# default values and metadata
#"""
+__version__ = '3.1.4'
+
[docs]def docstring_replace(**kwargs):
def d(f):
f.__doc__ = f.__doc__.format(**kwargs)
diff --git a/docs/_modules/tp/cli/options.html b/docs/_modules/tp/cli/options.html
index 4a1d12f..b2ad4f5 100644
--- a/docs/_modules/tp/cli/options.html
+++ b/docs/_modules/tp/cli/options.html
@@ -78,6 +78,10 @@ Source code for tp.cli.options
#Functions
#---------
#
+# administrative_options
+# function for help and version display.
+# axes_limit_function
+# function for setting the axis limits.
# direction_function:
# function for picking the --direction (-d).
# doping_type_option:
@@ -104,12 +108,100 @@ Source code for tp.cli.options
# function for picking the --temperature (-t).
# verbose_option:
# function for increasing the verbosity.
-# axes_limit_function
-# function for setting the axis limits.
#"""
import click
+[docs]def adminsitrative_options(f):
+ """Help and version options.
+
+ Allows -h for help (click-nonstandard).
+
+ Options
+ -------
+
+ --help, -h
+ show help and exit
+ --version
+ show version and exit
+ """
+
+ f = click.help_option('-h', '--help')(f)
+ f = click.version_option(package_name='tp')(f)
+
+ return f
+
+[docs]def axes_limit_function(multiple=False, c=False):
+ """Function for creating axes limit options.
+
+ Arguments
+ ---------
+
+ multiple : bool, optional
+ allow multiple limits. Default: False.
+ c : bool, optional
+ include colour limits. Default: False.
+
+ Returns
+ -------
+ decorator
+ axes limit options decorator.
+ """
+
+ def axes_limit_options(f):
+ """Options for axes limits.
+
+ Options
+ -------
+
+ --xmin : float, optional
+ override minimum x.
+ --xmax : float, optional
+ override maximum x.
+ --ymin : float, optional
+ override minimum y.
+ --ymax : float, optional
+ override maximum y.
+ --cmin : float, optional
+ override minimum colour.
+ --cmax : float, optional
+ override maximum colour.
+
+ Returns
+ -------
+
+ decorator
+ axes limits options decorator.
+ """
+
+ f = click.option('--xmin',
+ help='Override minimum x.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--xmax',
+ help='Override maximum x.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--ymin',
+ help='Override minimum y.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--ymax',
+ help='Override maximum y.',
+ multiple=multiple,
+ type=float)(f)
+ if c:
+ f = click.option('--cmin',
+ help='Override minimum colour value.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--cmax',
+ help='Override maximum colour value.',
+ multiple=multiple,
+ type=float)(f)
+ return f
+ return axes_limit_options
+
[docs]def direction_function(multiple=False):
"""Function to create direction options.
@@ -222,31 +314,6 @@ Source code for tp.cli.options
return f
return doping_option
-[docs]def heatmap_options(f):
- """Options for heatmaps."""
-
- f = click.option('--discrete/--continuous',
- help='Discretise colourmap. [default: continuous]',
- default=False,
- show_default=False)(f)
- f = click.option('-l', '--levels',
- help='Levels for discrete plots. Lists directly '
- 'specify the contour levels, while integers '
- 'specify the maximum-1 number of "nice" '
- 'levels to plot.',
- multiple=True,
- default=[None])(f)
- f = click.option('--contours',
- help='Contours to plot.',
- multiple=True,
- type=float,
- default=[None])(f)
- f = click.option('--contourcolours',
- help='contour colours',
- multiple=True,
- default=['black'])(f)
- return f
-
[docs]def dos_function(dosargs=['-c', '--colour']):
"""Function for creating DoS options.
@@ -341,6 +408,31 @@ Source code for tp.cli.options
return f
return dos_options
+[docs]def heatmap_options(f):
+ """Options for heatmaps."""
+
+ f = click.option('--discrete/--continuous',
+ help='Discretise colourmap. [default: continuous]',
+ default=False,
+ show_default=False)(f)
+ f = click.option('-l', '--levels',
+ help='Levels for discrete plots. Lists directly '
+ 'specify the contour levels, while integers '
+ 'specify the maximum-1 number of "nice" '
+ 'levels to plot.',
+ multiple=True,
+ default=[None])(f)
+ f = click.option('--contours',
+ help='Contours to plot.',
+ multiple=True,
+ type=float,
+ default=[None])(f)
+ f = click.option('--contourcolours',
+ help='contour colours',
+ multiple=True,
+ default=['black'])(f)
+ return f
+
[docs]def inputs_function(name='filenames', nargs=-1):
"""Function for creating input arguments.
@@ -700,77 +792,6 @@ Source code for tp.cli.options
show_default=False)(f)
return f
-
-[docs]def axes_limit_function(multiple=False, c=False):
- """Function for creating axes limit options.
-
- Arguments
- ---------
-
- multiple : bool, optional
- allow multiple limits. Default: False.
- c : bool, optional
- include colour limits. Default: False.
-
- Returns
- -------
- decorator
- axes limit options decorator.
- """
-
- def axes_limit_options(f):
- """Options for axes limits.
-
- Options
- -------
-
- --xmin : float, optional
- override minimum x.
- --xmax : float, optional
- override maximum x.
- --ymin : float, optional
- override minimum y.
- --ymax : float, optional
- override maximum y.
- --cmin : float, optional
- override minimum colour.
- --cmax : float, optional
- override maximum colour.
-
- Returns
- -------
-
- decorator
- axes limits options decorator.
- """
-
- f = click.option('--xmin',
- help='Override minimum x.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--xmax',
- help='Override maximum x.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--ymin',
- help='Override minimum y.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--ymax',
- help='Override maximum y.',
- multiple=multiple,
- type=float)(f)
- if c:
- f = click.option('--cmin',
- help='Override minimum colour value.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--cmax',
- help='Override maximum colour value.',
- multiple=multiple,
- type=float)(f)
- return f
- return axes_limit_options
diff --git a/docs/_modules/tp/plot/frequency.html b/docs/_modules/tp/plot/frequency.html
index ed34c24..e1ddf4a 100644
--- a/docs/_modules/tp/plot/frequency.html
+++ b/docs/_modules/tp/plot/frequency.html
@@ -968,7 +968,7 @@ Source code for tp.plot.frequency
cbar.set_alpha(1)
cbar.set_label(axlabels[projected])
tp.plot.utilities.set_locators(cbar.ax, y=cbar.ax.yaxis.get_scale())
- cbar.draw_all()
+ cbar._draw_all()
if main:
data[xquantity] = x
diff --git a/docs/_modules/tp/plot/heatmap.html b/docs/_modules/tp/plot/heatmap.html
index 4587142..12785d9 100644
--- a/docs/_modules/tp/plot/heatmap.html
+++ b/docs/_modules/tp/plot/heatmap.html
@@ -321,17 +321,16 @@ Source code for tp.plot.heatmap
# plotting
if discrete:
kwargs.pop('rasterized')
- if levels is None or levels == ():
- heat = ax.contourf(x[:-1], y[:-1], c, cmap=colours, norm=cnorm,
- **kwargs)
+ if levels in [None, (), [None], (None,)]:
+ levels = 10
else:
if isinstance(levels, (list, np.ndarray, tuple)) and len(levels) == 1:
levels = int(levels[0])
elif isinstance(levels, float):
- raise TypeError('levels must be an int or array-like, not float')
- if levels is not None and levels != ():
- heat = ax.contourf(x[:-1], y[:-1], c, cmap=colours, norm=cnorm,
- levels=levels, **kwargs)
+ raise TypeError(
+ 'levels must be an int or array-like, not float')
+ heat = ax.contourf(x[:-1], y[:-1], c, cmap=colours, norm=cnorm,
+ levels=levels, **kwargs)
else:
heat = ax.pcolormesh(x, y, c, cmap=colours, norm=cnorm, **kwargs)
fig = ax.get_figure()
@@ -342,7 +341,7 @@ Source code for tp.plot.heatmap
cbar = plt.colorbar(heat, ax=ax, extend=extend)
# contours
- if contours is not None and contours != ():
+ if contours not in [None, [None], (), (None,)]:
if contourkwargs == None:
contourkwargs = {}
if not isinstance(contours, (list, np.ndarray)):
diff --git a/docs/_modules/tp/plot/phonons.html b/docs/_modules/tp/plot/phonons.html
index d02d719..5151aa9 100644
--- a/docs/_modules/tp/plot/phonons.html
+++ b/docs/_modules/tp/plot/phonons.html
@@ -878,7 +878,7 @@ Source code for tp.plot.phonons
cbar.set_alpha(1)
cbar.set_label(axlabels[quantity])
tp.plot.utilities.set_locators(cbar.ax, y=cbar.ax.yaxis.get_scale())
- cbar.draw_all()
+ cbar._draw_all()
if main:
if round(np.amin(f), 1) == 0:
@@ -1120,7 +1120,7 @@ Source code for tp.plot.phonons
cbar.set_alpha(1)
cbar.set_label(axlabels[projected])
tp.plot.utilities.set_locators(cbar.ax, y=cbar.ax.yaxis.get_scale())
- cbar.draw_all()
+ cbar._draw_all()
if main:
ax.set_ylim(ymin, ymax)
diff --git a/docs/gallery.html b/docs/gallery.html
index c1217cd..b2bfdbb 100644
--- a/docs/gallery.html
+++ b/docs/gallery.html
@@ -129,7 +129,7 @@ Note:
ztmap heatmap (the power factor pfmap is also available):
Click on the plot to see the script, or one could use
-`tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete
+tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete
A related plot we hope people find useful for screening materials to
@@ -153,7 +153,7 @@
Note:
-tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR -doscolour '#d46ef9' --doscolour '#7b8eff' -c '#f0901f'
+tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR --doscolour '#d46ef9' --doscolour '#7b8eff' -c '#f0901f'
This is where some of the more useful functions of ThermoParser
diff --git a/docs/genindex.html b/docs/genindex.html
index 421f6ad..e48356b 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -125,10 +125,10 @@
A
add_multi() (in module tp.plot.phonons)
-
-
- add_pfmap() (in module tp.plot.heatmap)
- add_projected_dispersion() (in module tp.plot.phonons)
@@ -142,6 +142,8 @@
A
- add_ztdiff() (in module tp.plot.heatmap)
- add_ztmap() (in module tp.plot.heatmap)
+
+ - adminsitrative_options() (in module tp.cli.options)
- alphabetise() (in module tp.axes.legend)
diff --git a/docs/heatmaps.html b/docs/heatmaps.html
index 7ffa1ba..68b7531 100644
--- a/docs/heatmaps.html
+++ b/docs/heatmaps.html
@@ -89,7 +89,7 @@ Heatmaps
This shows the classic ZT against carrier concentration and temperature
heatmap. This can be plotted at the command line with:
-`tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete
+tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete
and in python with:
diff --git a/docs/index.html b/docs/index.html
index dd7b61b..c8881be 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -85,7 +85,7 @@
| | |___ ___ |___ |_____ ___ :|___/ ___ |___ ___ ___ |___ \
| | | | / \ | \ | | | / \:| / | | \ / / \ | \/
| | | | |___/ | | | | | |:| | | | \___ |___/ | \_____
-| | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.3\
+| | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.4\
|____________________________________:_______________________/____________:_____/
@@ -247,6 +247,10 @@ ContributorsJOSS reviewers, Evan Walter Clarke
+Spotte-Smith, Enric Tomás Grau-Luque, and Francesco Nattino; and the
+editor Mojtaba Barzegari. An unintimidating and productive review
+process, which I would recommend if the opportunity arises!
License¶
diff --git a/docs/objects.inv b/docs/objects.inv
index 75c8ec8..3faecc6 100644
Binary files a/docs/objects.inv and b/docs/objects.inv differ
diff --git a/docs/phonons.html b/docs/phonons.html
index 69c8ef2..844666e 100644
--- a/docs/phonons.html
+++ b/docs/phonons.html
@@ -89,7 +89,7 @@ Phonons
This shows a phonon dispersion and density of states (DoS). This is the
only combined plot currenty possible at the command line, with:
-tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR -doscolour '#d46ef9' --doscolour '#7b8eff' -c '#f0901f'
+tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR --doscolour '#d46ef9' --doscolour '#7b8eff' -c '#f0901f'
and in python:
diff --git a/docs/searchindex.js b/docs/searchindex.js
index ef53697..10d3c16 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["avg-rates","contents","cumkappa","dos","gallery","heatmaps","index","modules","phonons","prophon","tp","tp.axes","tp.cli","tp.data","tp.plot","tp.setup","tutorial-00","tutorial-01","tutorial-02","tutorial-03","tutorial-04","tutorial-05","tutorial-06","tutorial-0X","tutorials","waterfalls"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":3,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":2,"sphinx.domains.rst":2,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["avg-rates.rst","contents.rst","cumkappa.rst","dos.rst","gallery.rst","heatmaps.rst","index.rst","modules.rst","phonons.rst","prophon.rst","tp.rst","tp.axes.rst","tp.cli.rst","tp.data.rst","tp.plot.rst","tp.setup.rst","tutorial-00.rst","tutorial-01.rst","tutorial-02.rst","tutorial-03.rst","tutorial-04.rst","tutorial-05.rst","tutorial-06.rst","tutorial-0X.rst","tutorials.rst","waterfalls.rst"],objects:{"":{tp:[10,0,0,"-"]},"tp.axes":{large:[11,0,0,"-"],legend:[11,0,0,"-"],small:[11,0,0,"-"]},"tp.axes.large":{four_square:[11,1,1,""],four_square_colourbars:[11,1,1,""],one:[11,1,1,""],one_colourbar:[11,1,1,""],one_dos:[11,1,1,""],one_dos_colourbar:[11,1,1,""],three_h:[11,1,1,""],three_h_colourbars:[11,1,1,""],three_square:[11,1,1,""],three_square_colourbars:[11,1,1,""],two_h:[11,1,1,""],two_h_colourbars:[11,1,1,""],two_v:[11,1,1,""],two_v_colourbars:[11,1,1,""]},"tp.axes.legend":{add_add_legend:[11,1,1,""],alphabetise:[11,1,1,""],consolidate:[11,1,1,""]},"tp.axes.small":{four_square:[11,1,1,""],four_square_colourbars:[11,1,1,""],one:[11,1,1,""],one_colourbar:[11,1,1,""],one_dos:[11,1,1,""],one_dos_colourbar:[11,1,1,""],three_h:[11,1,1,""],three_h_colourbars:[11,1,1,""],three_square:[11,1,1,""],three_square_colourbars:[11,1,1,""],two_h:[11,1,1,""],two_h_colourbars:[11,1,1,""],two_v:[11,1,1,""],two_v_colourbars:[11,1,1,""]},"tp.calculate":{be_occupation:[10,1,1,""],cumulate:[10,1,1,""],dfdde:[10,1,1,""],fd_occupation:[10,1,1,""],from_tp:[10,1,1,""],gaussian:[10,1,1,""],interpolate:[10,1,1,""],kl:[10,1,1,""],kl_fromdict:[10,1,1,""],lifetime:[10,1,1,""],lorentzian:[10,1,1,""],mfp:[10,1,1,""],power_factor:[10,1,1,""],power_factor_fromdict:[10,1,1,""],thermal_conductivity:[10,1,1,""],to_tp:[10,1,1,""],zt:[10,1,1,""],zt_fromdict:[10,1,1,""]},"tp.cli":{cli:[12,0,0,"-"],options:[12,0,0,"-"]},"tp.cli.options":{axes_limit_function:[12,1,1,""],direction_function:[12,1,1,""],doping_function:[12,1,1,""],doping_type_option:[12,1,1,""],dos_function:[12,1,1,""],fill_options:[12,1,1,""],heatmap_options:[12,1,1,""],inputs_function:[12,1,1,""],interpolate_options:[12,1,1,""],kpoints_options:[12,1,1,""],legend_function:[12,1,1,""],line_options:[12,1,1,""],plot_io_function:[12,1,1,""],temperature_option:[12,1,1,""],verbose_option:[12,1,1,""]},"tp.data":{load:[13,0,0,"-"],run:[13,0,0,"-"],save:[13,0,0,"-"],utilities:[13,0,0,"-"]},"tp.data.load":{amset:[13,1,1,""],amset_mesh:[13,1,1,""],boltztrap:[13,1,1,""],get_path:[13,1,1,""],phono3py:[13,1,1,""],phonopy_dispersion:[13,1,1,""],phonopy_dos:[13,1,1,""],phonopy_gruneisen:[13,1,1,""],scale_to_path:[13,1,1,""]},"tp.data.run":{boltztrap:[13,1,1,""]},"tp.data.save":{cumkappa:[13,1,1,""],hdf5:[13,1,1,""],kappa_target:[13,1,1,""],phono3py:[13,1,1,""],prompt:[13,1,1,""],zt:[13,1,1,""]},"tp.data.utilities":{merge:[13,1,1,""],resolve:[13,1,1,""]},"tp.plot":{colour:[14,0,0,"-"],frequency:[14,0,0,"-"],heatmap:[14,0,0,"-"],mfp:[14,0,0,"-"],phonons:[14,0,0,"-"],utilities:[14,0,0,"-"]},"tp.plot.colour":{elbow:[14,1,1,""],highlight:[14,1,1,""],hsb2rgb:[14,1,1,""],linear:[14,1,1,""],skelton:[14,1,1,""],uniform:[14,1,1,""]},"tp.plot.frequency":{add_cum_kappa:[14,1,1,""],add_density:[14,1,1,""],add_dos:[14,1,1,""],add_projected_waterfall:[14,1,1,""],add_waterfall:[14,1,1,""],format_waterfall:[14,1,1,""]},"tp.plot.heatmap":{add_heatmap:[14,1,1,""],add_kappa_target:[14,1,1,""],add_pfdiff:[14,1,1,""],add_pfmap:[14,1,1,""],add_ztdiff:[14,1,1,""],add_ztmap:[14,1,1,""]},"tp.plot.mfp":{add_cum_kappa:[14,1,1,""],add_markers:[14,1,1,""]},"tp.plot.phonons":{add_alt_dispersion:[14,1,1,""],add_alt_projected_dispersion:[14,1,1,""],add_dispersion:[14,1,1,""],add_multi:[14,1,1,""],add_projected_dispersion:[14,1,1,""],add_wideband:[14,1,1,""],formatting:[14,1,1,""],get_equivalent_qpoint:[14,1,1,""],tile_properties:[14,1,1,""]},"tp.plot.utilities":{colour_scale:[14,1,1,""],parse_colours:[14,1,1,""],scale_to_axis:[14,1,1,""],set_locators:[14,1,1,""]},"tp.settings":{amset_conversions:[10,1,1,""],boltztrap_conversions:[10,1,1,""],boltztrap_dimensions:[10,1,1,""],conversions:[10,1,1,""],dimensions:[10,1,1,""],inverted_labels:[10,1,1,""],labels:[10,1,1,""],locator:[10,1,1,""],long_labels:[10,1,1,""],medium_labels:[10,1,1,""],phono3py_conversions:[10,1,1,""],phonopy_conversions:[10,1,1,""],short_labels:[10,1,1,""],to_amset:[10,1,1,""],to_boltztrap:[10,1,1,""],to_phono3py:[10,1,1,"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,8,11,12,13,14,19,20,25],renam:[],repeat:[13,14,16],repetit:13,replac:[17,25],repo:4,repres:[0,5,18,21],request:6,requir:[1,2,3,4,5,12,13,14,16,18,21,23,25],rerun:[3,4],rescal:[4,5,8],resolv:[0,4,13],respect:[0,5,18,19,21,22],rest:[22,23],result:[4,14,23],retriev:[4,6,14],rev:4,revers:20,review:6,rgb2arrai:[],rgb:[5,9,14],rgba:14,right:[2,3,4,11,19,21],roman:[11,21],roughli:6,round:[13,21],row:11,rrggbb:[12,14],run:[4,5,6,7,9,10,14,18,20,23],run_dir:13,runner:[],safe_load:13,same:[3,4,5,6,8,13,14,15,17,19,20,21,22,24],sampl:14,satur:14,save:[0,2,5,6,7,8,9,10,18,19,20,21,22,25],savefig:[0,2,3,5,6,8,9,17,18,19,20,21,25],scale:[2,5,8,11,13,14,20,21,25],scale_to_axi:14,scale_to_path:13,scalepo:13,scanlon:[4,6],scatter:[0,4,6,9,14,18,20,25],scattering_r:13,scheme:14,scienc:6,scipi:6,scope:[4,24],scratch:11,screen:[4,14],script:[4,5,6,14,18,20,24],scs:[8,20],sdata:14,sean:6,search:1,second:[2,14,19,23],section:[2,9,14,18,25],see:[0,2,4,6,13],seebeck:[10,13,14,21],seem:25,select:[0,2,9,12,13,14,19,24],self:[10,14,18],semi:[],separ:[3,8,13,19,22],sequenc:[11,14],seri:24,set:[0,1,2,3,5,6,7,9,11,12,13,14,15,17,19,20,21,22,23],set_loc:[0,14,20,21],set_xlabel:[0,20,21],set_ylabel:[0,20,21],set_ylim:[8,19],setup:[7,10,23],sever:[2,5,17,18,19,21],shade:14,shape:[11,13,14,17,21],share:[2,13,19,24],sheet:[6,9,10,11,18,22],shenanegan:0,shift:14,short_label:[10,21,22],shorten:[8,20],shorthand:18,shoul:2,should:[0,6,13,14,15,17,20,21,22,23],show:[0,2,3,4,5,8,9,12,17,19,20,21,23,25],shown:[9,19],shrink:10,shrunk:10,side:[8,11],sidewai:14,sigma:[3,4,10,14],significantli:[4,11],similar:[5,9,13,16],simpl:[0,8,21],simplest:[4,6,16],simpli:[16,17,25],simplic:4,simplifi:6,simul:[4,20],sinc:4,singh:13,singl:[5,6,9,11,13,14,18,19,20,25],singli:10,singular:[],six:22,size:[4,8,10,11,17,20,22],skelton:14,slash:16,slightli:4,slower:11,small:[2,3,5,7,9,10,17,19,20,21,22,25],smaller:20,smallest:10,smear:[3,4],smith:6,smooth:14,smtg:6,snyder:13,soc:13,solid:[12,14],solv:20,some:[4,5,9,11,17,18,20,21,23,24],someth:[14,16,20],sometim:14,somewhat:11,sort:[0,10],sourc:[6,10,11,12,13,14,15,17,21],space:[8,11,17,18,19,20],spacial:19,specialis:24,specialist:6,specif:[4,6,13,14,23],specifi:[0,2,3,5,13,14,18,19,20,21,22,23],sphinx:6,spin:13,split:[6,8,20],spooner:[4,6],spott:6,squar:[11,16],src:6,stage:[6,17],stand:[18,20],standard:[10,13,18,19,22],standardis:13,start:[3,11,14,16,20],state:[2,6,8,13,14,19,25],stdout:13,step:[6,13,17,18],still:[6,14],stitch:15,stop:[18,20],str:[10,11,12,13,14,15],straightforward:[0,6],streamlin:[4,12,19],string:[13,14,18,19],strong:20,structur:[2,6,13,14,16,24],stuff:18,style:[6,8,9,10,11,18,20,21,22,24],stylelib:18,stype:[0,13],sub:[],subdictionari:[13,21],subfig:17,submit:6,submodul:[1,7],subpackag:[1,7],subplot:6,subplots_adjust:21,subsequ:11,subset:14,substitut:6,suffix:[11,21],suggest:[15,23],suit:[6,9,11],suitabl:[9,23],sum:13,sumo:13,sup:5,supercel:[4,8,17,18,20],supplement:6,suppli:[2,5,9,14,15],support:[2,6,20],sure:[5,14,21],swap:[6,13],symmetri:[6,9,14,15,17],symmop:14,symop:14,symprec:15,tab10:14,tag:[0,2,9,16,25],take:[6,11,13,14,16,17,18,19,21],taken:[14,17],target:[4,5,6,13,14],tco:4,tdata:0,tell:18,temperatur:[0,2,4,5,6,9,10,12,13,14,18,20,21,25],temperature_opt:12,templat:[5,22],test:1,text:[11,16],than:[3,4,8,9,11,13,14,18,19,20,22,25],thank:6,thats:4,thei:[0,6,8,13,14,17,18,19,20],them:[0,4,8,17,18,19,20],themselv:16,therebi:0,therefor:[4,20],thermal:[4,5,6,10,13,14,17,18,20,21,25],thermal_conduct:10,thermoelectr:[4,6,21],thermopars:[0,4,5,6,10,16,17,18,19,21,24],thermoplott:[],thi:[0,2,3,4,5,6,8,9,10,13,14,15,16,17,18,19,20,21,24,25],thing:[3,4,11,14,16,17,21],third:[4,23],those:[5,6,14,22],three:[4,5,11,13,16,17,19],three_h:11,three_h_colourbar:11,three_squar:11,three_square_colourbar:11,through:[3,6,19,21],throughout:17,thrown:[5,17],thz:10,tick:[0,8,10,13,14,20,22],tick_label:14,tick_posit:14,ticklabel:14,tickpo:13,tidi:18,tidier:5,tile:14,tile_properti:14,time:[4,5,13,18,21,23],tinterp:13,tiresom:6,titl:[0,2,3,8,19,21],tmax:13,tmin:[13,21],to_amset:10,to_boltztrap:10,to_phono3pi:10,to_tp:10,to_xxx:22,togeth:[13,15,19],toggl:[12,16],tol:14,toler:14,too:[14,17,22,23],tool:[4,5,6,13,14,15,23],toolkit:6,top:[5,9,11,16,18,19,20,21,22,25],total:[0,3,4,13,14,16],totalcolour:14,totallabel:14,tprc:[6,10,14,24],tracker:6,tradit:14,translat:10,transpar:[4,18],transport:[4,6,10,13,19,21],transport_75x75x75:[4,5,21],transvers:14,transverse_1:[],transverse_2:[],treat:14,trend:4,trivial:17,trnasport:[],tstep:13,tupl:14,turn:[13,14,20],tutori:[0,1,4,6],twice:14,two:[2,3,5,6,8,9,11,14,15,17,18,21,23],two_h:[0,2,3,11,20],two_h_colourbar:11,two_v:[11,20],two_v_colourbar:11,type:[4,6,8,10,11,12,13,14,15,16,17,18,24],typic:16,ucl:[],unalik:19,under:[5,6,8,12,14],undercolour:14,underli:[17,22],uniform:[5,14,18],unintimid:6,unit:[6,10,13,17,21,22,24],unitest:6,unittest:6,unless:14,unoccupi:14,unsmear:3,unweight:23,unweighted_kpoint:23,updat:[10,22],url:4,usag:[2,16],use:[0,2,4,5,6,9,10,14,16,17,18,20,21,22,24,25],use_tprc:10,used:[0,2,3,4,5,6,8,9,10,11,14,16,17,18,19,20,21,24,25],useful:[4,6,8,9,11,14,19,21],user:[5,6,9,18,22,24],uses:[5,6,11,18,19,23],using:[0,4,5,6,10,13,14,17,19,21],usr:[0,2,3,5,8,9,17,18,19,20,21,25],usual:[8,16,19],util:[0,4,7,10,20,21,23],valu:[3,10,13,14,16,20,21,23],valuabl:5,vari:[4,13],variabl:[10,13,14,20,21],variable_nam:21,variat:21,variou:[6,8,14],vasp:[7,10,13,14,23,24],vasprun:13,veloc:[4,10,17],verbos:[6,12,14],verbose_opt:12,veri:[0,23],version:[2,4,9,12,13,17,18,19,20],vertic:[11,20],via:[0,4,5,9,16,17,19,21],vibrat:17,viridi:[9,14,20,25],viridis_r:14,visibl:[14,20],volum:[],wai:[3,4,5,6,14,16,17,18,19],walter:6,want:[0,2,5,6,9,14,18,19,22,23],warda:6,waterfal:[2,6,14,20],wavevector:13,weight:[0,4,13,15],weighted_kpoint:23,weighted_mfp:0,weighted_r:[0,13],welcom:[6,22],well:[3,4,10,14,20,24,25],wether:5,wget:4,what:[15,18,21,23],when:[0,4,6,10,21,23,24],where:[4,5,6,11,14,17,18,20,21,25],wherea:14,whether:[6,12],which:[0,2,3,4,5,6,8,9,11,13,14,15,16,17,18,19,20,21,22,23,24,25],whilst:11,white:[5,9,14],who:6,whole:[3,13,14,17],wide:[6,18],wideband:[4,9,18],widen:4,widest:9,width:[10,11,14],wiedemann:13,willi:6,wink:[],winter_r:[14,20],within:[5,14,17],without:[5,13,15,20,22,23],work:[4,9,11,12,13,14,20,21],worker:14,workflow:4,worri:22,worth:[13,20],would:[6,13,14,15,20,22,23],wrap:5,wrapper:[6,10,13,14],write:[13,14,15,22],written:[16,18],wrt:[10,13],x_tick:14,xdata:13,xinterp:14,xmarker:[2,14],xmarkkwarg:14,xmax:14,xmin:14,xml:13,xquantiti:14,xscale:14,xxx:[],xxx_name:22,xy_limit_opt:[],y_tick:14,yaml:[4,6,8,9,10,13,14,17,18,19,20,24],yamldata:13,year:[],yet:[2,20],yinterp:14,ymarker:[2,14],ymax:14,ymin:14,you:[0,2,4,5,6,9,11,13,14,15,16,17,18,19,20,21,22,23,24,25],your:[4,5,6,11,17,18,19,22],your_hdf5_path:6,yourself:14,yourstyl:22,yquantiti:14,yscale:14,yyi:[],zdiff:4,zero:[5,13,14,15],zero_weight:15,zhu:6,zno:[2,4,5,8,9,17,18,19],zt_fromdict:10,ztdiff:[4,5,16],ztmap:[4,5]},titles:["Average Rates","ThermoParser","Cumulative Lattice Thermal Conductivity","Density of States (DoS)","Gallery","Heatmaps","Installation","tp","Phonons","Projected Phonons","tp package","tp.axes package","tp.cli package","tp.data package","tp.plot package","tp.setup package","Tutorial-00: CLI Fundamentals","Tutorial-01: Python Foundations","Tutorial-02: Individual Customisation","Tutorial-03: Compound Axes","Tutorial-04: Layered Plots","Tutorial-05: Helper Functions","Tutorial-06: Package Customisation","Tutorial-0X: Miscellaneous Assists","Tutorials","Waterfall"],titleterms:{"function":21,Axes:[17,18,19,20,21],DoS:3,assist:23,averag:0,axes:11,calcul:10,cli:[6,12,16],colour:14,colourmap:18,command:6,compound:19,conducit:23,conduct:2,content:[10,11,12,13,14,15],contribut:6,contributor:6,cumul:2,customis:[18,22],data:13,densiti:3,extend:22,format:20,foundat:17,frequenc:14,fundament:16,galleri:4,heatmap:[5,14],help:17,helper:21,indic:1,individu:18,instal:6,interfac:6,label:21,larg:11,lattic:[2,23],layer:20,legend:[11,19,21],licens:6,line:[6,17,18,19,20,21],load:[13,17,18,20],locat:21,mac:6,merg:23,mfp:14,miscellan:23,modul:[10,11,12,13,14,15],more:17,note:4,option:12,packag:[10,11,12,13,14,15,22],phonon:[8,9,14],plot:[14,17,18,19,20],point:23,project:9,python:[6,17],rate:0,refer:4,requir:6,resolv:21,run:13,save:[13,17],set:10,setup:15,small:11,state:3,submodul:[10,11,12,13,14,15],subpackag:10,tabl:1,target:23,test:6,thermal:[2,23],thermopars:[1,22],thermoplott:[],tick:21,tprc:22,tutori:[16,17,18,19,20,21,22,23,24],usag:[],util:[13,14],variabl:18,vasp:15,waterfal:25,weight:23,yaml:22,zero:23}})
\ No newline at end of file
diff --git a/docs/tp.cli.html b/docs/tp.cli.html
index 83259da..b5cc40c 100644
--- a/docs/tp.cli.html
+++ b/docs/tp.cli.html
@@ -108,6 +108,23 @@ Submodules
tp.cli.options module¶
Provides groups of options to streamline the CLI
+
+-
+
tp.cli.options.adminsitrative_options(f)[source]¶
+Help and version options.
+Allows -h for help (click-nonstandard).
+
+
+- --help, -h
+show help and exit
+- --version
+show version and exit
+
+
+
+
-
tp.cli.options.axes_limit_function(multiple=False, c=False)[source]¶
diff --git a/docs/tutorial-00.html b/docs/tutorial-00.html
index 58ef80a..84eb876 100644
--- a/docs/tutorial-00.html
+++ b/docs/tutorial-00.html
@@ -94,7 +94,7 @@ Tutorial-00: CLI Fundamentalstp get zt.
If further arguments have been given, this can be accessed with
---help, but note -h is not a substitute for --help.
+--help or -h.
Typically, you will need one or more data files, which are inputted
directly after the command, e.g. tp plot avg-rates mesh.h5. The
type of file is hinted at at the top of the --help, e.g.
diff --git a/examples/00-cli-fundamentals/README.rst b/examples/00-cli-fundamentals/README.rst
index f6424df..fe0ed46 100644
--- a/examples/00-cli-fundamentals/README.rst
+++ b/examples/00-cli-fundamentals/README.rst
@@ -10,7 +10,7 @@ type the full thing in, e.g. ``tp get``, to get a similar list of the
available functions. Then type in all three parts to get a detailed
description of how to use the function, e.g. ``tp get zt``.
If further arguments have been given, this can be accessed with
-``--help``, but note ``-h`` is *not* a substitute for ``--help``.
+``--help`` or ``-h``.
Typically, you will need one or more data files, which are inputted
directly after the command, e.g. ``tp plot avg-rates mesh.h5``. The
diff --git a/examples/heatmaps/plot-zt.sh b/examples/heatmaps/plot-zt.sh
index 3fd08c4..348feb0 100644
--- a/examples/heatmaps/plot-zt.sh
+++ b/examples/heatmaps/plot-zt.sh
@@ -1 +1 @@
-`tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete
\ No newline at end of file
+tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete
\ No newline at end of file
diff --git a/examples/phonons/plot-phonons.sh b/examples/phonons/plot-phonons.sh
index 2d84d7c..2fddee2 100644
--- a/examples/phonons/plot-phonons.sh
+++ b/examples/phonons/plot-phonons.sh
@@ -1 +1 @@
-tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR -doscolour '#d46ef9' --doscolour '#7b8eff' -c '#f0901f'
\ No newline at end of file
+tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR --doscolour '#d46ef9' --doscolour '#7b8eff' -c '#f0901f'
\ No newline at end of file
diff --git a/setup.py b/setup.py
index cfd008c..9a4e996 100644
--- a/setup.py
+++ b/setup.py
@@ -3,10 +3,10 @@
__name__ = 'ThermoParser'
__author__ = 'Kieran B. Spooner'
__copyright__ = 'Copyright Scanlon Materials Theory Group (2024)'
-__version__ = '3.1.3'
+__version__ = '3.1.4' # Remember to update the main README header too!
__maintainer__ = 'Kieran B. Spooner'
__email__ = 'k.b.spooner@bham.ac.uk'
-__date__ = 'March 21st 2024'
+__date__ = 'April 1st 2024'
import os
import setuptools
@@ -62,8 +62,7 @@ def __init__(self, *args, **kwargs):
test_suite='setup.load_test_suite',
install_requires=['click', 'h5py', 'matplotlib', 'numpy', 'pymatgen',
'pyyaml', 'scipy', 'setuptools', 'wheel'],
- extras_require={'docs': ['sphinx', 'sphinx_rtd_theme'],
- 'tests': ['unitest']},
- python_requires='>=3.6',
+ extras_require={'docs': ['sphinx', 'sphinx_rtd_theme']},
+ python_requires='>=3.8',
cmdclass={'install': PostInstallMoveFile},
entry_points={'console_scripts': ['tp = tp.cli.cli:tp_cli']})
diff --git a/tp/__init__.py b/tp/__init__.py
index ea1758b..7a12336 100644
--- a/tp/__init__.py
+++ b/tp/__init__.py
@@ -9,6 +9,8 @@
# default values and metadata
#"""
+__version__ = '3.1.4'
+
def docstring_replace(**kwargs):
def d(f):
f.__doc__ = f.__doc__.format(**kwargs)
diff --git a/tp/cli/README.rst b/tp/cli/README.rst
index 7e7ae79..306f436 100644
--- a/tp/cli/README.rst
+++ b/tp/cli/README.rst
@@ -8,8 +8,8 @@ practical differences for the user:
1. The modular structure: the overarching command is ``tp``, running
this lists the sub commands, likewise with each of those (e.g. ``tp
plot``). The full command currently has three parts, e.g. ``tp plot
- waterfall``, after which you add the arguments. ``--help`` grants
- information at every step.
+ waterfall``, after which you add the arguments. ``--help`` or ``-h``
+ grants information at every step.
2. Multiple arguments must use the ``--thing`` every time, i.e. in
``argparse`` you may type ``-d a b c``, but in ``click`` you must
type ``-d a -d b -d c``. The exception is in ``ztdiff``, where kappa
diff --git a/tp/cli/cli.py b/tp/cli/cli.py
index 08925d2..962a07a 100644
--- a/tp/cli/cli.py
+++ b/tp/cli/cli.py
@@ -64,18 +64,21 @@
from tp.cli.options import *
@click.group()
+@adminsitrative_options
def tp_cli():
"""Command line tools for transport properties."""
return
@tp_cli.group()
+@adminsitrative_options
def gen():
"""Tools for generating calculation inputs."""
return
@gen.command(no_args_is_help=True)
+@adminsitrative_options
@kpoints_options
def kpar(kpoints, mesh, poscar):
"""Suggests KPAR values for VASP.
@@ -99,6 +102,7 @@ def kpar(kpoints, mesh, poscar):
@gen.command(no_args_is_help=True)
+@adminsitrative_options
@kpoints_options
@click.option('-z', '--zero-kpoints', '--zero-ibzkpt',
help='IBZKPT file path. Overrides --zero-mesh.',
@@ -137,12 +141,14 @@ def kpoints(kpoints, mesh, poscar, zero_kpoints, zero_mesh, output):
@tp_cli.group()
+@adminsitrative_options
def get():
"""Tools for accessing data."""
return
@get.command('amset', no_args_is_help=True)
+@adminsitrative_options
@inputs_function('amset_file', nargs=1)
@click.option('-q', '--quantity',
help='Quantity to read.',
@@ -270,6 +276,7 @@ def get_amset(amset_file, quantity, dtype, doping, direction, temperature, spin,
return
@get.command('occupation')
+@adminsitrative_options
@inputs_function('amset_mesh_file', nargs=1)
@doping_type_option
@doping_function()
@@ -340,6 +347,7 @@ def get_occupation(amset_mesh_file, dtype, doping, temperature, spin, poscar):
@get.command('boltztrap')
+@adminsitrative_options
@inputs_function('boltztrap_hdf5', nargs=1)
@click.option('-q', '--quantity',
help='Quantity to read.',
@@ -399,6 +407,7 @@ def get_boltztrap(boltztrap_hdf5, quantity, dtype, doping, direction, temperatur
@get.command('phono3py', no_args_is_help=True)
+@adminsitrative_options
@inputs_function('kappa_hdf5', nargs=1)
@click.option('-q', '--quantity',
help='Quantity to read.',
@@ -492,6 +501,7 @@ def get_phono3py(kappa_hdf5, quantity, direction, temperature, band, qpoint,
@get.command('zt', no_args_is_help=True)
+@adminsitrative_options
@inputs_function('transport_file', nargs=1)
@click.option('-k', '--kappa',
help='Phono3py kappa-mxxx.hdf5.',
@@ -559,12 +569,14 @@ def get_zt(transport_file, kappa, dtype, doping, direction, temperature, max):
@tp_cli.group()
+@adminsitrative_options
def run():
"""Tools for transport properties postprocessing."""
return
@run.command(no_args_is_help=True)
+@adminsitrative_options
@click.option('--tmin',
help='Set minimum temperature in K. Does not speed up '
@@ -651,12 +663,14 @@ def boltztrap(tmin, tmax, tstep, dmin, dmax, ndope, relaxation_time, lpfac,
@tp_cli.group()
+@adminsitrative_options
def save():
"""Tools for saving data."""
return
@save.command('cumkappa', no_args_is_help=True)
+@adminsitrative_options
@inputs_function('kappa_hdf5', nargs=1)
@click.option('--mfp/--frequency',
help='x-axis quantity. [default: frequency]',
@@ -690,6 +704,7 @@ def save_cumkappa(kappa_hdf5, mfp, direction, temperature, output, extension):
@save.command('kappa', no_args_is_help=True)
+@adminsitrative_options
@inputs_function('kappa_hdf5', nargs=1)
@direction_function(multiple=True)
@click.option('-o', '--output',
@@ -720,6 +735,7 @@ def save_kappa(kappa_hdf5, direction, output):
@save.command('zt', no_args_is_help=True)
+@adminsitrative_options
@inputs_function('transport_file', nargs=1)
@click.option('-k', '--kappa',
help='Phono3py kappa-mxxx.hdf5.',
@@ -749,12 +765,14 @@ def save_zt(transport_file, kappa, dtype, direction, interpolate, kind, output):
@tp_cli.group()
+@adminsitrative_options
def plot():
"""Tools for plotting."""
return
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('mesh_h5')
@click.option('--mfp/--rate',
help='Plot mfp instead of rate. [default: rate]',
@@ -978,6 +996,7 @@ def avg_rates(mesh_h5, mfp, total, x, crt, exclude, doping, direction,
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('kappa_hdf5')
@click.option('--mfp/--frequency',
help='x-axis quantity. [default: frequency]',
@@ -1098,6 +1117,7 @@ def cumkappa(kappa_hdf5, mfp, percent, xmarkers, ymarkers, direction,
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('dos_dat', nargs=1)
@dos_function()
@fill_options
@@ -1160,6 +1180,7 @@ def dos(dos_dat, poscar, atoms, sigma, projected, total, total_label,
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@click.option('-k', '--kfile',
help='Thermal data filename(s). Required for a '
'--component of lattice or total.',
@@ -1413,6 +1434,7 @@ def kappa(kfile, efile, component, direction, tmin, tmax, dtype, doping,
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('transport_file', nargs=1)
@click.option('-z', '--zt',
help='Target ZT.',
@@ -1489,6 +1511,7 @@ def kappa_target(transport_file, zt, direction, interpolate, kind, colour,
@plot.command('phonons', no_args_is_help=True)
+@adminsitrative_options
@inputs_function('band_yaml')
@click.option('--bandmin',
help='Minimum band index.',
@@ -1600,6 +1623,7 @@ def converge_phonons(band_yaml, bandmin, bandmax, colour, alpha, linestyle,
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('transport_file')
@click.option('-k', '--kfile',
help='Thermal data filename(s). Required for a --quantity '
@@ -1994,6 +2018,7 @@ def transport(transport_file, kfile, quantity, direction, tmin, tmax, dtype,
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('kappa_hdf5', nargs=1)
@click.option('-y',
help='y-axis quantity. Options include frequency, kappa, '
@@ -2149,6 +2174,7 @@ def waterfall(kappa_hdf5, y, x, projected, direction, temperature, colour, alpha
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('band_yaml', nargs=1)
@inputs_function('kappa_hdf5', nargs=1)
@@ -2204,6 +2230,7 @@ def wideband(band_yaml, kappa_hdf5, temperature, poscar, colour, smoothing, styl
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('transport_file', nargs=1)
@click.option('--pf/--zt',
help='Power factor instead of ZT. [default: zt]',
@@ -2280,6 +2307,7 @@ def ztmap(transport_file, pf, kappa, direction, dtype, interpolate, kind,
@plot.command(no_args_is_help=True)
+@adminsitrative_options
@inputs_function('transport_files', nargs=2)
@click.option('--pf/--zt',
help='Power factor instead of ZT. [default: zt]',
diff --git a/tp/cli/options.py b/tp/cli/options.py
index 179c615..4b83bb2 100644
--- a/tp/cli/options.py
+++ b/tp/cli/options.py
@@ -3,6 +3,10 @@
#Functions
#---------
#
+# administrative_options
+# function for help and version display.
+# axes_limit_function
+# function for setting the axis limits.
# direction_function:
# function for picking the --direction (-d).
# doping_type_option:
@@ -29,12 +33,100 @@
# function for picking the --temperature (-t).
# verbose_option:
# function for increasing the verbosity.
-# axes_limit_function
-# function for setting the axis limits.
#"""
import click
+def adminsitrative_options(f):
+ """Help and version options.
+
+ Allows -h for help (click-nonstandard).
+
+ Options
+ -------
+
+ --help, -h
+ show help and exit
+ --version
+ show version and exit
+ """
+
+ f = click.help_option('-h', '--help')(f)
+ f = click.version_option(package_name='tp')(f)
+
+ return f
+
+def axes_limit_function(multiple=False, c=False):
+ """Function for creating axes limit options.
+
+ Arguments
+ ---------
+
+ multiple : bool, optional
+ allow multiple limits. Default: False.
+ c : bool, optional
+ include colour limits. Default: False.
+
+ Returns
+ -------
+ decorator
+ axes limit options decorator.
+ """
+
+ def axes_limit_options(f):
+ """Options for axes limits.
+
+ Options
+ -------
+
+ --xmin : float, optional
+ override minimum x.
+ --xmax : float, optional
+ override maximum x.
+ --ymin : float, optional
+ override minimum y.
+ --ymax : float, optional
+ override maximum y.
+ --cmin : float, optional
+ override minimum colour.
+ --cmax : float, optional
+ override maximum colour.
+
+ Returns
+ -------
+
+ decorator
+ axes limits options decorator.
+ """
+
+ f = click.option('--xmin',
+ help='Override minimum x.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--xmax',
+ help='Override maximum x.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--ymin',
+ help='Override minimum y.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--ymax',
+ help='Override maximum y.',
+ multiple=multiple,
+ type=float)(f)
+ if c:
+ f = click.option('--cmin',
+ help='Override minimum colour value.',
+ multiple=multiple,
+ type=float)(f)
+ f = click.option('--cmax',
+ help='Override maximum colour value.',
+ multiple=multiple,
+ type=float)(f)
+ return f
+ return axes_limit_options
+
def direction_function(multiple=False):
"""Function to create direction options.
@@ -147,31 +239,6 @@ def doping_option(f):
return f
return doping_option
-def heatmap_options(f):
- """Options for heatmaps."""
-
- f = click.option('--discrete/--continuous',
- help='Discretise colourmap. [default: continuous]',
- default=False,
- show_default=False)(f)
- f = click.option('-l', '--levels',
- help='Levels for discrete plots. Lists directly '
- 'specify the contour levels, while integers '
- 'specify the maximum-1 number of "nice" '
- 'levels to plot.',
- multiple=True,
- default=[None])(f)
- f = click.option('--contours',
- help='Contours to plot.',
- multiple=True,
- type=float,
- default=[None])(f)
- f = click.option('--contourcolours',
- help='contour colours',
- multiple=True,
- default=['black'])(f)
- return f
-
def dos_function(dosargs=['-c', '--colour']):
"""Function for creating DoS options.
@@ -266,6 +333,31 @@ def dos_options(f):
return f
return dos_options
+def heatmap_options(f):
+ """Options for heatmaps."""
+
+ f = click.option('--discrete/--continuous',
+ help='Discretise colourmap. [default: continuous]',
+ default=False,
+ show_default=False)(f)
+ f = click.option('-l', '--levels',
+ help='Levels for discrete plots. Lists directly '
+ 'specify the contour levels, while integers '
+ 'specify the maximum-1 number of "nice" '
+ 'levels to plot.',
+ multiple=True,
+ default=[None])(f)
+ f = click.option('--contours',
+ help='Contours to plot.',
+ multiple=True,
+ type=float,
+ default=[None])(f)
+ f = click.option('--contourcolours',
+ help='contour colours',
+ multiple=True,
+ default=['black'])(f)
+ return f
+
def inputs_function(name='filenames', nargs=-1):
"""Function for creating input arguments.
@@ -625,74 +717,3 @@ def verbose_option(f):
show_default=False)(f)
return f
-
-def axes_limit_function(multiple=False, c=False):
- """Function for creating axes limit options.
-
- Arguments
- ---------
-
- multiple : bool, optional
- allow multiple limits. Default: False.
- c : bool, optional
- include colour limits. Default: False.
-
- Returns
- -------
- decorator
- axes limit options decorator.
- """
-
- def axes_limit_options(f):
- """Options for axes limits.
-
- Options
- -------
-
- --xmin : float, optional
- override minimum x.
- --xmax : float, optional
- override maximum x.
- --ymin : float, optional
- override minimum y.
- --ymax : float, optional
- override maximum y.
- --cmin : float, optional
- override minimum colour.
- --cmax : float, optional
- override maximum colour.
-
- Returns
- -------
-
- decorator
- axes limits options decorator.
- """
-
- f = click.option('--xmin',
- help='Override minimum x.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--xmax',
- help='Override maximum x.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--ymin',
- help='Override minimum y.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--ymax',
- help='Override maximum y.',
- multiple=multiple,
- type=float)(f)
- if c:
- f = click.option('--cmin',
- help='Override minimum colour value.',
- multiple=multiple,
- type=float)(f)
- f = click.option('--cmax',
- help='Override maximum colour value.',
- multiple=multiple,
- type=float)(f)
- return f
- return axes_limit_options
diff --git a/tp/plot/frequency.py b/tp/plot/frequency.py
index a5202a5..ceb5a04 100644
--- a/tp/plot/frequency.py
+++ b/tp/plot/frequency.py
@@ -893,7 +893,7 @@ def add_projected_waterfall(ax, data, quantity, projected,
cbar.set_alpha(1)
cbar.set_label(axlabels[projected])
tp.plot.utilities.set_locators(cbar.ax, y=cbar.ax.yaxis.get_scale())
- cbar.draw_all()
+ cbar._draw_all()
if main:
data[xquantity] = x
diff --git a/tp/plot/heatmap.py b/tp/plot/heatmap.py
index 96b162d..c541d1c 100644
--- a/tp/plot/heatmap.py
+++ b/tp/plot/heatmap.py
@@ -246,17 +246,16 @@ def add_heatmap(ax, x, y, c, xinterp=None, yinterp=None, kind='linear',
# plotting
if discrete:
kwargs.pop('rasterized')
- if levels is None or levels == ():
- heat = ax.contourf(x[:-1], y[:-1], c, cmap=colours, norm=cnorm,
- **kwargs)
+ if levels in [None, (), [None], (None,)]:
+ levels = 10
else:
if isinstance(levels, (list, np.ndarray, tuple)) and len(levels) == 1:
levels = int(levels[0])
elif isinstance(levels, float):
- raise TypeError('levels must be an int or array-like, not float')
- if levels is not None and levels != ():
- heat = ax.contourf(x[:-1], y[:-1], c, cmap=colours, norm=cnorm,
- levels=levels, **kwargs)
+ raise TypeError(
+ 'levels must be an int or array-like, not float')
+ heat = ax.contourf(x[:-1], y[:-1], c, cmap=colours, norm=cnorm,
+ levels=levels, **kwargs)
else:
heat = ax.pcolormesh(x, y, c, cmap=colours, norm=cnorm, **kwargs)
fig = ax.get_figure()
@@ -267,7 +266,7 @@ def add_heatmap(ax, x, y, c, xinterp=None, yinterp=None, kind='linear',
cbar = plt.colorbar(heat, ax=ax, extend=extend)
# contours
- if contours is not None and contours != ():
+ if contours not in [None, [None], (), (None,)]:
if contourkwargs == None:
contourkwargs = {}
if not isinstance(contours, (list, np.ndarray)):
diff --git a/tp/plot/phonons.py b/tp/plot/phonons.py
index 2c7f693..2a4e639 100644
--- a/tp/plot/phonons.py
+++ b/tp/plot/phonons.py
@@ -803,7 +803,7 @@ def add_projected_dispersion(ax, data, pdata, quantity, bandmin=None,
cbar.set_alpha(1)
cbar.set_label(axlabels[quantity])
tp.plot.utilities.set_locators(cbar.ax, y=cbar.ax.yaxis.get_scale())
- cbar.draw_all()
+ cbar._draw_all()
if main:
if round(np.amin(f), 1) == 0:
@@ -1045,7 +1045,7 @@ def add_alt_projected_dispersion(ax, data, pdata, quantity, projected,
cbar.set_alpha(1)
cbar.set_label(axlabels[projected])
tp.plot.utilities.set_locators(cbar.ax, y=cbar.ax.yaxis.get_scale())
- cbar.draw_all()
+ cbar._draw_all()
if main:
ax.set_ylim(ymin, ymax)