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Ignore deprecation warnings issued by pmg if py2.7

This commit is contained in:
Matteo Giantomassi 2017-10-28 00:08:36 +02:00
parent ebbf4a9c44
commit 8f7a36e6f7
7 changed files with 67 additions and 33 deletions
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7
abipy/abio/robots.py
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@ -428,12 +428,15 @@ class Robot(object):
Return list of (label, ncfile, param) tuples where param is obtained via `func_or_string`.
Args:
func_or_string: Either string or callable defining the quantity to be used for sorting.
func_or_string: Either None, string, callable defining the quantity to be used for sorting.
If string, it's assumed that the ncfile has an attribute with the same name and getattr is invoked.
If callable, the output of callable(ncfile) is used.
If None, no sorting is performed.
reverse: If set to True, then the list elements are sorted as if each comparison were reversed.
"""
if callable(func_or_string):
if func_or_string is None:
return [(label, ncfile, label) for (label, ncfile) in self]
elif callable(func_or_string):
items = [(label, ncfile, func_or_string(ncfile)) for (label, ncfile) in self]
else:
# Assume string and attribute with the same name.

6
abipy/electrons/optic.py
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@ -523,7 +523,8 @@ class OpticRobot(Robot, RobotWithEbands, NotebookWriter):
"all" if all components available on file should be plotted on the same ax.
what_list: List of quantities to plot. "re" for real part, "im" for imaginary.
Accepts also "abs", "angle".
sortby: Define the convergence parameter, sort files and produce plot labels. Can be string or function.
sortby: Define the convergence parameter, sort files and produce plot labels. Can be None, string or function.
If None, no sorting is performed.
If string, it's assumed that the ncfile has an attribute with the same name and getattr is invoked.
If callable, the output of callable(ncfile) is used.
itemp: Temperature index.
@ -584,7 +585,8 @@ class OpticRobot(Robot, RobotWithEbands, NotebookWriter):
itemp: Temperature index.
what_list: List of quantities to plot. "re" for real part, "im" for imaginary.
Accepts also "abs", "angle".
sortby: Define the convergence parameter, sort files and produce plot labels. Can be string or function.
sortby: Define the convergence parameter, sort files and produce plot labels. Can be None, string or function.
If None, no sorting is performed.
If string, it's assumed that the ncfile has an attribute with the same name and getattr is invoked.
If callable, the output of callable(ncfile) is used.
decompose: True to plot individual contributions.

49
abipy/eph/eph.py
View File

@ -63,7 +63,7 @@ class A2F(object):
# """Computes the momenta of a2F(w)"""
# raise NotImplementedError()
#def get_mcmillan_Tc(self, mustar):
#def get_mcmillan_tc(self, mustar):
# """
# Computes the critical temperature with the McMillan equation and the input mustar.
# """
@ -203,15 +203,16 @@ class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
self.reader.close()
@add_fig_kwargs
def plot_eph_strength(self, what="lambda", ylims=None, ax=None, **kwargs):
def plot_eph_strength(self, what="lambda", ylims=None, ax=None, label=None, **kwargs):
"""
Plot phonon bands with eph coupling strenght lambda(q, nu)
Args:
what: `lambda` for eph strength, gamma for ph linewidth.
what: `lambda` for eph strength, gamma for phonon linewidths.
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
ax: matplotlib :class:`Axes` or None if a new figure should be created.
label: String used to label the plot in the legend.
Returns:
`matplotlib` figure
@ -242,15 +243,15 @@ class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
xvals = np.arange(len(self.phbands.qpoints))
for nu in self.phbands.branches:
ax.plot(xvals, yvals[:, nu])
ax.plot(xvals, yvals[:, nu],
label=label if (nu == 0 and label) else None)
#if "color" not in kwargs and not match_bands:
# kwargs["color"] = "black"
#if "linewidth" not in kwargs:
# kwargs["linewidth"] = 2.0
#if "color" not in kwargs and not match_bands: kwargs["color"] = "black"
#if "linewidth" not in kwargs: kwargs["linewidth"] = 2.0
#ax.plot(xvals, yvals.T)
#set_axlims(ax, ylims, "y")
set_axlims(ax, ylims, "y")
if label: ax.legend(loc="best")
return fig
@add_fig_kwargs
@ -425,13 +426,39 @@ class EphRobot(Robot, RobotWithEbands, RobotWithPhbands, NotebookWriter):
"""
EXT = "EPH"
@add_fig_kwargs
def plot_lambda_convergence(self, what="lambda", sortby="nkpt", ylims=None, ax=None, **kwargs):
"""
Plot the convergence of the lambda(q, nu) parameters wrt to `sortby` parameter.
Args:
what: `lambda` for eph strength, gamma for phonon linewidths.
sortby: Define the convergence parameter, sort files and produce plot labels. Can be None, string or function.
If None, no sorting is performed.
If string, it's assumed that the ncfile has an attribute with the same name and getattr is invoked.
If callable, the output of callable(ncfile) is used.
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
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns:
`matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
for label, ncfile, param in self.sortby(sortby):
ncfile.plot_eph_strength(what=what, ax=ax, ylims=ylims,
label="%s %s" % (sortby, param) if not callable(sortby) else str(param),
show=False)
return fig
@add_fig_kwargs
def plot_a2f_convergence(self, sortby="nkpt", ax=None, xlims=None, **kwargs):
"""
Plot the convergence of the Eliashberg function wrt to `sortby` parameter.
Args:
sortby: Define the convergence parameter, sort files and produce plot labels. Can be string or function.
sortby: Define the convergence parameter, sort files and produce plot labels. Can be None, string or function.
If None, no sorting is performed.
If string, it's assumed that the ncfile has an attribute with the same name and getattr is invoked.
If callable, the output of callable(ncfile) is used.
ax: matplotlib :class:`Axes` or None if a new figure should be created.
@ -462,7 +489,9 @@ class EphRobot(Robot, RobotWithEbands, RobotWithPhbands, NotebookWriter):
nb.cells.extend([
#nbv.new_markdown_cell("# This is a markdown cell"),
nbv.new_code_cell("robot = abilab.EphRobot(*%s)\nrobot.trim_paths()\nrobot" % str(args)),
nbv.new_code_cell("robot.plot_lambda_convergence();"),
nbv.new_code_cell("robot.plot_a2f_convergence();"),
#nbv.new_code_cell("robot.plot_a2ftr_convergence();"),
])
return self._write_nb_nbpath(nb, nbpath)

5
abipy/eph/sigeph.py
View File

@ -28,7 +28,7 @@ class SigEPhFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter)
.. code-block:: python
with SigEPhFile("out_SIGMAPH.nc") as ncfile:
with SigEPhFile("out_SIGEPH.nc") as ncfile:
print(ncfile)
ncfile.ebands.plot()
"""
@ -154,11 +154,10 @@ class SigEPhFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter)
return self._write_nb_nbpath(nb, nbpath)
class SigmaPhReader(ElectronsReader):
class SigmaPhReader(ElectronsReader):
"""
Reads data from file and constructs objects.
"""
def read_phbands_qpath(self):
"""Read and return PhononBands."""
structure = self.read_structure()

5
abipy/eph/tests/test_eph.py
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@ -62,8 +62,9 @@ class EphRobotTest(AbipyTest):
#assert [t[2] for t in robot.sortby("nkpt")] == [10, 60, 182]
# Test plot methods
#if self.has_matplotlib():
# assert robot.plot_a2f_convergence(show=False)
if self.has_matplotlib():
assert robot.plot_lambda_convergence(show=False)
#assert robot.plot_a2f_convergence(show=False)
if self.has_nbformat():
robot.write_notebook(nbpath=self.get_tmpname(text=True))

14
abipy/examples/plot/plot_optic.py
View File

@ -3,38 +3,36 @@
This example shows how to plot the optical properties computed by optic within
the independent-particle approximation, no local-field effects and no excitonic effects.
"""
from abipy.abilab import abiopen
from abipy import abilab
import abipy.data as abidata
# Here we use one of the OPTIC.nc files shipped with abipy.
# Replace filename with the path to your OPTIC.nc file.
filename = abidata.ref_file("gaas_121212_OPTIC.nc")
ncfile = abiopen(filename)
ncfile = abilab.abiopen(filename)
# Optic files have a Structure and an ElectronBands object.
#ncfile.ebands.plot()
# To plot linear dielectric tensor for all
# tensor components available in the file:
# To plot linear dielectric tensor and other optical
# properties for all tensor components available in the file:
ncfile.plot_linopt(title="Linear dielectric function")
# To plot linear dielectric tensor:
# To plot the second Harmonic tensor
ncfile.plot_shg(title="Second Harmonic Generation")
# Remember to close the file.
ncfile.close()
# Use OpticRobot to analyze multiple file e.g convergence studies.
from abipy.electrons.optic import OpticRobot
filenames = [
abidata.ref_file("gaas_444_OPTIC.nc"),
abidata.ref_file("gaas_888_OPTIC.nc"),
abidata.ref_file("gaas_121212_OPTIC.nc"),
]
robot = OpticRobot.from_files(filenames)
robot = abilab.OpticRobot.from_files(filenames)
robot.plot_linopt_convergence(title="Convergence of $\epsilon$ wrt nkpt")

14
tests/test_scripts.py
View File

@ -36,8 +36,8 @@ class ScriptTest(AbipyTest):
verbose = "-vv"
# Don’t raise an exception if anything is printed to stderr
#if sys.version_info[0] <= 2 else str(s)
expect_stderr = True # else tests fail due to warnings and deprecation messages
# else tests fail due to deprecation warnings issued by pymatgen if oy2.7
expect_stderr = sys.version_info[0] <= 2
def get_env(self, check_help_version=True):
#import tempfile
@ -51,7 +51,7 @@ class ScriptTest(AbipyTest):
if check_help_version:
# Start with --help. If this does not work...
r = env.run(self.script, "--help")
r = env.run(self.script, "--help", expect_stderr=self.expect_stderr)
assert r.returncode == 0
# Script must provide a version option
@ -297,9 +297,11 @@ class TestAbicomp(ScriptTest):
#args = abidata.ref_files()
#r = env.run(self.script, "dfpt2_scf", *args, self.loglevel, self.verbose,
# expect_stderr=self.expect_stderr)
#args = abidata.ref_files()
#r = env.run(self.script, "time", *args, self.loglevel, self.verbose,
# expect_stderr=self.expect_stderr)
class TestAbirun(ScriptTest):
@ -312,10 +314,10 @@ class TestAbirun(ScriptTest):
# Test doc_manager
r = env.run(self.script, "doc_manager", self.loglevel, self.verbose, *no_logo_colors,
expect_stderr=self.expect_stderr)
expect_stderr=self.expect_stderr)
for qtype in QueueAdapter.all_qtypes():
r= env.run(self.script, ".", "doc_manager", qtype, self.loglevel, self.verbose, *no_logo_colors,
expect_stderr=self.expect_stderr)
r = env.run(self.script, ".", "doc_manager", qtype, self.loglevel, self.verbose, *no_logo_colors,
expect_stderr=self.expect_stderr)
# Test doc_sheduler
r = env.run(self.script, "doc_scheduler", self.loglevel, self.verbose, *no_logo_colors,