Fix cf and doc

CHANGES.rst

@@ -12,6 +12,8 @@ New features
 
 Breaking changes
 ----------------
+- The :meth:`xoa.cf.CFSpecs.decode` no uses the :class:`SGLocator` instance provided by
+  :func:`xoa.cf.get_sglocator_pivot` to manage staggered grid locations for the pivot format.
 - The :meth:`xoa.cf.CFSpecs.decode` no longer sets the "cf_specs" encoding [:pull:`96`].
 - The default `name_format` option of the :cfsec:`sglocator` Cf specication option is set to False to prevent parsing the grid location in names [:pull:`96`].
 - :func:`xoa.filter.tidal_filter` raises an :class:`~xoa.XoaError` instead of a simple warning when the time step is greater than an hour.

doc/conf.py

@@ -125,9 +125,7 @@
 genoptions_declarations = 'genoptions/declarations.txt'
 
 # %% Cfgm
-import xoa.cf
-
-cfgm_get_cfgm_func = xoa.cf._get_cfgm_
+cfgm_get_cfgm_func = "xoa.cf._get_cfgm_"
 cfgm_rst_file = "cf.txt"
 
 # %% Extlinks

doc/ext/genlogos.py

@@ -28,7 +28,7 @@ def genlogo(outfile, dark=False):
     circlecolor = tuple(c / 255 for c in shomlightblue)
 
     with plt.rc_context({"font.sans-serif": [font]}):
-        plt.figure(figsize=(width, height))
+        fig = plt.figure(figsize=(width, height))
         ax = plt.axes([0, 0, 1, 1], aspect=1, facecolor="b")
         kw = dict(
             family="sans-serif",
@@ -40,8 +40,8 @@ def genlogo(outfile, dark=False):
         )
         ax.text(0.05, 0.5, "X", ha="left", **kw)
         ax.text(0.95, 0.5, "A", ha="right", **kw)
-        plt.xlim(0, width)
-        plt.ylim(0, height)
+        ax.set_xlim(0, width)
+        ax.set_ylim(0, height)
 
         clip_height = 0.26
         for y0 in (0, 1 - clip_height):
@@ -61,7 +61,9 @@ def genlogo(outfile, dark=False):
             circle.set_clip_box(clip)
 
         ax.axis("off")
-        plt.savefig(outfile, transparent=True)
+        fig.savefig(outfile, transparent=True)
+        plt.close(fig)
+        del fig
 
 
 def genlogos(app):

doc/uses.cf.rst

@@ -27,14 +27,15 @@ default behaviors for user's special datasets.
 
 
 .. note:: This module shares common feature with the excellent and long
-    awaited `xf_xarray <https://cf-xarray.readthedocs.io/en/latest/>`_
+    awaited `cf_xarray <https://cf-xarray.readthedocs.io/en/latest/>`_
     package and started a long time before with the Vacumm package.
     The most notable differences differences include:
 
-    - The current module is also designed for data variables, not only
+    - The current module is also designed for data variables an dimensions, not only
       coordinates.
-    - It search for items not only using standard_names but also
-      specialized names.
+    - It searches for items not only using standard_names but also
+      specialized names. It means that objetcs can be found a dataset or data array
+      even if they are not properly formatted.
     - It is not only available as accessors, but also as independant
       objects that can be configured for each type of dataset or in
       contexts by the user.
@@ -801,5 +802,6 @@ Now we can read, decode and merge all files without any conflict:
 
     dsv = xoa.open_data_sample("hycom.gdp.u.nc").xoa.decode()
     dsh = xoa.open_data_sample("hycom.gdp.h.nc").xoa.decode()
+    print(dsu)
     ds = xr.merge([dsu, dsv, dsh])
     ds

examples/plot_croco_section.py

@@ -4,7 +4,7 @@
 Interpolate a meridional section of CROCO outputs to regular depths
 ===================================================================
 
-This notebook, we show:
+In this notebook, we show:
 
 * how to compute the depths from s-coordinates,
 * how to easily find the name of variables and coordinates,
@@ -146,5 +146,5 @@
 axs[0].set_title("Original")
 axs[1].set_title("Interpolated")
 
-# # %%
-# # Et voilà!
+# %%
+# Et voilà!

examples/plot_mercator_argo.py

@@ -4,7 +4,7 @@
 Compare Mercator to ARGO
 ========================
 
-This notebook, we show:
+In this notebook, we show:
 
 * how to easily rename variables and coordinates in an ARGO and a Mercator datasets,
 * how to plot a T-S diagram,
@@ -99,7 +99,7 @@
     scatter_cmap="cmo.deep",
     axes=axs[1],
 )
-axs[1].axvline(x=35.65, ls="--", color="k");
+axs[1].axvline(x=35.65, ls="--", color="k")
 
 # %%
 # Here we select the last ARGO profile as a reference profile
@@ -161,7 +161,7 @@
 ax.scatter(ds_merc_ens_rect.lon, ds_merc_ens_rect.lat, label="Rejected", alpha=0.15, **kws)
 ax.scatter(ds_merc_ens.lon, ds_merc_ens.lat, label='Mercator', **kws)
 ax.scatter(ds_argo_prof.lon, ds_argo_prof.lat, s=100, c="C2", transform=pcar, label='ARGO')
-plt.legend();
+plt.legend()
 
 # %%
 # We used the :func:`xoa.geo.get_extent` to compute a square geographical extent based
@@ -191,7 +191,11 @@
 ds_argo_prof.sal.plot(y="depth", label="ARGO", color="C0")
 plt.title("Uncertain profile")
 plt.legend()
-xplot.plot_double_minimap(ds_argo_prof, regional_ax="left", global_ax=(0.88, 0.88, 0.11),);
+xplot.plot_double_minimap(
+    ds_argo_prof,
+    regional_ax="left",
+    global_ax=(0.88, 0.88, 0.11),
+)
 
 # %%
 # Therefore, if we accept an uncertainty in the positioning of the ocean
@@ -228,7 +232,7 @@
 sal_argo_prof_m.plot(y="depth", label="ARGO", color="C0", ax=axes[1])
 plt.stairs(sal_argo_prof_m, merc_prof_edges, orientation="horizontal", color="C0", lw=0.5)
 axes[1].set_title("On Mercator depths")
-axes[1].axis(axis);
+axes[1].axis(axis)
 
 # %%
 # These plots show that the model is too haline, except at the

xoa/_samples/gdp.cfg

@@ -1,3 +1,6 @@
+[sglocator]
+name_format=False
+
 [coords]
 
     [[lon]]

xoa/_samples/hycom.cfg

@@ -4,6 +4,10 @@ name=hycom
     [[attrs]]
     nsigma = "[0-9]?"
 
+[sglocator]
+name_format="{root}_{loc}"
+valid_locations=u,v
+
 [vertical]
 positive=down
 type=dz

xoa/cf.py

@@ -731,6 +731,14 @@ def add_loc(self, da, loc, to_name=True, to_attrs=True):
         )
 
 
+def get_sglocator_pivot():
+    """Get the :class:`SGLocator` instance that is used as a pivot format"""
+    cache = _get_cache_()
+    if "sglocator_pivot" not in cache:
+        cache["sglocator_pivot"] = SGLocator()
+    return cache["sglocator_pivot"]
+
+
 def _solve_rename_conflicts_(rename_args):
     """Skip renaming items that overwride previous items"""
     used = {}
@@ -933,6 +941,17 @@ def sglocator(self):
         """:class:`SGLocator` instance"""
         return self._sgl
 
+    def get_sglocator(self, specialize):
+        """Get the right :class:`SGLocator` instance
+
+        Parameters
+        ----------
+        specialize: book
+            If True, the locator is the one of this dataset, as given by :attr:`sglocator`.
+            Else, if is the pivot locator as given by :func:`get_sglocator_pivot`.
+        """
+        return self._sgl if specialize else get_sglocator_pivot()
+
     @property
     def cfgspecs(self):
         return self._cfgspecs
@@ -2746,8 +2765,11 @@ def format_dataarray(
         elif not attrs:
             attrs = {}
 
+        # Get the appropriate sglocator for formatting
+        sglocator = self.parent.get_sglocator(specialize)
+
         # Format array
-        new_da = self.sglocator.format_dataarray(
+        new_da = sglocator.format_dataarray(
             da,
             loc=loc,
             name=new_name,
@@ -2763,8 +2785,8 @@ def format_dataarray(
         # Return new name but don't rename
         if not rename:
             if old_name is None:
-                return self.sglocator.format_attr("name", new_name, loc)
-            return self.sglocator.merge_attr("name", old_name, new_name, loc)
+                return sglocator.format_attr("name", new_name, loc)
+            return sglocator.merge_attr("name", old_name, new_name, loc)
 
         # # Rename dim if axis coordinate
         # rename_dim = rename and rename_dim

xoa/cfgm.py

@@ -33,6 +33,7 @@
 from collections import OrderedDict
 from warnings import warn
 import logging
+import importlib
 
 try:
     import configobj.validate as validate
@@ -584,7 +585,7 @@ def is_dict(value, default={}, vtype=None):
     "cmap": is_cmap,
     "color": is_color,
     "dict": is_dict,
-    "boolstr": is_boolstr
+    "boolstr": is_boolstr,
     # lists validators for these scalars will be automatically generated
 }
 
@@ -2175,7 +2176,10 @@ def gen_cfgm_rst(app):
 
     logging.info("Generating rst declarations for the ConfigManager")
 
-    rst = app.config.cfgm_get_cfgm_func().to_rst(secrole="cfgmsec", optrole="cfgmopt")
+    mname, fname = os.path.splitext(app.config.cfgm_get_cfgm_func)
+    mloaded = importlib.import_module(mname)
+    func = getattr(mloaded, fname[1:])
+    rst = func().to_rst(secrole="cfgmsec", optrole="cfgmopt")
 
     outfile = os.path.abspath(app.config.cfgm_rst_file)
     outdir = os.path.dirname(outfile)
@@ -2192,7 +2196,10 @@ def gen_cfgm_cfg(app):
         return
 
     logging.info("Generating the default config from the ConfigManager")
-    cfg = app.config.cfgm_get_cfgm_func().defaults
+    mname, fname = os.path.splitext(app.config.cfgm_get_cfgm_func)
+    mloaded = importlib.import_module(mname)
+    func = getattr(mloaded, fname[1:])
+    cfg = func().defaults
     outfile = os.path.abspath(app.config.cfgm_cfg_file)
     outdir = os.path.dirname(outfile)
     if not os.path.exists(outdir):