Update the docs

src/aiida_quantumespresso/calculations/functions/xspectra/get_powder_spectrum.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
-"""CalcFunction to compute the powder spectrum of a set of XANES spectra from `XspectraCalculation`s."""
-
+"""CalcFunction to compute the powder spectrum of a set of XANES spectra from ``XspectraCalculation``."""
 from aiida.common import ValidationError
 from aiida.engine import calcfunction
 from aiida.orm import XyData
@@ -10,10 +9,9 @@
 def get_powder_spectrum(**kwargs): # pylint: disable=too-many-statements
  """Combine the given spectra into a single "Powder" spectrum, representing the XAS of a powder sample.
 
- The function expects between 1 and 3 XyData nodes from `XspectraCalculation`s whose
+ The function expects between 1 and 3 XyData nodes from ``XspectraCalculation`` whose
  polarisation vectors are the basis vectors of the original crystal structure (100, 010, 001).
  """
-
  spectra = [node for node in kwargs.values() if isinstance(node, XyData)]
  vectors = [node.creator.res['xepsilon'] for node in spectra]
 

src/aiida_quantumespresso/calculations/functions/xspectra/merge_spectra.py

@@ -1,22 +1,20 @@
 # -*- coding: utf-8 -*-
-"""CalcFunction to merge multiple XyData nodes of calculated XANES spectra into a new XyData node."""
-
+"""CalcFunction to merge multiple ``XyData`` nodes of calculated XANES spectra into a new ``XyData`` node."""
 from aiida.engine import calcfunction
 from aiida.orm import XyData
 
 
 @calcfunction
 def merge_spectra(**kwargs):
- """Compile all calculated spectra into a single XyData node for easier plotting.
+ """Compile all calculated spectra into a single ``XyData`` node for easier plotting.
 
- The keyword arguments must be an arbitrary number of XyData nodes from
+ The keyword arguments must be an arbitrary number of ``XyData`` nodes from
  the `output_spectra` of `XspectraCalculation`s, all other `kwargs` will be discarded at
  runtime.
 
- Returns a single XyData node where each set of y values is labelled
+ Returns a single ``XyData`` node where each set of y values is labelled
  according to the polarisation vector used for the `XspectraCalculation`.
  """
-
  output_spectra = XyData()
  y_arrays_list = []
  y_units_list = []

src/aiida_quantumespresso/workflows/xspectra/core.py

@@ -26,45 +26,41 @@
 class XspectraCoreWorkChain(ProtocolMixin, WorkChain):
  """Workchain to compute X-ray absorption spectra for a given structure using Quantum ESPRESSO.
 
- The workflow follows the process required to compute the XAS of an input structure:
- an SCF calculation is performed using the provided structure, which is then followed by
- the calculation of the XAS itself by XSpectra. The calculations performed by the WorkChain
- in a typical run will be:
- - PwSCF calculation with pw.x of the input structure with a core-hole present.
- - Generation of core-wavefunction data with upf2plotcore.sh (if requested).
- - XAS calculation with xspectra.x to compute the Lanczos coefficients and print the
- XANES spectra for the polarisation vectors requested in the input.
- - Collation of output data from pw.x and xspectra.x calculations, including a
- combination of XANES dipole spectra based on polarisation vectors to represent the
- powder spectrum of the structure (if requested).
- If ``run_replot = True`` is set in the inputs (defaults to False), the WorkChain will run
- a second xspectra.x calculation which replots the spectra produced from the ``xs_prod``
- step. This option can be very useful for obtaining a final spectrum at low levels of
- broadening (relative to the default of 0.5 eV), particularly as higher levels of
- broadening significantly speed up the convergence of the Lanczos procedure. Inputs for the
- replot calculation are found in the ``xs_plot`` namespace.
-
- The core-wavefunction plot derived from the ground-state of the absorbing element can
- be provided as a top-level input or produced by the WorkChain. If left to the WorkChain,
- the ground-state pseudopotential assigned to the absorbing element will be used to
- generate this data using the upf2plotcore.sh utility script (via the ``aiida-shell``
- plugin).
+ The workflow follows the process required to compute the XAS of an input structure: an SCF calculation is performed
+ using the provided structure, which is then followed by the calculation of the XAS itself by XSpectra. The
+ calculations performed by the WorkChain in a typical run will be:
+
+ - PwSCF calculation with pw.x of the input structure with a core-hole present.
+ - Generation of core-wavefunction data with upf2plotcore.sh (if requested).
+ - XAS calculation with xspectra.x to compute the Lanczos coefficients and print the XANES spectra for the
+ polarisation vectors requested in the input.
+ - Collation of output data from pw.x and xspectra.x calculations, including a combination of XANES dipole spectra
+ based on polarisation vectors to represent the powder spectrum of the structure (if requested).
+
+ If ``run_replot = True`` is set in the inputs (defaults to False), the WorkChain will run a second xspectra.x
+ calculation which replots the spectra produced from the ``xs_prod`` step. This option can be very useful for
+ obtaining a final spectrum at low levels of broadening (relative to the default of 0.5 eV), particularly as higher
+ levels of broadening significantly speed up the convergence of the Lanczos procedure. Inputs for the replot
+ calculation are found in the ``xs_plot`` namespace.
+
+ The core-wavefunction plot derived from the ground-state of the absorbing element can be provided as a top-level
+ input or produced by the WorkChain. If left to the WorkChain, the ground-state pseudopotential assigned to the
+ absorbing element will be used to generate this data using the upf2plotcore.sh utility script (via the
+ ``aiida-shell`` plugin).
 
  In its current stage of development, the workflow requires the following:
- - An input structure where the desired absorbing atom in the system is marked as a
- separate Kind. The default behaviour for the WorkChain is to set the Kind name as
- 'X', however this can be changed via the `overrides` dictionary.
- - A code node for ``upf2plotcore``, configured for the ``aiida-shell`` plugin
- (https://github.com/sphuber/aiida-shell). Alternatively, a ``SinglefileData`` node
- from a previous ``ShellJob`` run can be supplied under ``inputs.core_wfc_data``.
- - A suitable pair of pseudopotentials for the element type of the absorbing atom,
- one for the ground-state occupancy which contains GIPAW informtation for the core
- level of interest for the XAS (e.g. 1s in the case of a K-edge calculation) and
- the other containing a core hole.
- - For the moment this can be passed either via the ``core_hole_pseudos`` field
- in ``get_builder_from_protocol`` or via the overrides, but will be
- changed later once full families of core-hole pseudopotentials become
- available.
+
+ - An input structure where the desired absorbing atom in the system is marked as a separate Kind. The default
+ behaviour for the WorkChain is to set the Kind name as 'X', however this can be changed via the `overrides`
+ dictionary.
+ - A code node for ``upf2plotcore``, configured for the ``aiida-shell`` plugin
+ (https://github.com/sphuber/aiida-shell). Alternatively, a ``SinglefileData`` node from a previous ``ShellJob``
+ run can be supplied under ``inputs.core_wfc_data``.
+ - A suitable pair of pseudopotentials for the element type of the absorbing atom, one for the ground-state occupancy
+ which contains GIPAW informtation for the core level of interest for the XAS (e.g. 1s in the case of a K-edge
+ calculation) and the other containing a core hole. (For the moment this can be passed either via the
+ ``core_hole_pseudos`` field in ``get_builder_from_protocol`` or via the overrides, but will be changed later once
+ full families of core-hole pseudopotentials become available).
  """
 
  # pylint: disable=too-many-public-methods, too-many-statements

tests/workflows/xspectra/test_core.py

@@ -1,21 +1,20 @@
 # -*- coding: utf-8 -*-
 """Tests for the `XspectraCoreWorkChain` class."""
-
 import io
 
 from aiida import engine, orm
 from aiida.common import LinkType
-from aiida.engine.utils import instantiate_process
 from aiida.manage.manager import get_manager
 from plumpy import ProcessState
 import pytest
 
 
 def instantiate_process(cls_or_builder, inputs=None):
  """Instantiate a process, from a ``Process`` class or ``ProcessBuilder`` instance."""
+ from aiida.engine.utils import instantiate_process as _instantiate_process
  manager = get_manager()
  runner = manager.get_runner()
- return instantiate_process(runner, cls_or_builder **{inputs or {})
+ return _instantiate_process(runner, cls_or_builder, **(inputs or {}))
 
 
 @pytest.fixture