scnc
/
abipy
mirror of https://github.com/abinit/abipy.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fix flak8 warnings, make ipython hard-dep

This commit is contained in:
gmatteo 2021-05-26 23:26:17 +02:00
parent 084fa939a0
commit 313703278b
31 changed files with 68 additions and 62 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
abipy/abilab.py
View File

@ -356,7 +356,7 @@ def software_stack(as_dataframe=False):
try:
mod = import_module(pkg_name)
return mod.__version__
except:
except Exception:
return None
try:

2
abipy/abio/abivars.py
View File

@ -749,7 +749,7 @@ def structure_from_abistruct_fmt(string):
v = xred[iatom]
lines.append("%.16f %.16f %.16f" % (v[0], v[1], v[2]))
s = "\n".join(head) + "\n" + "\n".join(lines) #; print(s)
s = "\n".join(head) + "\n" + "\n".join(lines) #; print(s)
return AbinitInputFile.from_string(s).structure

2
abipy/abio/factories.py
View File

@ -1503,7 +1503,7 @@ def conduc_kerange_from_inputs(scf_input, nscf_input, tmesh, ddb_ngqpt, eph_ngqp
sigma_kerange[0] += epad
if e_range > 0:
sigma_kerange[1] += epad
# Modify the second nscf input to get a task that calculate the kpt in the sigma interval (Kerange.nc file)
multi[2].set_vars(optdriver=8, wfk_task='"wfk_kpts_erange"', kptopt=1,
sigma_ngkpt=sigma_ngkpt, einterp=einterp, sigma_erange=sigma_kerange)

2
abipy/core/kpoints.py
View File

@ -1138,7 +1138,7 @@ class KpointList(collections.abc.Sequence):
def plotly(self, fig=None, **kwargs):
"""Plot k-points with plotly."""
from abipy.tools.plotting import plotly_wigner_seitz, plotly_brillouin_zone
from abipy.tools.plotting import plotly_brillouin_zone
fold = False
if self.is_path:
labels = {k.name: k.frac_coords for k in self if k.name}

3
abipy/core/mixins.py
View File

@ -729,6 +729,7 @@ abilab.enable_notebook(with_seaborn=True)
nbformat.write(nb, fh)
return nbpath
class NotebookWriter(HasNotebookTools, metaclass=abc.ABCMeta):
"""
Mixin class for objects that are able to generate jupyter_ notebooks.
@ -850,7 +851,7 @@ class NotebookWriter(HasNotebookTools, metaclass=abc.ABCMeta):
This function *generates* a predefined list of plotly figures with minimal input from the user.
Relies on yield_plotly_figs implemented by the subclass to generate the figures.
"""
print("in plotly expose")
#print("in plotly expose")
pn, template = self._get_panel_and_template()
pn.config.sizing_mode = 'stretch_width'

7
abipy/core/structure.py
View File

@ -1315,7 +1315,6 @@ class Structure(pmg_Structure, NotebookWriter):
Args:
with_cart_coords: True if Cartesian coordinates should be added as well.
"""
from collections import defaultdict
if with_cart_coords:
group = {symb: {"site_idx": [], "frac_coords": [], "cart_coords": []} for symb in self.symbol_set}
else:
@ -1339,8 +1338,8 @@ class Structure(pmg_Structure, NotebookWriter):
@add_fig_kwargs
def plot(self, **kwargs):
"""
Plot structure in 3D with matplotlib. Return matplotlib Figure
See plot_structure for kwargs
Plot structure in 3D with matplotlib. Return matplotlib Figure.
See plot_structure for kwargs.
"""
from abipy.tools.plotting import plot_structure
return plot_structure(self, **kwargs)
@ -1348,7 +1347,7 @@ class Structure(pmg_Structure, NotebookWriter):
@add_plotly_fig_kwargs
def plotly(self, **kwargs):
"""
Plot structure in 3D with plotly. Return plotly Figure
Plot structure in 3D with plotly. Return plotly Figure.
See plot_structure for kwargs
"""
from abipy.tools.plotting import plotly_structure

4
abipy/dfpt/phonons.py
View File

@ -1124,8 +1124,8 @@ See also <https://forum.abinit.org/viewtopic.php?f=10&t=545>
# Scatter plot with Bose-Einstein occupation factors for T = temp
factor = abu.phfactor_ev2units(units)
if temp < 1: temp = 1
fig.layout.annotations=[dict(text="T = %.1f K" % temp, font_size=fontsize, x=0.5, xref='paper',
xanchor='center', y=1, yref='paper', yanchor='bottom' ,showarrow=False)]
fig.layout.annotations = [dict(text="T = %.1f K" % temp, font_size=fontsize, x=0.5, xref='paper',
xanchor='center', y=1, yref='paper', yanchor='bottom', showarrow=False)]
xs = np.arange(self.num_qpoints)
for nu in self.branches:
ws = self.phfreqs[:, nu]

12
abipy/dfpt/vsound.py
View File

@ -10,7 +10,7 @@ from abipy.dfpt.ddb import DdbFile
from abipy.dfpt.phonons import PhononBands, get_dyn_mat_eigenvec, match_eigenvectors
from abipy.abio.inputs import AnaddbInput
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, set_visible, get_fig_plotly, get_figs_plotly, \
add_plotly_fig_kwargs, plotlyfigs_to_browser, push_to_chart_studio, PlotlyRowColDesc
add_plotly_fig_kwargs, plotlyfigs_to_browser, PlotlyRowColDesc
from pymatgen.core.units import bohr_to_angstrom, eV_to_Ha
@ -353,10 +353,10 @@ class SoundVelocity(Has_Structure, NotebookWriter):
if fig is None:
fig, _ = get_fig_plotly()
fig.layout=dict(annotations=[dict(text=title, font_size=fontsize, x=0.5, xref='paper', xanchor='center',
y=1, yref='paper', yanchor='bottom' ,showarrow=False)],
yaxis_title_text=abu.wlabel_from_units(units, unicode=True),
xaxis_title_text= "Wave Vector")
fig.layout = dict(annotations=[dict(text=title, font_size=fontsize, x=0.5, xref='paper', xanchor='center',
y=1, yref='paper', yanchor='bottom' ,showarrow=False)],
yaxis_title_text=abu.wlabel_from_units(units, unicode=True),
xaxis_title_text="Wave Vector")
else:
fig.layout.annotations[idir].text = title
fig.layout.annotations[idir].font.size = fontsize
@ -429,7 +429,7 @@ class SoundVelocity(Has_Structure, NotebookWriter):
horizontal_spacing=0.05)
for i in range(self.n_directions):
rcd = PlotlyRowColDesc(i//2, i%2, nrows, ncols)
rcd = PlotlyRowColDesc(i // 2, i % 2, nrows, ncols)
self.plotly_fit_freqs_dir(i, fig, rcd, units=units, fontsize=fontsize, show=False)
return fig

1
abipy/dynamics/hist.py
View File

@ -449,7 +449,6 @@ class HistFile(AbinitNcFile, NotebookWriter):
# yield self.plotly(show=False)
# yield self.plotly_energies(show=False)
def mvplot_trajectories(self, colormap="hot", sampling=1, figure=None, show=True,
with_forces=True, **kwargs): # pragma: no cover
"""

2
abipy/electrons/denpot.py
View File

@ -1,7 +1,7 @@
# coding: utf-8
"""Density/potential files in netcdf/fortran format."""
import os
import tempfile
#import tempfile
#import numpy as np
from monty.string import marquee

11
abipy/electrons/ebands.py
View File

@ -1410,7 +1410,7 @@ class ElectronBands(Has_Structure):
if unicode:
import re
numl=re.findall(r'\d', formula)
numl = re.findall(r'\d', formula)
for s in numl:
formula = formula.replace(s,SUBSCRIPT_UNICODE[s])
@ -1459,7 +1459,6 @@ class ElectronBands(Has_Structure):
k0_list.append(k)
effmass_bands_f90.append(v)
# Set small values to zero.
k0_list = np.reshape(k0_list, (-1, 3))
k0_list = np.where(np.abs(k0_list) > 1e-12, k0_list, 0.0)
@ -2105,7 +2104,7 @@ class ElectronBands(Has_Structure):
ply_row, ply_col = rcd.ply_row, rcd.ply_col
# Decorate the axis (e.g add ticks and labels).
self.decorate_plotly(fig, klabels=klabels, iax = rcd.iax)
self.decorate_plotly(fig, klabels=klabels, iax=rcd.iax)
plotly_set_lims(fig, ylims, "y")
# Plot the band energies.
@ -2386,12 +2385,12 @@ class ElectronBands(Has_Structure):
fig.add_scatter(x=xx, y=yy, mode="lines", name=label, showlegend=showlegend, line=line_opts, **kwargs,
row=ply_row, col=ply_col)
label = ''
showlegend=False
showlegend = False
if with_linewidths:
w = self.linewidths[spin, :, band] * lw_fact / 2
lw_color = lines[-1].get_color()
raise NotImplementedError
#lw_color = lines[-1].get_color()
# solution 1: Use scater points to fill
# solution 2: add two traces and fill the area between
# color problem
@ -3978,7 +3977,7 @@ class ElectronDos(object):
fig.add_scatter(x=x, y=y, mode='lines', name=trace_name, showlegend=showlegend, line=opts, **kwargs)
xlabel, ylabel = 'Energy (eV)', 'DOS (states/eV)'
if exchange_xy: xlabel, ylabel = ylabel, xlabel
if exchange_xy: xlabel, ylabel = ylabel, xlabel
fig.layout.xaxis.title = xlabel
fig.layout.yaxis.title = ylabel
plotly_set_lims(fig, xlims, "x")

9
abipy/eph/rta.py
View File

@ -625,7 +625,8 @@ class RtaRobot(Robot, RobotWithEbands):
#def get_mobility_mu_dataframe(self, eh=0, component='xx', itemp=0, spin=0, **kwargs):
@add_fig_kwargs
def plot_mobility_kconv(self, eh=0, bte=['serta','mrta','ibte'], component='xx', itemp=0, spin=0, fontsize=14, ax=None, **kwargs):
def plot_mobility_kconv(self, eh=0, bte=('serta', 'mrta', 'ibte'), component='xx', itemp=0, spin=0,
fontsize=14, ax=None, **kwargs):
"""
Plot the convergence of the mobility as a function of the number of k-points,
for different transport formalisms included in the computation.
@ -662,9 +663,9 @@ class RtaRobot(Robot, RobotWithEbands):
if 'serta' in bte:
mob_serta = ncfile.reader.read_variable("mobility_mu")[0, spin, itemp, eh, j, i]
if 'mrta' in bte:
mob_mrta = ncfile.reader.read_variable("mobility_mu")[1, spin, itemp, eh, j, i]
mob_mrta = ncfile.reader.read_variable("mobility_mu")[1, spin, itemp, eh, j, i]
if 'ibte' in bte:
mob_ibte = ncfile.reader.read_variable("ibte_mob")[spin, itemp, eh, j, i]
mob_ibte = ncfile.reader.read_variable("ibte_mob")[spin, itemp, eh, j, i]
res.append([kptrlattx, mob_serta, mob_mrta, mob_ibte])
temps.append(ncfile.tmesh[itemp])
@ -789,7 +790,7 @@ class RtaRobot(Robot, RobotWithEbands):
#if self.all_have_ibte:
yield self.plot_ibte_mrta_serta_conv(show=False)
yield self.plot_ibte_vs_rta_rho(show=False)
# Determine the independent component. For the time being,
# only consider the cubic case separately
abifile = self.abifiles[0]

1
abipy/examples/flows/run_becs_and_epsilon_vs_kpts.py
View File

@ -15,6 +15,7 @@ import abipy.data as abidata
from abipy import flowtk
def make_scf_input(ngkpt, paral_kgb=0):
"""
This function constructs the input file for the GS calculation for a given IBZ sampling.

2
abipy/examples/flows/run_eph_mob.py
View File

@ -13,8 +13,6 @@ import abipy.abilab as abilab
import abipy.flowtk as flowtk
import abipy.core.abinit_units as abu
from abipy.abilab import abiopen
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")

1
abipy/examples/flows/run_nonlinear.py
View File

@ -14,6 +14,7 @@ from abipy import abilab
# NB: This flow requires abinit >= "8.5.2"
def make_scf_input(ecut=10, ngkpt=(8, 8, 8)):
"""
This function constructs an `AbinitInput` for performing a

5
abipy/examples/flows/run_phonopy_si.py
View File

@ -1,10 +1,11 @@
#!/usr/bin/env python
r"""
Phonopy + Abinit Flow
=====================
Phonopy with AbiPy Flow
=======================
This example shows how to compute phonon frequencies with phonopy
(supercells and finite-difference method).
This approach could be useful to obtain vibrational properties with XC functionals
for which DFPT is not yet implemented.

2
abipy/examples/plot/plot_a2f.py
View File

@ -11,7 +11,7 @@ import abipy.data as abidata
phdos_path = abidata.ref_file("al_161616q_PHDOS.nc")
ncfile = abilab.abiopen(abidata.ref_file("al_888k_161616q_A2F.nc"))
ncfile = abilab.abiopen(abidata.ref_file("al_888k_161616q_A2F.nc"))
print(ncfile)
#ncfile.phbands.plot()

13
abipy/flowtk/tasks.py
View File

@ -582,7 +582,7 @@ qadapters:
qname: localhost
job:
mpi_runner: mpirun
pre_run:
pre_run:
# List of shell commands executed before running abinit
# Change this part according to your Abinit installation and the location of the shared libs
- export OMP_NUM_THREADS=1
@ -623,15 +623,15 @@ Cannot locate `{cls.YAML_FILE}` neither in current directory nor in `{path}`
!!! PLEASE READ THIS !!!
To run AbiPy flows you need a manager.yaml describing your computer/cluster
To run AbiPy flows you need a manager.yaml describing your computer/cluster
as well as the job submission engine being used (shell, Slurm, PBS, etc).
Examples are provided in the `abipy/data/managers` directory.
Use `abidoc.py manager` to access the documentation from the terminal.
See also https://abinit.github.io/abipy/workflows/manager_examples.html for examples.
A minimalistic example of manager.yml for a laptop with the shell engine is reported below:
{cls.get_simple_manager()}
""", color="red"))
@ -3945,7 +3945,8 @@ class KerangeTask(AbinitTask):
"""
Class for kerange calculations.
"""
color_rgb = np.array((255, 128, 0)) / 255
color_rgb = np.array((255, 128, 128)) / 255
class ManyBodyTask(AbinitTask):
"""

6
abipy/flowtk/works.py
View File

@ -468,9 +468,9 @@ class NodeContainer(metaclass=abc.ABCMeta):
kwargs.update({"manager": seq_manager})
if eph_inp.get("eph_task",0) == -4:
max_cores = TaskManager.from_user_config().qadapter.max_cores
natom3 = 3 * len(eph_inp.structure)
nprocs = max(max_cores - max_cores % natom3, 1)
max_cores = TaskManager.from_user_config().qadapter.max_cores
natom3 = 3 * len(eph_inp.structure)
nprocs = max(max_cores - max_cores % natom3, 1)
new_manager = TaskManager.from_user_config().new_with_fixed_mpi_omp(nprocs, 1)
kwargs.update({"manager": new_manager})

2
abipy/integration_tests/itest_phonons.py
View File

@ -160,7 +160,7 @@ def itest_phonon_restart(fwp):
tolvrs=1.0e-5,
)
multi = abilab.MultiDataset(structure=structure,
multi = abilab.MultiDataset(structure=structure,
pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"),
ndtset=1 + len(qpoints))

11
abipy/panels/core.py
View File

@ -77,7 +77,7 @@ def get_template_cls_from_name(name):
if hasattr(pn.template, name):
return getattr(pn.template, name)
try_name = name + "Template"
try_name = name + "Template"
if hasattr(pn.template, try_name):
return getattr(pn.template, try_name)
@ -87,7 +87,6 @@ Possible templates are: {list(pn.template.__dict__.keys())}
""")
def depends_on_btn_click(btn_name):
def decorator(func):
@ -190,9 +189,11 @@ If everything is properly configured, a new window is automatically created in y
""")
btn = pnw.Button(name="Upload to chart studio server")
def push_to_cs(event):
with ButtonContext(btn):
push_to_chart_studio(fig)
btn.on_click(push_to_cs)
if with_help:
@ -397,7 +398,6 @@ class AbipyParameterized(param.Parameterized):
Please **refresh** the page using the refresh button of the browser if plotly figures are not shown.
""")
#def __repr__(self):
# # https://github.com/holoviz/param/issues/396
# return f"AbiPyParametrized(name='{self.name}')"
@ -516,7 +516,6 @@ class HasStructureParams(AbipyParameterized):
objects=[None, "jsmol", "vesta", "xcrysden", "vtk", "crystalk", "ngl",
"matplotlib", "plotly", "ase_atoms", "mayavi"])
#def __init__(self, **params):
# self.struct_view_btn = pnw.Button(name="View structure", button_type='primary')
# super(self).__init__(**params)
@ -639,7 +638,7 @@ def get_structure_info(structure):
df_len = pd.DataFrame(rows, index=["Å", "Bohr"]).transpose().rename_axis("Lattice lenghts")
# Build dataframe with lattice angles.
rows = []; keys = ("alpha", "beta", "gamma")
rows = []; keys = ("alpha", "beta", "gamma")
rows.append({k: d[k] for k in keys})
rows.append({k: np.radians(d[k]) for k in keys})
df_ang = pd.DataFrame(rows, index=["Degrees", "Radians"]).transpose().rename_axis("Lattice angles")
@ -713,7 +712,7 @@ class PanelWithElectronBands(AbipyParameterized):
# e-DOS plot.
edos_method = param.ObjectSelector(default="gaussian", objects=["gaussian", "tetra"], doc="e-DOS method")
edos_step_ev = param.Number(0.1, bounds=(1e-6, None), step=0.1, doc='e-DOS step in eV')
edos_width_ev = param.Number(0.2, step=0.05, bounds=(1e-6, None), doc='e-DOS Gaussian broadening in eV' )
edos_width_ev = param.Number(0.2, step=0.05, bounds=(1e-6, None), doc='e-DOS Gaussian broadening in eV')
# SKW interpolation of the KS band energies.
skw_lpratio = param.Integer(5, bounds=(1, None))

1
abipy/panels/ddb.py
View File

@ -600,6 +600,7 @@ class DdbRobotPanel(BaseRobotPanel, HasAnaddbParams):
"""Return tabs with widgets to interact with the DDB file."""
robot = self.robot
d = {}
d["Summary"] = pn.Row(
bkw.PreText(text=robot.to_string(verbose=self.verbose), sizing_mode="scale_both")
)

2
abipy/panels/hist.py
View File

@ -4,7 +4,7 @@ import panel as pn
import panel.widgets as pnw
import bokeh.models.widgets as bkw
from abipy.panels.core import AbipyParameterized, ButtonContext, mpl, ply, depends_on_btn_click
from abipy.panels.core import AbipyParameterized, mpl, ply, depends_on_btn_click
_what_list = ["pressure", "forces", "energy", "abc", "angles", "volume"]

2
abipy/panels/outputs.py
View File

@ -4,7 +4,7 @@
import panel as pn
#import panel.widgets as pnw
import bokeh.models.widgets as bkw
from abipy.panels.core import AbipyParameterized, mpl, ply, dfc #, ButtonContext
from abipy.panels.core import AbipyParameterized, mpl, ply, dfc
class AbinitOutputFilePanel(AbipyParameterized):

2
abipy/panels/phonons.py
View File

@ -3,7 +3,7 @@ import param
import panel as pn
import panel.widgets as pnw
from abipy.panels.core import AbipyParameterized, ButtonContext, mpl, ply, dfc, depends_on_btn_click
from abipy.panels.core import AbipyParameterized, mpl, ply, dfc, depends_on_btn_click
class PhononBandsPlotterPanel(AbipyParameterized):

2
abipy/panels/structure.py
View File

@ -5,7 +5,7 @@ import panel as pn
import panel.widgets as pnw
import bokeh.models.widgets as bkw
from abipy.panels.core import HasStructureParams, ButtonContext, dfc, mpl, ply, depends_on_btn_click
from abipy.panels.core import HasStructureParams, dfc, mpl, ply, depends_on_btn_click
class StructurePanel(HasStructureParams):

4
abipy/scripts/abicomp.py
View File

@ -676,9 +676,9 @@ def _invoke_robot(options):
if options.plotly:
# plotly version.
if hasattr(robot, "plotly_expose"):
robot.plotly_expose(chart_studio=options.chart_studio, verbose=options.verbose)
robot.plotly_expose(chart_studio=options.chart_studio, verbose=options.verbose)
else:
cprint("<%s> does not implement plotly_expose method" % type(robot), color="red")
cprint("<%s> does not implement plotly_expose method" % type(robot), color="red")
elif hasattr(robot, "expose"):
# matplotlib version.

2
abipy/tools/devtools.py
View File

@ -123,6 +123,8 @@ def display_top(snapshot, key_type='lineno', limit=3):
snapshot = tracemalloc.take_snapshot()
display_top(snapshot)
"""
import tracemalloc
import linecache
snapshot = snapshot.filter_traces((
tracemalloc.Filter(False, "<frozen importlib._bootstrap>"),
tracemalloc.Filter(False, "<unknown>"),

6
abipy/tools/plotting.py
View File

@ -566,7 +566,7 @@ class PanelExpose(object): # pragma: no cover
self.verbose = verbose
if self.verbose:
print("\nLoading all figures before showing them. It may take some time...")
print("\nLoading all figures before showing them. It may take some time...")
self.start_time = time.time()
@ -979,7 +979,7 @@ class PlotlyRowColDesc(object):
# Assume list with 4 integers
try:
return cls(*obj)
except exc:
except Exception as exc:
raise TypeError(f"Dont know how to convert `{type(obj)}` into `{cls}`")
def __init__(self, py_row, py_col, nrows, ncols):
@ -1328,6 +1328,7 @@ def push_to_chart_studio(figs):
####################################################
import plotly.graph_objects as go
def go_points(points, size=4, color="black", labels=None, **kwargs):
#textposition = 'top right',
@ -1486,7 +1487,6 @@ def plot_fcc_prim():
fcc_conv = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
fcc_conv_box = get_box(fcc_conv, name="conv lattice")
fig = go.Figure(data=[*fcc_prim_box, *fcc_prim_vectors, *fcc_conv_box, atoms])
return fig

2
requirements-optional.txt
View File

@ -1,4 +1,3 @@
ipython
jupyter
nbformat
pygments
@ -11,7 +10,6 @@ ase
param
panel
bokeh
chart-studio
XlsxWriter # For DataFrame.to_excel()
# Unit tests
python-coveralls

7
tasks.py
View File

@ -59,10 +59,15 @@ pytest -n 2 --cov-config=.coveragerc --cov=abipy -v --doctest-modules abipy \
def style(ctx):
with cd(ABIPY_ROOTDIR):
ctx.run("pycodestyle 2>&1 | tee style.log", pty=True)
ctx.run("flake8 --count --show-source --statistics | tee -a style.log", pty=True)
#ctx.run("pydocstyle abipy | tee -a style.log", pty=True)
@task
def flake(ctx):
with cd(ABIPY_ROOTDIR):
ctx.run("flake8 --count --show-source --statistics | tee -a style.log", pty=True)
@task
def plots(ctx):
with cd(os.path.join(ABIPY_ROOTDIR, "abipy", "examples")):