pre-commit run --all-files

Author: ocefpaf

.travis.yml

@@ -64,15 +64,15 @@ script:
       check-manifest --verbose ;
       twine check dist/* ;
     fi
-  
+
   - |
     if [[ $TRAVIS_JOB_NAME == 'docs' ]]; then
       set -e
       cp notebooks/quick_intro.ipynb docs/source/
       pushd docs
       make clean html linkcheck
       popd
-      if [[ -z "$TRAVIS_TAG" ]]; then 
+      if [[ -z "$TRAVIS_TAG" ]]; then
         python -m doctr deploy --build-tags --key-path github_deploy_key_pyoceans_python_ctd.enc --built-docs docs/build/html/ dev
       else
         python -m doctr deploy --build-tags --key-path github_deploy_key_pyoceans_python_ctd.enc --built-docs docs/build/html/ "version-$TRAVIS_TAG"
@@ -92,4 +92,4 @@ deploy:
     repo: pyoceans/python-ctd
     tags: true
     all_branches: master
-    condition: '$TRAVIS_JOB_NAME == "tarball"'
+    condition: '$TRAVIS_JOB_NAME == "tarball"'

MANIFEST.in

@@ -1,4 +1,4 @@
 include *.txt
 include README.md
 recursive-include ctd *.py
-prune tests
+prune tests

ctd/extras.py

@@ -1,6 +1,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import numpy.ma as ma
+
 from pandas import Series
 
 
@@ -17,9 +18,7 @@ def pointwise(x):
         if x < xs[0]:
             return ys[0] + (x - xs[0]) * (ys[1] - ys[0]) / (xs[1] - xs[0])
         elif x > xs[-1]:
-            return ys[-1] + (x - xs[-1]) * (ys[-1] - ys[-2]) / (
-                xs[-1] - xs[-2]
-            )
+            return ys[-1] + (x - xs[-1]) * (ys[-1] - ys[-2]) / (xs[-1] - xs[-2])
         else:
             return interpolator(x)
 
@@ -143,9 +142,7 @@ def gen_topomask(h, lon, lat, dx=1.0, kind="linear", plot=False):
 def plot_section(self, reverse=False, filled=False, **kw):
     import gsw
 
-    lon, lat, data = list(
-        map(np.asanyarray, (self.lon, self.lat, self.values))
-    )
+    lon, lat, data = list(map(np.asanyarray, (self.lon, self.lat, self.values)))
     data = ma.masked_invalid(data)
     h = self.get_maxdepth()
     if reverse:
@@ -167,8 +164,7 @@ def plot_section(self, reverse=False, filled=False, **kw):
     labelsize = kw.pop("labelsize", 11)
     cmap = kw.pop("cmap", plt.cm.rainbow)
     levels = kw.pop(
-        "levels",
-        np.arange(np.floor(data.min()), np.ceil(data.max()) + 0.5, 0.5),
+        "levels", np.arange(np.floor(data.min()), np.ceil(data.max()) + 0.5, 0.5),
     )
 
     # Colorbar key words.
@@ -218,14 +214,7 @@ def plot_section(self, reverse=False, filled=False, **kw):
 
     # Color version.
     cs = ax.contourf(
-        x,
-        z,
-        data,
-        cmap=cmap,
-        levels=levels,
-        alpha=1.0,
-        extend=extend,
-        zorder=2,
+        x, z, data, cmap=cmap, levels=levels, alpha=1.0, extend=extend, zorder=2,
     )  # manual=True
     # Colorbar.
     cb = fig.colorbar(

ctd/plotting.py

@@ -1,5 +1,6 @@
 import matplotlib.pyplot as plt
 import pandas as pd
+
 from pandas_flavor import register_dataframe_method, register_series_method
 
 

ctd/processing.py

@@ -1,6 +1,7 @@
 import numpy as np
 import numpy.ma as ma
 import pandas as pd
+
 from pandas_flavor import register_dataframe_method, register_series_method
 
 
@@ -145,9 +146,7 @@ def _despike(series, n1, n2, block, keep):
     # Use the last value to fill-up.
     std = np.r_[std, np.tile(std[-1], block - 1)]
     mean = np.r_[mean, np.tile(mean[-1], block - 1)]
-    mask = np.abs(data - mean.filled(fill_value=np.NaN)) > std.filled(
-        fill_value=np.NaN
-    )
+    mask = np.abs(data - mean.filled(fill_value=np.NaN)) > std.filled(fill_value=np.NaN)
     data[mask] = np.NaN
 
     # Pass two recompute the mean and std without the flagged values from pass

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/conf.py

@@ -61,6 +61,7 @@
 #
 from ctd import __version__ as VERSION
 
+
 version = VERSION
 # The full version, including alpha/beta/rc tags.
 release = VERSION

github_deploy_key_pyoceans_python_ctd.enc

@@ -1 +1 @@
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requirements.txt

@@ -1,6 +1,6 @@
 gsw>=3.3.0
 matplotlib
 numpy
-pandas-flavor==0.1.2
 pandas>=0.24.0
+pandas-flavor==0.1.2
 scipy

tests/test_plotting.py

@@ -7,6 +7,7 @@
 
 import ctd
 
+
 matplotlib.use("Agg", warn=True)
 
 data_path = Path(__file__).parent.joinpath("data")