Checkpoint commit: continuing reorganization of the package

.gitignore

@@ -45,6 +45,7 @@ Thumbs.db
 
 # Things specific to this project #
 ###################################
+*.list
 
 # Documentation generated files #
 #################################

gsw/__init__.py

@@ -1,3 +1,12 @@
-#from ._gsw_ufuncs import *
+"""
+Python implementation of the Gibbs SeaWater (GSW) Oceanographic
+Toolbox of TEOS-10.
+"""
+
+
 from ._wrapped_ufuncs import *
-from ._pyfunctions import *
+
+from .stability import *
+from . import stability
+
+from . import conversions

gsw/conversions.py

@@ -0,0 +1,33 @@
+"""
+Conversions involving temperature, salinity, entropy, pressure,
+and height.
+"""
+from ._wrapped_ufuncs import (
+adiabatic_lapse_rate_from_CT,
+C_from_SP,
+CT_from_enthalpy,
+CT_from_entropy,
+CT_from_pt,
+CT_from_rho,
+CT_from_t,
+deltaSA_from_SP,
+entropy_from_pt,
+entropy_from_t,
+pt0_from_t,
+pt_from_CT,
+pt_from_entropy,
+pt_from_t,
+SA_from_rho,
+SA_from_SP,
+SA_from_Sstar,
+SP_from_C,
+SP_from_SA,
+SP_from_SK,
+SP_from_SR,
+SP_from_Sstar,
+SR_from_SP,
+Sstar_from_SA,
+Sstar_from_SP,
+t_from_CT,
+z_from_p,
+)

gsw/_pyfunctions.py → gsw/stability.py

@@ -1,3 +1,19 @@
+"""
+Vertical stability functions.
+
+These work with ndarrays of profiles; use the `axis` keyword
+argument to specify the axis along which pressure varies.
+For example, the default, following the Matlab versions, is
+`axis=0`, meaning the pressure varies along the first dimension.
+Use `axis=-1` if pressure varies along the last dimension--that
+is, along a row, as the column index increases, in the 2-D case.
+
+Docstrings are not yet available; they will be added later via
+an automated mechanism.
+
+"""
+
+
 import numpy as np
 
 from ._utilities import match_args_return, axis_slicer
@@ -44,6 +60,7 @@ def Nsquared(SA, CT, p, lat=None, axis=0):
 
     return N2, p_mid
 
+
 @match_args_return
 def Turner_Rsubrho(SA, CT, p, axis=0):
     SA = np.clip(SA, 0, 50)
@@ -70,6 +87,7 @@ def Turner_Rsubrho(SA, CT, p, axis=0):
 
     return Tu, Rsubrho, p_mid
 
+
 @match_args_return
 def IPV_vs_fNsquared_ratio(SA, CT, p, p_ref=0, axis=0):
     SA = np.clip(SA, 0, 50)

tools/_utilities.py

@@ -0,0 +1 @@
+../gsw/_utilities.py

tools/categories.py

@@ -0,0 +1,24 @@
+"""
+Use 'wrapped_ufuncs.list' and the function names from parsing
+Matlab to generate lists of wrapped functions in categories.
+"""
+
+from matlab_parser import get_sigdicts_by_subdir
+
+sigdicts = get_sigdicts_by_subdir()
+with open('wrapped_ufuncs.list') as f:
+    lines = f.readlines()
+    uflist = [name.strip() for name in lines]
+
+def write_basic_conversions():
+    out = []
+    nlist = [n for n in uflist if 'from' in n]
+    for name in nlist:
+        if not('ice' in name or 'freezing' in name or 'exact' in name):
+            try:
+                out.append(sigdicts['toolbox'][name]['name'])
+            except KeyError:
+                pass
+    out.append('')
+    with open('basic_conversions.list', 'w') as f:
+        f.write(',\n'.join(out))

tools/matlab_parser.py

@@ -22,7 +22,7 @@
                             r"\((?P<input>.*)\)")
 
 
-def list_functions(matdir=gsw_matlab_dir):
+def list_functions(matdir=gsw_matlab_dir, subdir=''):
     rawlist = glob.glob(os.path.join(matdir, '*.m'))
     signatures = []
     rejects = []
@@ -65,6 +65,13 @@ def get_complete_sigdict():
     return to_sigdict(get_all_signatures())
 
 
+def get_sigdicts_by_subdir():
+    out = dict(toolbox=to_sigdict(list_functions()[0]))
+    for subdir in gsw_matlab_subdirs:
+        out[subdir] = to_sigdict(list_functions(subdir=subdir)[0])
+    return out
+
+
 def variables_from_signatures(signatures):
     inputs = set()
     outputs = set()