Merge pull request #4 from rcaneill/rc_dev_orga

Re-organizing code

.gitignore

@@ -1,6 +1,9 @@
 # macOS noise
 .DS_Store
 
+# emacs tmp
+*~
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

gsw_xarray/__init__.py

@@ -1,75 +1,7 @@
 __version__ = "0.1.0"
-from functools import wraps
 
 import gsw
-import xarray as xr
-
-
-_func_standard_name_units = (
-    ("CT_from_enthalpy", "sea_water_conservative_temperature", "degC"),
-    ("CT_from_enthalpy_exact", "sea_water_conservative_temperature", "degC"),
-    ("CT_from_entropy", "sea_water_conservative_temperature", "degC"),
-    ("CT_from_pt", "sea_water_conservative_temperature", "degC"),
-    ("CT_from_rho", "sea_water_conservative_temperature", "degC"),
-    ("CT_from_t", "sea_water_conservative_temperature", "degC"),
-    ("C_from_SP", "sea_water_electrical_conductivity", "mS cm-1"),
-    ("SA_from_SP", "sea_water_absolute_salinity", "g kg-1"),
-    ("SA_from_SP_Baltic", "sea_water_absolute_salinity", "g kg-1"),
-    ("SA_from_Sstar", "sea_water_absolute_salinity", "g kg-1"),
-    ("SA_from_rho", "sea_water_absolute_salinity", "g kg-1"),
-    ("SP_from_C", "sea_water_practical_salinity", "1"),
-    ("SP_from_SA", "sea_water_practical_salinity", "1"),
-    ("SP_from_SA_Baltic", "sea_water_practical_salinity", "1"),
-    ("SP_from_SK", "sea_water_practical_salinity", "1"),
-    ("SP_from_SR", "sea_water_practical_salinity", "1"),
-    ("SP_from_Sstar", "sea_water_practical_salinity", "1"),
-    ("SP_salinometer", "sea_water_practical_salinity", "1"),
-    ("SR_from_SP", "sea_water_reference_salinity", "g kg-1"),
-    ("Sstar_from_SA", "sea_water_preformed_salinity", "g kg-1"),
-    ("Sstar_from_SP", "sea_water_preformed_salinity", "g kg-1"),
-    ("f", "coriolis_parameter", "s-1"),
-    ("p_from_z", "sea_water_pressure", "dbar"),
-    ("pt0_from_t", "sea_water_potential_temperature", "degC"),
-    ("pt_from_CT", "sea_water_potential_temperature", "degC"),
-    ("pt_from_entropy", "sea_water_potential_temperature", "degC"),
-    # if p_ref is not 0 this next standard name is incorrect
-    ("pt_from_t", "sea_water_potential_temperature", "degC"),
-    ("rho", "sea_water_density", "kg m-3"),
-    ("rho_t_exact", "sea_water_density", "kg m-3"),
-    ("sigma0", "sea_water_sigma_t", "kg m-3"),  # only applies to pressure=0
-    ("sound_speed", "speed_of_sound_in_sea_water", "m s-1"),
-    ("sound_speed_t_exact", "speed_of_sound_in_sea_water", "m s-1"),
-    ("t_from_CT", "sea_water_temperature", "degC"),
-    # not sure how I feel about this next one
-    ("z_from_p", "height_above_mean_sea_level", "m"),
-)
-
-
-def cf_attrs(standard_name, units, extra=None):
-    def cf_attrs_decorator(func):
-        @wraps(func)
-        def cf_attrs_wrapper(*args, **kwargs):
-            rv = func(*args, **kwargs)
-            if isinstance(rv, xr.DataArray):
-                rv.attrs["standard_name"] = standard_name
-                rv.attrs["units"] = units
-
-            return rv
-
-        return cf_attrs_wrapper
-
-    return cf_attrs_decorator
-
-
-def _init_funcs():
-    _wrapped_funcs = {}
-    for func, name, units in _func_standard_name_units:
-        _wrapped_funcs[func] = cf_attrs(name, units)(getattr(gsw, func))
-    return _wrapped_funcs
-
-
-_wrapped_funcs = _init_funcs()
-
+from ._core import _wrapped_funcs
 
 # See PEP 562
 def __getattr__(name):
@@ -83,6 +15,5 @@ def __getattr__(name):
                 f"module {__name__} has no attribute {name}"
             ) from error
 
-
 def __dir__():
     return list(sorted(set([*_wrapped_funcs.keys(), *dir(gsw)])))

gsw_xarray/_cf_names.py

@@ -0,0 +1,38 @@
+_func_standard_name_units = (
+    ("CT_from_enthalpy", "sea_water_conservative_temperature", "degC"),
+    ("CT_from_enthalpy_exact", "sea_water_conservative_temperature", "degC"),
+    ("CT_from_entropy", "sea_water_conservative_temperature", "degC"),
+    ("CT_from_pt", "sea_water_conservative_temperature", "degC"),
+    ("CT_from_rho", "sea_water_conservative_temperature", "degC"),
+    ("CT_from_t", "sea_water_conservative_temperature", "degC"),
+    ("C_from_SP", "sea_water_electrical_conductivity", "mS cm-1"),
+    ("SA_from_SP", "sea_water_absolute_salinity", "g kg-1"),
+    ("SA_from_SP_Baltic", "sea_water_absolute_salinity", "g kg-1"),
+    ("SA_from_Sstar", "sea_water_absolute_salinity", "g kg-1"),
+    ("SA_from_rho", "sea_water_absolute_salinity", "g kg-1"),
+    ("SP_from_C", "sea_water_practical_salinity", "1"),
+    ("SP_from_SA", "sea_water_practical_salinity", "1"),
+    ("SP_from_SA_Baltic", "sea_water_practical_salinity", "1"),
+    ("SP_from_SK", "sea_water_practical_salinity", "1"),
+    ("SP_from_SR", "sea_water_practical_salinity", "1"),
+    ("SP_from_Sstar", "sea_water_practical_salinity", "1"),
+    ("SP_salinometer", "sea_water_practical_salinity", "1"),
+    ("SR_from_SP", "sea_water_reference_salinity", "g kg-1"),
+    ("Sstar_from_SA", "sea_water_preformed_salinity", "g kg-1"),
+    ("Sstar_from_SP", "sea_water_preformed_salinity", "g kg-1"),
+    ("f", "coriolis_parameter", "s-1"),
+    ("p_from_z", "sea_water_pressure", "dbar"),
+    ("pt0_from_t", "sea_water_potential_temperature", "degC"),
+    ("pt_from_CT", "sea_water_potential_temperature", "degC"),
+    ("pt_from_entropy", "sea_water_potential_temperature", "degC"),
+    # if p_ref is not 0 this next standard name is incorrect
+    ("pt_from_t", "sea_water_potential_temperature", "degC"),
+    ("rho", "sea_water_density", "kg m-3"),
+    ("rho_t_exact", "sea_water_density", "kg m-3"),
+    ("sigma0", "sea_water_sigma_t", "kg m-3"),  # only applies to pressure=0
+    ("sound_speed", "speed_of_sound_in_sea_water", "m s-1"),
+    ("sound_speed_t_exact", "speed_of_sound_in_sea_water", "m s-1"),
+    ("t_from_CT", "sea_water_temperature", "degC"),
+    # not sure how I feel about this next one
+    ("z_from_p", "height_above_mean_sea_level", "m"),
+)

gsw_xarray/_core.py

@@ -0,0 +1,30 @@
+from functools import wraps
+
+import gsw
+import xarray as xr
+
+from ._cf_names import _func_standard_name_units
+
+def cf_attrs(standard_name, units, extra=None):
+    def cf_attrs_decorator(func):
+        @wraps(func)
+        def cf_attrs_wrapper(*args, **kwargs):
+            rv = func(*args, **kwargs)
+            if isinstance(rv, xr.DataArray):
+                rv.attrs["standard_name"] = standard_name
+                rv.attrs["units"] = units
+
+            return rv
+
+        return cf_attrs_wrapper
+
+    return cf_attrs_decorator
+
+def _init_funcs():
+    _wrapped_funcs = {}
+    for func, name, units in _func_standard_name_units:
+        _wrapped_funcs[func] = cf_attrs(name, units)(getattr(gsw, func))
+    return _wrapped_funcs
+
+
+_wrapped_funcs = _init_funcs()

gsw_xarray/tests/test_gsw_xarray.py

@@ -1,5 +1,29 @@
 from gsw_xarray import __version__
+import gsw_xarray as gsw
+import xarray as xr
 
+def _create_ds():
+    import numpy as np
+    ds = xr.Dataset()
+    id = np.arange(3)
+    ds['id'] = xr.DataArray(id, coords={'id':id})
+    ds['CT'] = ds['id'] * 10
+    ds['CT'].attrs = {'standard_name':'sea_water_conservative_temperature'}
+    ds['SA'] = ds['id'] * 0.1 + 34
+    ds['SA'].attrs = {'standard_name':'sea_water_absolute_salinity'}
+    return ds
 
 def test_version():
     assert __version__ == "0.1.0"
+
+def test_func_standard():
+    """Basic test"""
+    ds = _create_ds()
+    sigma0 = gsw.sigma0(SA=ds.SA, CT=ds.CT)
+    assert sigma0.attrs['standard_name'] == 'sea_water_sigma_t'
+
+def test_func_standard_module():
+    """gsw can be used with modules, e.g. gsw.density"""
+    ds = _create_ds()
+    sigma0 = gsw.density.sigma0(SA=ds.SA, CT=ds.CT)
+    assert sigma0.attrs['standard_name'] == 'sea_water_sigma_t'