +503,6 @@ def anacompare_phdos(self, nqsmalls, asr=2, chneut=1, dipdip=1, dos_method="tetr
 
         Return:
             `namedtuple` with the following attributes:
-
                 phdoses: List of :class:`PhononDos` objects
                 plotter: :class:`PhononDosPlotter` object. Client code can use `plotter.gridplot()`
                     to visualize the results.

abipy/dfpt/gruneisen.py

@@ -149,7 +149,7 @@ def plot_doses(self, xlims=None, dos_names="all", with_idos=True, **kwargs):
             xlims: Set the data limits for the x-axis in eV. Accept tuple e.g. `(left, right)`
                 or scalar e.g. `left`. If left (right) is None, default values are used
             dos_names: List of strings defining the DOSes to plot. Use `all` to plot all DOSes available.
-            with_idos: True to display integrated doses
+            with_idos: True to display integrated doses.
 
         Returns:
             matplotlib figure.

abipy/dfpt/phonons.py

@@ -880,7 +880,7 @@ def plot(self, ax=None, units="eV", qlabels=None, branch_range=None, match_bands
             units: Units for phonon plots. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz").
                 Case-insensitive.
             qlabels: dictionary whose keys are tuples with the reduced coordinates of the q-points.
-                The values are the labels. e.g. qlabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}.
+                The values are the labels. e.g. ``qlabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}``.
             branch_range: Tuple specifying the minimum and maximum branch index to plot (default: all branches are plotted).
             match_bands: if True the bands will be matched based on the scalar product between the eigenvectors.
 
@@ -951,7 +951,7 @@ def plot_colored_matched(self, ax=None, units="eV", qlabels=None, branch_range=N
             ax: matplotlib :class:`Axes` or None if a new figure should be created.
             units: Units for phonon plots. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz"). Case-insensitive.
             qlabels: dictionary whose keys are tuples with the reduced coordinates of the q-points.
-                The values are the labels. e.g. qlabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}
+                The values are the labels. e.g. ``qlabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}``
             branch_range: Tuple specifying the minimum and maximum branch_i index to plot (default: all branches are plotted).
             colormap: matplotlib colormap to determine the colors available. The colors will be chosen not in a
                 sequential order to avoid difficulties in distinguishing the lines.
@@ -1203,7 +1203,7 @@ def plot_fatbands(self, units="eV", colormap="jet", phdos_file=None,
             ylims: Set the data limits for the y-axis. Accept tuple e.g. `(left, right)`
                    or scalar e.g. `left`. If left (right) is None, default values are used
             qlabels: dictionary whose keys are tuples with the reduced coordinates of the q-points.
-                The values are the labels. e.g. qlabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}.
+                The values are the labels. e.g. ``qlabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}``.
 
         Returns:
             `matplotlib` figure.
@@ -1320,7 +1320,7 @@ def plot_with_phdos(self, phdos, units="eV", qlabels=None, axlist=None, **kwargs
             phdos: An instance of :class:`PhononDos` or netcdf file providing a PhononDos object.
             units: Units for phonon plots. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz"). Case-insensitive.
             qlabels: dictionary whose keys are tuples with the reduced coordinates of the q-points.
-                The values are the labels e.g. qlabels = {(0.0,0.0,0.0):"$\Gamma$", (0.5,0,0):"L"}.
+                The values are the labels e.g. ``qlabels = {(0.0,0.0,0.0):"$\Gamma$", (0.5,0,0):"L"}``.
             axlist: The axes for the bandstructure plot and the DOS plot. If axlist is None, a new figure
                 is created and the two axes are automatically generated.
 
@@ -1436,7 +1436,7 @@ def to_pymatgen(self, qlabels=None):
 
         Args:
             qlabels: dictionary whose keys are tuples with the reduced coordinates of the q-points.
-                The values are the labels e.g. qlabels = {(0.0,0.0,0.0):"$\Gamma$", (0.5,0,0):"L"}.
+                The values are the labels e.g. ``qlabels = {(0.0,0.0,0.0):"$\Gamma$", (0.5,0,0):"L"}``.
                 If None labels will be determined automatically.
         """
         # pymatgen labels dict is inverted
@@ -2291,12 +2291,10 @@ def phbands_gridplot(phb_objects, titles=None, phdos_objects=None, phdos_kwargs=
         phb_objects: List of objects from which the phonon band structures are extracted.
             Each item in phb_objects is either a string with the path of the netcdf file,
             or one of the abipy object with an `phbands` attribute or a :class:`PhononBands` object.
-        phdos_objects:
-            List of objects from which the phonon DOSes are extracted.
+        phdos_objects: List of objects from which the phonon DOSes are extracted.
             Accept filepaths or :class:`PhononDos` objects. If phdos_objects is not None,
             each subplot in the grid contains a band structure with DOS else a simple bandstructure plot.
-        titles:
-            List of strings with the titles to be added to the subplots.
+        titles: List of strings with the titles to be added to the subplots.
         phdos_kwargs: optional dictionary with the options passed to `get_phdos` to compute the phonon DOS.
             Used only if `phdos_objects` is not None.
         units: Units for phonon plots. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz"). Case-insensitive.
@@ -2555,7 +2553,7 @@ def combiplot(self, qlabels=None, units='eV', ylims=None, **kwargs):
         Args:
             units: Units for phonon plots. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz"). Case-insensitive.
             qlabels: dictionary whose keys are tuples with the reduced coordinates of the k-points.
-                The values are the labels e.g. klabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}.
+                The values are the labels e.g. ``klabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}``.
             ylims: Set the data limits for the y-axis. Accept tuple e.g. `(left, right)`
                    or scalar e.g. `left`. If left (right) is None, default values are used
 

abipy/dynamics/hist.py

@@ -104,7 +104,7 @@ def etotals(self):
 
     def get_relaxation_analyzer(self):
         """
-        Return a pymatgen :class:`RelaxationAnalyzer object to analyze the relaxation in a calculation.
+        Return a pymatgen :class:`RelaxationAnalyzer` object to analyze the relaxation in a calculation.
         """
         from pymatgen.analysis.structure_analyzer import RelaxationAnalyzer
         return RelaxationAnalyzer(self.initial_structure, self.final_structure)

abipy/electrons/bse.py

@@ -101,7 +101,7 @@ def plot(self, ax=None, *args, **kwargs):
         Plot all the components of the tensor
 
         Args:
-            ax: matplotlib :class:`Axes` or None if a new figure should be created.
+            ax: matplotlib `Axes` or None if a new figure should be created.
 
         ==============  ==============================================================
         kwargs          Meaning
@@ -249,7 +249,7 @@ def plot(self, ax=None, **kwargs):
         Plot the MDF.
 
         Args:
-            ax: matplotlib :class:`Axes` or None if a new figure should be created.
+            ax: matplotlib `Axes` or None if a new figure should be created.
 
         ==============  ==============================================================
         kwargs          Meaning
@@ -576,7 +576,7 @@ def plot(self, ax=None, cplx_mode="Im", qpoint=None, xlims=None, ylims=None, **k
         Get a matplotlib plot showing the MDFs.
 
         Args:
-            ax: matplotlib :class:`Axes` or None if a new figure should be created.
+            ax: matplotlib `Axes` or None if a new figure should be created.
             cplx_mode: string defining the data to print (case-insensitive).
                 Possible choices are `re` for the real part, `im` for imaginary part only. `abs` for the absolute value.
                 Options can be concated with "-".
@@ -808,7 +808,7 @@ def plot_mdftype_cplx(self, mdf_type, cplx_mode, qpoint=None, ax=None,
         Helper function to plot data corresponds to `mdf_type`, `cplx_mode`, `qpoint`.
 
         Args:
-            ax: matplotlib :class:`Axes` or None if a new figure should be created.
+            ax: matplotlib `Axes` or None if a new figure should be created.
             mdf_type:
             cplx_mode: string defining the data to print (case-insensitive).
                 Possible choices are `re` for the real part, `im` for imaginary part only. `abs` for the absolute value.

abipy/examples/plot/plot_optic.py

@@ -29,7 +29,7 @@
 # Remember to close the file.
 ncfile.close()
 
-# Use OpticRobot to analyze multiple file e.g convergence studies.
+# Use OpticRobot to analyze multiple file e.g. convergence studies.
 filenames = [
     abidata.ref_file("gaas_444_OPTIC.nc"),
     abidata.ref_file("gaas_888_OPTIC.nc"),

abipy/examples/plot/plot_qpbands_with_interpolation.py

@@ -58,7 +58,7 @@
 plotter.combiplot(title="Combiplot")
 plotter.boxplot(swarm=True, title="Boxplot")
 plotter.combiboxplot(swarm=True, title="Combiboxplot")
-# sphinx_gallery_thumbnail_number = 6
+# sphinx_gallery_thumbnail_number = 4
 plotter.gridplot(title="Gridplot")
 
 sigres.close()

abipy/examples/plot/plot_scr_matrix.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 r"""
-SCF matrix
+SCR matrix
 ==========
 
-This examples shows how to plot the matrix elements of the 
+This examples shows how to plot the matrix elements of the
 inverse dielectric function stored in the SCR file (optdriver 3)
 See also `plot_scr.py` for the optical spectrum.
 """

docs/README.rst → docs/README.md

@@ -1,5 +1,4 @@
-AbiPy documentation
-===================
+## AbiPy documentation
 
 This is the top level build directory for the AbiPy documentation.  
 All of the documentation is written using sphinx, a python documentation system built on top of ReST.  
@@ -23,10 +22,14 @@ This directory contains:
 
   * _templates - used by the sphinx build system
 
-To build the HTML documentation, install sphinx  then type "make html" that will execute::
+To build the HTML documentation, install sphinx then type `make html` that will execute::
 
   sphinx-build -b html -d _build/doctrees . _build/html
 
 The documentation is produced in `_build/html`.
 
 You can run ``make help`` to see information on all possible make targets.
+
+To deploy to gh-pages::
+
+   ghp-import _build/html/ -n -p

docs/api/display_api.rst

@@ -1,9 +1,8 @@
 display Package
 ===============
 
-
 :mod:`display` Module
-=====================
+---------------------
 
 .. automodule:: abipy.display
    :members: