pre-commit

.github/workflows/pre-commit.yml

@@ -12,4 +12,3 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
     - uses: pre-commit/action@v2.0.0
-

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
   hooks:
     - id: check-ast
     - id: end-of-file-fixer
+      exclude: github_deploy_key.enc
     - id: check-docstring-first
     - id: check-added-large-files
     - id: requirements-txt-fixer
@@ -14,18 +15,18 @@ repos:
     - id: debug-statements
 
 - repo: https://gitlab.com/pycqa/flake8
-  rev: 3.8.4
+  rev: 3.9.0
   hooks:
     - id: flake8
       exclude: docs/source/conf.py
-      args: [--max-line-length=105]
+      args: [--max-line-length=105, "--ignore=E203,W503"]
 
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: v5.7.0
+- repo: https://github.com/pycqa/isort
+  rev: 5.7.0
   hooks:
-  - id: isort
-    additional_dependencies: [toml]
-    args: [--project=oceans, --multi-line=3, --lines-after-imports=2, --lines-between-types=1, --trailing-comma, --force-grid-wrap=0, --use-parentheses, --line-width=88]
+    - id: isort
+      additional_dependencies: [toml]
+      args: ["--profile", "black", "--filter-files"]
 
 - repo: https://github.com/psf/black
   rev: 20.8b1
@@ -43,4 +44,4 @@ repos:
 - repo: https://github.com/asottile/add-trailing-comma
   rev: v2.1.0
   hooks:
-    - id: add-trailing-comma
+    - id: add-trailing-comma

.travis.yml

@@ -20,8 +20,6 @@ matrix:
       env: PY=3.8
     - name: "doctests"
       env: PY=3
-    - name: "coding_standards"
-      env: PY=3
     - name: "tarball"
       env: PY=3
     - name: "docs"
@@ -60,10 +58,6 @@ script:
   - if [[ $TRAVIS_JOB_NAME == doctests ]]; then
       pytest -vv oceans --doctest-modules ;
     fi
-
-  - if [[ $TRAVIS_JOB_NAME == 'coding_standards' ]]; then
-      pytest --flake8 -m flake8 ;
-    fi
 
   - |
     if [[ $TRAVIS_JOB_NAME == 'docs' ]]; then

CHANGES.txt

@@ -80,4 +80,4 @@ Version 0.1.0
 
 Version 0.0.1
 
-* Initial release.
+* Initial release.

docs/Makefile

@@ -16,4 +16,4 @@ 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/RPSstuff.rst

@@ -4,4 +4,4 @@
 .. automodule:: oceans.RPSstuff
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/source/colormaps.rst

@@ -4,4 +4,4 @@
 .. automodule:: oceans.colormaps
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/source/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -25,7 +24,6 @@
 
 from oceans._version import get_versions
 
-
 version = release = get_versions()["version"]
 del get_versions
 
@@ -116,7 +114,7 @@
         "relations.html",  # needs 'show_related': True theme option to display
         "searchbox.html",
         "donate.html",
-    ]
+    ],
 }
 
 

docs/source/datasets.rst

@@ -4,4 +4,4 @@
 .. automodule:: oceans.datasets
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/source/filters.rst

@@ -4,4 +4,4 @@
 .. automodule:: oceans.filters
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/source/ocfis.rst

@@ -4,4 +4,4 @@
 .. automodule:: oceans.ocfis
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/source/plotting.rst

@@ -4,4 +4,4 @@
 .. automodule:: oceans.plotting
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

oceans/RPSstuff.py

@@ -3,7 +3,6 @@
 import numpy as np
 import numpy.ma as ma
 
-
 earth_radius = 6371.0e3
 
 

oceans/__init__.py

@@ -1,5 +1,4 @@
 from ._version import get_versions  # noqa
 
-
 __version__ = get_versions()["version"]
 del get_versions

oceans/_version.py

@@ -68,9 +68,7 @@ def decorate(f):
     return decorate
 
 
-def run_command(
-    commands, args, cwd=None, verbose=False, hide_stderr=False, env=None
-):
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
     """Call the given command(s)."""
     assert isinstance(commands, list)
     p = None
@@ -86,7 +84,7 @@ def run_command(
                 stderr=(subprocess.PIPE if hide_stderr else None),
             )
             break
-        except EnvironmentError:
+        except OSError:
             e = sys.exc_info()[1]
             if e.errno == errno.ENOENT:
                 continue
@@ -96,7 +94,7 @@ def run_command(
             return None, None
     else:
         if verbose:
-            print("unable to find command, tried %s" % (commands,))
+            print(f"unable to find command, tried {commands}")
         return None, None
     stdout = p.communicate()[0].strip()
     if sys.version_info[0] >= 3:
@@ -135,7 +133,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     if verbose:
         print(
             "Tried directories %s but none started with prefix %s"
-            % (str(rootdirs), parentdir_prefix)
+            % (str(rootdirs), parentdir_prefix),
         )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
@@ -149,7 +147,7 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        f = open(versionfile_abs, "r")
+        f = open(versionfile_abs)
         for line in f.readlines():
             if line.strip().startswith("git_refnames ="):
                 mo = re.search(r'=\s*"(.*)"', line)
@@ -164,7 +162,7 @@ def git_get_keywords(versionfile_abs):
                 if mo:
                     keywords["date"] = mo.group(1)
         f.close()
-    except EnvironmentError:
+    except OSError:
         pass
     return keywords
 
@@ -243,9 +241,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(
-        GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True
-    )
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -297,9 +293,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = (
-                "unable to parse git-describe output: '%s'" % describe_out
-            )
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 
         # tag
@@ -308,7 +302,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
+            pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format(
                 full_tag,
                 tag_prefix,
             )
@@ -324,9 +318,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(
-            GITS, ["rev-list", "HEAD", "--count"], cwd=root
-        )
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
@@ -523,9 +515,7 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(
-            get_keywords(), cfg.tag_prefix, verbose
-        )
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
     except NotThisMethod:
         pass
 

oceans/colormaps.py

@@ -1,14 +1,11 @@
 import os
-
 from colorsys import hsv_to_rgb
 from glob import glob
 
 import matplotlib.pyplot as plt
 import numpy as np
-
 from matplotlib import colors
 
-
 cmap_path = os.path.join(os.path.dirname(__file__), "cmap_data")
 
 
@@ -26,7 +23,7 @@ def get_color(color):
     for hue in range(color):
         hue = 1.0 * hue / color
         col = [int(x) for x in hsv_to_rgb(hue, 1.0, 230)]
-        yield "#{0:02x}{1:02x}{2:02x}".format(*col)
+        yield "#{:02x}{:02x}{:02x}".format(*col)
 
 
 def cmat2cmpl(rgb, reverse=False):
@@ -160,7 +157,7 @@ def demo():
     data = np.outer(np.arange(0, 1, 0.01), np.ones(10))
     fig = plt.figure(figsize=(10, 5))
     fig.subplots_adjust(top=0.8, bottom=0.05, left=0.01, right=0.99)
-    cmaps = sorted((m for m in cm.keys() if not m.endswith("_r")))
+    cmaps = sorted(m for m in cm.keys() if not m.endswith("_r"))
     length = len(cmaps)
     for k, cmap in enumerate(cmaps):
         plt.subplot(1, length + 1, k + 1)

oceans/datasets.py

@@ -1,7 +1,6 @@
 import warnings
 
 import numpy as np
-
 from netCDF4 import Dataset
 
 from oceans.ocfis import get_profile, wrap_lon180
@@ -21,7 +20,7 @@ def _woa_variable(variable):
     v = _VAR.get(variable)
     if not v:
         raise ValueError(
-            f'Unrecognizable variable. Expected one of {list(_VAR.keys())}, got "{variable}".'
+            f'Unrecognizable variable. Expected one of {list(_VAR.keys())}, got "{variable}".',
         )
     return v
 
@@ -35,7 +34,7 @@ def _woa_url(variable, time_period, resolution):
         pref = "woa09"
         warnings.warn(
             f'The variable "{variable}" is only available at 1 degree resolution, '
-            f'annual time period, and "{pref}".'
+            f'annual time period, and "{pref}".',
         )
         return f"{base}/" f"{pref}/" f"{variable}_annual_1deg.nc"
     else:
@@ -50,7 +49,7 @@ def _woa_url(variable, time_period, resolution):
     grid = grids.get(resolution)
     if not grid:
         raise ValueError(
-            f'Unrecognizable resolution. Expected one of {list(grids.keys())}, got "{resolution}".'
+            f'Unrecognizable resolution. Expected one of {list(grids.keys())}, got "{resolution}".',
         )
     res = grid[0]
     gg = grid[1]
@@ -90,7 +89,7 @@ def _woa_url(variable, time_period, resolution):
     if not tt:
         raise ValueError(
             f"Unrecognizable time_period. "
-            f'Expected one of {list(time_periods.keys())}, got "{time_period}".'
+            f'Expected one of {list(time_periods.keys())}, got "{time_period}".',
         )
 
     url = (
@@ -102,9 +101,7 @@ def _woa_url(variable, time_period, resolution):
     return url
 
 
-def woa_profile(
-    lon, lat, variable="temperature", time_period="annual", resolution="1"
-):
+def woa_profile(lon, lat, variable="temperature", time_period="annual", resolution="1"):
     """
     Return an iris.cube instance from a World Ocean Atlas variable at a
     given lon, lat point.
@@ -143,9 +140,7 @@ def woa_profile(
     """
     import iris
 
-    url = _woa_url(
-        variable=variable, time_period=time_period, resolution=resolution
-    )
+    url = _woa_url(variable=variable, time_period=time_period, resolution=resolution)
 
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")
@@ -222,9 +217,7 @@ def woa_subset(
     url = _woa_url(variable, time_period, resolution)
     cubes = iris.load_raw(url)
     cubes = [
-        cube.intersection(
-            longitude=(bbox[0], bbox[1]), latitude=(bbox[2], bbox[3])
-        )
+        cube.intersection(longitude=(bbox[0], bbox[1]), latitude=(bbox[2], bbox[3]))
         for cube in cubes
     ]