Rename misc module to _helpers

There is no reason to expose those functions in the public API.
`rprof.plot_rprofs` as well as `time_series.plot_time_series` now take a
string to specify the variables to plot (akin to the `--plot` command
line option of the `rprof` and `tseries` subcommands).

Author: amorison

docs/index.rst

@@ -43,7 +43,6 @@ Welcome to StagPy's documentation!
    sources/apiref/config
    sources/apiref/error
    sources/apiref/field
-   sources/apiref/misc
    sources/apiref/parfile
    sources/apiref/phyvars
    sources/apiref/plates

docs/sources/apiref/misc.rst

@@ -1,4 +1,4 @@
-"""Miscellaneous definitions."""
+"""Various helper functions and classes."""
 
 from inspect import getdoc
 

stagpy/misc.py stagpy/_helpers.pystagpy/misc.py renamed to stagpy/_helpers.py

@@ -12,8 +12,8 @@
 
 import numpy as np
 
-from . import error, misc, phyvars, stagyyparsers
-from .misc import CachedReadOnlyProperty as crop
+from . import error, phyvars, stagyyparsers, _helpers
+from ._helpers import CachedReadOnlyProperty as crop
 
 
 class _Geometry:
@@ -440,7 +440,7 @@ def __getitem__(self, name):
         elif name in phyvars.RPROF_EXTRA:
             meta = phyvars.RPROF_EXTRA[name]
             rprof, rad = meta.description(step)
-            meta = phyvars.Varr(misc.baredoc(meta.description),
+            meta = phyvars.Varr(_helpers.baredoc(meta.description),
                                 meta.kind, meta.dim)
             self._cached_extra[name] = rprof, rad, meta
         else:

stagpy/_step.py

@@ -9,7 +9,7 @@
 from . import __doc__ as doc_module
 from . import conf, PARSING_OUT, load_mplstyle
 from . import commands, field, rprof, time_series, refstate, plates
-from .misc import baredoc
+from ._helpers import baredoc
 from .config import CONFIG_DIR
 
 

stagpy/args.py

@@ -12,7 +12,7 @@
 from . import conf, phyvars, __version__
 from . import stagyydata
 from .config import CONFIG_FILE, CONFIG_LOCAL
-from .misc import baredoc
+from ._helpers import baredoc
 
 
 def info_cmd():

stagpy/commands.py

@@ -8,7 +8,7 @@
 import matplotlib.patches as mpat
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 
-from . import conf, misc, phyvars
+from . import conf, phyvars, _helpers
 from .error import NotAvailableError
 from .stagyydata import StagyyData
 
@@ -166,7 +166,7 @@ def plot_scalar(step, var, field=None, axis=None, **extra):
         meta = phyvars.FIELD[var]
     else:
         meta = phyvars.FIELD_EXTRA[var]
-        meta = phyvars.Varf(misc.baredoc(meta.description), meta.dim)
+        meta = phyvars.Varf(_helpers.baredoc(meta.description), meta.dim)
     if step.geom.threed and step.geom.spherical:
         raise NotAvailableError(
             'plot_scalar not implemented for 3D spherical geometry')
@@ -318,7 +318,7 @@ def cmd():
         conf.core
     """
     sdat = StagyyData()
-    lovs = misc.list_of_vars(conf.field.plot)
+    lovs = _helpers.list_of_vars(conf.field.plot)
     # no more than two fields in a subplot
     lovs = [[slov[:2] for slov in plov] for plov in lovs]
     minmax = {}
@@ -346,9 +346,9 @@ def cmd():
                         plot_vec(axis, step, var[1])
             if conf.field.timelabel:
                 time, unit = sdat.scale(step.timeinfo['t'], 's')
-                time = misc.scilabel(time)
+                time = _helpers.scilabel(time)
                 axes[0, 0].text(0.02, 1.02, f'$t={time}$ {unit}',
                                 transform=axes[0, 0].transAxes)
             oname = '_'.join(chain.from_iterable(vfig))
             plt.tight_layout(w_pad=3)
-            misc.saveplot(fig, oname, step.isnap)
+            _helpers.saveplot(fig, oname, step.isnap)

stagpy/field.py

@@ -6,7 +6,8 @@
 import numpy as np
 from scipy.signal import argrelextrema
 
-from . import conf, error, field, misc, phyvars
+from . import conf, error, field, phyvars
+from ._helpers import saveplot
 from .stagyydata import StagyyData
 
 
@@ -283,7 +284,7 @@ def plot_plates(step, time, vrms_surface, trench, ridge, agetrench,
     plot_plate_limits(ax3, ridge, trench, conf.plates.vmin,
                       conf.plates.vmax)
 
-    misc.saveplot(fig0, 'sveltempconc', timestep)
+    saveplot(fig0, 'sveltempconc', timestep)
 
     # plotting velocity and velocity derivative
     fig0, (ax1, ax2) = plt.subplots(2, 1, sharex=True, figsize=(12, 8))
@@ -314,7 +315,7 @@ def plot_plates(step, time, vrms_surface, trench, ridge, agetrench,
         conf.plates.dvmax, facecolor='#8b6914', alpha=0.2)
     ax2.set_ylim(conf.plates.dvmin, conf.plates.dvmax)
 
-    misc.saveplot(fig0, 'sveldvel', timestep)
+    saveplot(fig0, 'sveldvel', timestep)
 
     # plotting velocity and second invariant of stress
     if 'str' in conf.plates.plot:
@@ -350,7 +351,7 @@ def plot_plates(step, time, vrms_surface, trench, ridge, agetrench,
             conf.plates.dvmax,
             facecolor='#8B6914', alpha=0.2)
 
-        misc.saveplot(fig0, 'svelstress', timestep)
+        saveplot(fig0, 'svelstress', timestep)
 
     # plotting velocity
     fig1, (ax1, ax2) = plt.subplots(2, 1, sharex=True, figsize=(12, 8))
@@ -449,7 +450,7 @@ def plot_plates(step, time, vrms_surface, trench, ridge, agetrench,
     plot_plate_limits(ax2, ridge, trench, conf.plates.topomin,
                       conf.plates.topomax)
     ax1.set_title(timestep)
-    misc.saveplot(fig1, 'sveltopo', timestep)
+    saveplot(fig1, 'sveltopo', timestep)
 
     if 'age' in conf.plates.plot:
         ax4.set_ylabel("Seafloor age [My]")
@@ -463,7 +464,7 @@ def plot_plates(step, time, vrms_surface, trench, ridge, agetrench,
         plot_plate_limits(ax4, ridge, trench, conf.plates.agemin,
                           conf.plates.agemax)
         ax3.set_title(timestep)
-        misc.saveplot(fig2, 'svelage', timestep)
+        saveplot(fig2, 'svelage', timestep)
 
     # writing the output into a file, all time steps are in one file
     for isubd in np.arange(len(distance_subd)):
@@ -505,7 +506,7 @@ def lithospheric_stress(step, trench, ridge, time):
     # Annotation with time and step
     axis.text(1., 0.9, str(round(time, 0)) + ' My', transform=axis.transAxes)
     axis.text(1., 0.1, str(timestep), transform=axis.transAxes)
-    misc.saveplot(fig, 'lith', timestep)
+    saveplot(fig, 'lith', timestep)
 
     # velocity
     vphi = step.fields['v2'][0, :, :, 0]
@@ -576,7 +577,7 @@ def lithospheric_stress(step, trench, ridge, time):
         conf.plates.lstressmax, facecolor='#8b6914', alpha=0.2)
     ax2.set_ylim(conf.plates.stressmin, conf.plates.lstressmax)
 
-    misc.saveplot(fig0, 'svelslith', timestep)
+    saveplot(fig0, 'svelslith', timestep)
 
 
 def set_of_vars(arg_plot):
@@ -686,7 +687,7 @@ def main_plates(sdat):
             # Put arrow where ridges and trenches are
             plot_plate_limits_field(axis, rcmb, ridges, trenches)
 
-            misc.saveplot(fig, 'eta', timestep, close=False)
+            saveplot(fig, 'eta', timestep, close=conf.plates.zoom is None)
 
             # Zoom
             if conf.plates.zoom is not None:
@@ -704,8 +705,7 @@ def main_plates(sdat):
                 yzoom = (rcmb + 1) * np.sin(np.radians(conf.plates.zoom))
                 axis.set_xlim(xzoom - ladd, xzoom + radd)
                 axis.set_ylim(yzoom - dadd, yzoom + uadd)
-                misc.saveplot(fig, 'etazoom', timestep, close=False)
-            plt.close(fig)
+                saveplot(fig, 'etazoom', timestep)
 
             # plot stress field with position of trenches and ridges
             if 'str' in conf.plates.plot:
@@ -721,14 +721,13 @@ def main_plates(sdat):
                 # Put arrow where ridges and trenches are
                 plot_plate_limits_field(axis, rcmb, ridges, trenches)
 
-                misc.saveplot(fig, 's', timestep, close=False)
+                saveplot(fig, 's', timestep, close=conf.plates.zoom is None)
 
                 # Zoom
                 if conf.plates.zoom is not None:
                     axis.set_xlim(xzoom - ladd, xzoom + radd)
                     axis.set_ylim(yzoom - dadd, yzoom + uadd)
-                    misc.saveplot(fig, 'szoom', timestep, close=False)
-                plt.close(fig)
+                    saveplot(fig, 'szoom', timestep)
 
                 # calculate stresses in the lithosphere
                 lithospheric_stress(step, trenches, ridges, time)
@@ -759,7 +758,7 @@ def main_plates(sdat):
                 # Put arrow where ridges and trenches are
                 plot_plate_limits_field(axis, rcmb, ridges, trenches)
 
-                misc.saveplot(fig, 'sx', timestep)
+                saveplot(fig, 'sx', timestep)
 
 
 def cmd():
@@ -814,7 +813,7 @@ def cmd():
             plt.hist(sizeplates, 10, (0, nphi / 2))
             plt.subplot(224)
             plt.plot(water_profile)
-            misc.saveplot(fig, 'plates', step.isnap)
+            saveplot(fig, 'plates', step.isnap)
 
             nb_plates.append(len(limits))
 
@@ -829,4 +828,4 @@ def cmd():
             plt.plot(time, nb_plates)
             plt.subplot(122)
             plt.plot(time, ch2o)
-            misc.saveplot(figt, f'plates_{istart}_{iend}')
+            saveplot(figt, f'plates_{istart}_{iend}')

stagpy/plates.py

@@ -2,7 +2,7 @@
 
 import matplotlib.pyplot as plt
 
-from . import conf, misc
+from . import conf, _helpers
 from .phyvars import REFSTATE
 from .stagyydata import StagyyData
 
@@ -31,7 +31,7 @@ def plot_ref(sdat, var):
     axis.set_ylabel('z Position')
     if len(adbts) > 2:
         axis.legend()
-    misc.saveplot(fig, f'refstate_{var}')
+    _helpers.saveplot(fig, f'refstate_{var}')
 
 
 def cmd():

stagpy/refstate.py

@@ -1,26 +1,26 @@
 """Plot radial profiles."""
 import matplotlib.pyplot as plt
 
-from . import conf, misc
+from . import conf, _helpers
 from .stagyydata import StagyyData
 
 
-def plot_rprofs(rprofs, lovs):
+def plot_rprofs(rprofs, names):
     """Plot requested radial profiles.
 
     Args:
         rprofs (:class:`~stagpy._step._Rprofs`): a radial profile viewer
             such as :attr:`Step.rprofs` and :attr:`_StepsView.rprofs_averaged`.
-        lovs (nested list of str): nested list of profile names such as the one
-            produced by :func:`stagpy.misc.list_of_vars`.
+        names (str): profile names separated by ``-`` (figures), ``.``
+            (subplots) and ``,`` (same subplot).
     """
     try:
         stepstr = rprofs.steps.stepstr
     except AttributeError:
         stepstr = str(rprofs.step.istep)
     sdat = rprofs.step.sdat
 
-    for vfig in lovs:
+    for vfig in _helpers.list_of_vars(names):
         fig, axes = plt.subplots(ncols=len(vfig), sharey=True,
                                  figsize=(4 * len(vfig), 6))
         axes = [axes] if len(vfig) == 1 else axes
@@ -56,7 +56,7 @@ def plot_rprofs(rprofs, lovs):
         _, unit = sdat.scale(1, 'm')
         ylabel += f' ({unit})' if unit else ''
         axes[0].set_ylabel(ylabel)
-        misc.saveplot(fig, fname + stepstr)
+        _helpers.saveplot(fig, fname + stepstr)
 
 
 def plot_grid(step):
@@ -79,7 +79,7 @@ def plot_grid(step):
     ax2.set_ylabel('$dr$' + unit)
     ax2.set_xlim([-0.5, len(rad) - 0.5])
     ax2.set_xlabel('Cell number')
-    misc.saveplot(fig, 'grid', step.istep)
+    _helpers.saveplot(fig, 'grid', step.istep)
 
 
 def cmd():
@@ -95,12 +95,8 @@ def cmd():
         for step in sdat.walk.filter(rprofs=True):
             plot_grid(step)
 
-    lovs = misc.list_of_vars(conf.rprof.plot)
-    if not lovs:
-        return
-
     if conf.rprof.average:
-        plot_rprofs(sdat.walk.rprofs_averaged, lovs)
+        plot_rprofs(sdat.walk.rprofs_averaged, conf.rprof.plot)
     else:
         for step in sdat.walk.filter(rprofs=True):
-            plot_rprofs(step.rprofs, lovs)
+            plot_rprofs(step.rprofs, conf.rprof.plot)