add pre-commit

.github/workflows/pre-commit.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [master]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+    - uses: pre-commit/action@v2.0.0

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.0.1
+  hooks:
+    - id: check-ast
+    - id: debug-statements
+    - id: check-added-large-files
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.1.0
+  hooks:
+    - id: codespell
+      exclude: >
+          (?x)^(
+              .*\.c
+          )$
+      args:
+        - --ignore-words-list=nin,preformed,wih,

MANIFEST.in

@@ -14,6 +14,7 @@ prune *.egg-info
 global-exclude *.so
 
 exclude *.yml
+exclude *.yaml
 exclude *.enc
 exclude .gitignore
 exclude .isort.cfg

README.md

@@ -47,7 +47,11 @@ C99 complex data type used in original GSW-C.
 
 To test, after installation, run "pytest" from the source directory.
 
-### Note for xarray users
+## Note for xarray users
 
 A wrapper around gsw called [gsw-xarray](https://github.com/DocOtak/gsw-xarray)
 exists for xarray. It adds CF compliant attributes when possible, units, and name.
+
+## Note for on generating the docstrings
+The autogenerated docstrings are checked with codespell in the CIs.
+when autogenerating them the we need to run `pre-commit run --all-files` and fix the documentation issues found.

gsw/_wrapped_ufuncs.py

@@ -960,7 +960,7 @@ def enthalpy_first_derivatives(SA, CT, p):
     (1) h_SA, the derivative with respect to Absolute Salinity at
     constant CT and p, and
     (2) h_CT, derivative with respect to CT at constant SA and p.
-    Note that h_P is specific volume (1/rho) it can be caclulated by calling
+    Note that h_P is specific volume (1/rho) it can be calculated by calling
     gsw_specvol(SA,CT,p).
 
     Parameters
@@ -993,7 +993,7 @@ def enthalpy_first_derivatives_CT_exact(SA, CT, p):
     (1) h_SA, the derivative with respect to Absolute Salinity at
     constant CT and p, and
     (2) h_CT, derivative with respect to CT at constant SA and p.
-    Note that h_P is specific volume, v, it can be calulated by calling
+    Note that h_P is specific volume, v, it can be calculated by calling
     gsw_specvol_CT_exact(SA,CT,p).
 
     Parameters
@@ -1322,7 +1322,7 @@ def frazil_properties(SA_bulk, h_bulk, p):
     """
     Calculates the mass fraction of ice (mass of ice divided by mass of ice
     plus seawater), w_Ih_final, which results from given values of the bulk
-    Absolute Salinity, SA_bulk, bulk enthalpy, h_bulk, occuring at pressure
+    Absolute Salinity, SA_bulk, bulk enthalpy, h_bulk, occurring at pressure
     p.  The final values of Absolute Salinity, SA_final, and Conservative
     Temperature, CT_final, of the interstitial seawater phase are also
     returned.  This code assumes that there is no dissolved air in the
@@ -1344,7 +1344,7 @@ def frazil_properties(SA_bulk, h_bulk, p):
         Absolute Salinity of the seawater in the final state,
         whether or not any ice is present.
     CT_final : array-like, deg C
-        Conservative Temperature of the seawater in the the final
+        Conservative Temperature of the seawater in the final
         state, whether or not any ice is present.
     w_Ih_final : array-like, unitless
         mass fraction of ice in the final seawater-ice mixture.
@@ -1364,11 +1364,11 @@ def frazil_properties_potential(SA_bulk, h_pot_bulk, p):
     Calculates the mass fraction of ice (mass of ice divided by mass of ice
     plus seawater), w_Ih_eq, which results from given values of the bulk
     Absolute Salinity, SA_bulk, bulk potential enthalpy, h_pot_bulk,
-    occuring at pressure p.  The final equilibrium values of Absolute
+    occurring at pressure p.  The final equilibrium values of Absolute
     Salinity, SA_eq, and Conservative Temperature, CT_eq, of the
     interstitial seawater phase are also returned.  This code assumes that
     there is no dissolved air in the seawater (that is, saturation_fraction
-    is assumed to be zero thoughout the code).
+    is assumed to be zero throughout the code).
 
     Parameters
     ----------
@@ -1385,7 +1385,7 @@ def frazil_properties_potential(SA_bulk, h_pot_bulk, p):
         Absolute Salinity of the seawater in the final state,
         whether or not any ice is present.
     CT_final : array-like, deg C
-        Conservative Temperature of the seawater in the the final
+        Conservative Temperature of the seawater in the final
         state, whether or not any ice is present.
     w_Ih_final : array-like, unitless
         mass fraction of ice in the final seawater-ice mixture.
@@ -1405,11 +1405,11 @@ def frazil_properties_potential_poly(SA_bulk, h_pot_bulk, p):
     Calculates the mass fraction of ice (mass of ice divided by mass of ice
     plus seawater), w_Ih_eq, which results from given values of the bulk
     Absolute Salinity, SA_bulk, bulk potential enthalpy, h_pot_bulk,
-    occuring at pressure p.  The final equilibrium values of Absolute
+    occurring at pressure p.  The final equilibrium values of Absolute
     Salinity, SA_eq, and Conservative Temperature, CT_eq, of the
     interstitial seawater phase are also returned.  This code assumes that
     there is no dissolved air in the seawater (that is, saturation_fraction
-    is assumed to be zero thoughout the code).
+    is assumed to be zero throughout the code).
 
     Parameters
     ----------
@@ -1426,7 +1426,7 @@ def frazil_properties_potential_poly(SA_bulk, h_pot_bulk, p):
         Absolute Salinity of the seawater in the final state,
         whether or not any ice is present.
     CT_final : array-like, deg C
-        Conservative Temperature of the seawater in the the final
+        Conservative Temperature of the seawater in the final
         state, whether or not any ice is present.
     w_Ih_final : array-like, unitless
         mass fraction of ice in the final seawater-ice mixture.
@@ -1509,8 +1509,8 @@ def frazil_ratios_adiabatic_poly(SA, p, w_Ih):
 @match_args_return
 def gibbs_ice_part_t(t, p):
     """
-    part of the the first temperature derivative of Gibbs energy of ice
-    that is the outout is gibbs_ice(1,0,t,p) + S0
+    part of the first temperature derivative of Gibbs energy of ice
+    that is the output is gibbs_ice(1,0,t,p) + S0
 
     Parameters
     ----------
@@ -1531,8 +1531,8 @@ def gibbs_ice_part_t(t, p):
 @match_args_return
 def gibbs_ice_pt0(pt0):
     """
-    part of the the first temperature derivative of Gibbs energy of ice
-    that is the outout is "gibbs_ice(1,0,pt0,0) + s0"
+    part of the first temperature derivative of Gibbs energy of ice
+    that is the output is "gibbs_ice(1,0,pt0,0) + s0"
 
     Parameters
     ----------
@@ -1983,7 +1983,7 @@ def melting_ice_into_seawater(SA, CT, p, w_Ih, t_Ih):
         Absolute Salinity of the seawater in the final state,
         whether or not any ice is present.
     CT_final : array-like, deg C
-        Conservative Temperature of the seawater in the the final
+        Conservative Temperature of the seawater in the final
         state, whether or not any ice is present.
     w_Ih_final : array-like, unitless
         mass fraction of ice in the final seawater-ice mixture.
@@ -2149,10 +2149,10 @@ def melting_seaice_into_seawater(SA, CT, p, w_seaice, SA_seaice, t_seaice):
     -------
     SA_final : array-like, g/kg
         Absolute Salinity of the mixture of the melted sea ice
-        (or ice) and the orignal seawater
+        (or ice) and the original seawater
     CT_final : array-like, deg C
         Conservative Temperature of the mixture of the melted
-        sea ice (or ice) and the orignal seawater
+        sea ice (or ice) and the original seawater
 
 
     """
@@ -2633,7 +2633,7 @@ def pt_from_CT(SA, CT):
     Calculates potential temperature (with a reference sea pressure of
     zero dbar) from Conservative Temperature.  This function uses 1.5
     iterations through a modified Newton-Raphson (N-R) iterative solution
-    proceedure, starting from a rational-function-based initial condition
+    procedure, starting from a rational-function-based initial condition
     for both pt and dCT_dpt.
 
     Parameters
@@ -2842,7 +2842,7 @@ def rho(SA, CT, p):
 @match_args_return
 def rho_alpha_beta(SA, CT, p):
     """
-    Calculates in-situ density, the appropiate thermal expansion coefficient
+    Calculates in-situ density, the appropriate thermal expansion coefficient
     and the appropriate saline contraction coefficient of seawater from
     Absolute Salinity and Conservative Temperature.  This function uses the
     computationally-efficient expression for specific volume in terms of
@@ -2944,7 +2944,7 @@ def rho_ice(t, p):
     """
     Calculates in-situ density of ice from in-situ temperature and pressure.
     Note that the output, rho_ice, is density, not density anomaly;  that
-    is, 1000 kg/m^3 is not subracted from it.
+    is, 1000 kg/m^3 is not subtracted from it.
 
     Parameters
     ----------
@@ -3050,7 +3050,7 @@ def rho_t_exact(SA, t, p):
     """
     Calculates in-situ density of seawater from Absolute Salinity and
     in-situ temperature.  Note that the output, rho, is density,
-    not density anomaly; that is, 1000 kg/m^3 is not subracted from it.
+    not density anomaly; that is, 1000 kg/m^3 is not subtracted from it.
 
     Parameters
     ----------
@@ -3773,7 +3773,7 @@ def specvol(SA, CT, p):
 @match_args_return
 def specvol_alpha_beta(SA, CT, p):
     """
-    Calculates specific volume, the appropiate thermal expansion coefficient
+    Calculates specific volume, the appropriate thermal expansion coefficient
     and the appropriate saline contraction coefficient of seawater from
     Absolute Salinity and Conservative Temperature.  This function uses the
     computationally-efficient expression for specific volume in terms of
@@ -3809,9 +3809,9 @@ def specvol_anom_standard(SA, CT, p):
     Calculates specific volume anomaly from Absolute Salinity, Conservative
     Temperature and pressure. It uses the computationally-efficient
     expression for specific volume as a function of SA, CT and p (Roquet
-    et al., 2015).  The reference value to which the anomally is calculated
+    et al., 2015).  The reference value to which the anomaly is calculated
     has an Absolute Salinity of SSO and Conservative Temperature equal to
-    0 degress C.
+    0 degrees C.
 
     Parameters
     ----------
@@ -4264,7 +4264,7 @@ def t_freezing_first_derivatives(SA, p, saturation_fraction):
 @match_args_return
 def t_freezing_first_derivatives_poly(SA, p, saturation_fraction):
     """
-    Calculates the frist derivatives of the in-situ temperature at which
+    Calculates the first derivatives of the in-situ temperature at which
     seawater freezes with respect to Absolute Salinity SA and pressure P (in
     Pa).  These expressions come from differentiating the expression that
     defines the freezing temperature, namely the equality between the

gsw/tests/test_xarray.py

@@ -121,7 +121,7 @@ def test_xarray_with_coords():
     CT_chunk = CT.chunk(chunks={'y':1,'t':1})
     lat_chunk = lat.chunk(chunks={'y':1})
 
-    # Dimensions and cordinates match:
+    # Dimensions and coordinates match:
     expected = gsw.sigma0(SA_vals, CT_vals)
     xarray = gsw.sigma0(SA, CT)
     chunked = gsw.sigma0(SA_chunk, CT_chunk)

setup.py

@@ -20,7 +20,7 @@ def read(*parts):
 
 
 class build_ext(_build_ext):
-    # Extention builder from pandas without the cython stuff
+    # Extension builder from pandas without the cython stuff
     def build_extensions(self):
         numpy_incl = pkg_resources.resource_filename('numpy', 'core/include')