ruff auto fixs

docs/source/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # ioos_qc documentation build configuration file, created by
 # sphinx-quickstart on Thu Aug 18 10:56:41 2016.
@@ -21,7 +20,7 @@
 import sys
 
 p = os.path.abspath(
-    os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
+    os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
 )
 sys.path.insert(0, p)
 
@@ -35,13 +34,13 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.todo',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx_autodoc_typehints',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx_autodoc_typehints",
     "nbsphinx",
 ]
 
@@ -59,25 +58,25 @@
 napoleon_use_rtype = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = ['.rst']
+source_suffix = [".rst"]
 
 # The encoding of source files.
 #
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'ioos_qc'
-copyright = '2022, IOOS'
-author = 'IOOS'
+project = "ioos_qc"
+copyright = "2022, IOOS"
+author = "IOOS"
 
 # The version info for the project yo're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -108,8 +107,8 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-exclude_patterns += ['examples/usage/*.ipynb']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns += ["examples/usage/*.ipynb"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -131,7 +130,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -148,17 +147,17 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
 html_theme_options = {
-    'description': 'IOOS QARTOD and other Quality Control tests implemented in Python',
-    'github_user': 'ioos',
-    'github_repo': 'ioos_qc',
-    'github_button': 'true',
+    "description": "IOOS QARTOD and other Quality Control tests implemented in Python",
+    "github_user": "ioos",
+    "github_repo": "ioos_qc",
+    "github_button": "true",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -187,7 +186,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -267,7 +266,7 @@
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'ioos_qcdoc'
+htmlhelp_basename = "ioos_qcdoc"
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -293,8 +292,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'ioos_qc.tex', 'ioos_qc Documentation',
-     'IOOS', 'manual'),
+    (master_doc, "ioos_qc.tex", "ioos_qc Documentation",
+     "IOOS", "manual"),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -337,11 +336,11 @@
 man_pages = [
     (
         master_doc,
-        'ioos_qc',
-        'ioos_qc Documentation',
+        "ioos_qc",
+        "ioos_qc Documentation",
         [author],
-        1
-    )
+        1,
+    ),
 ]
 
 # If true, show URL addresses after external links.
@@ -357,12 +356,12 @@
 texinfo_documents = [
     (
         master_doc,
-        'ioos_qc',
-        'ioos_qc Documentation',
+        "ioos_qc",
+        "ioos_qc Documentation",
         author,
-        'ioos_qc',
-        'Collection of utilities, scripts and tests to assist in automated quality assurance and quality control for oceanographic datasets and observing systems.',
-        'Miscellaneous'
+        "ioos_qc",
+        "Collection of utilities, scripts and tests to assist in automated quality assurance and quality control for oceanographic datasets and observing systems.",
+        "Miscellaneous",
     ),
 ]
 

ioos_qc/__init__.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# coding=utf-8
 
 try:
     from ._version import __version__

ioos_qc/argo.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# coding=utf-8
 """Tests based on the ARGO QC manual."""
 import logging
 import warnings
@@ -9,29 +8,30 @@
 import numpy as np
 
 from ioos_qc.qartod import QartodFlags
-from ioos_qc.utils import add_flag_metadata
-from ioos_qc.utils import great_circle_distance
-from ioos_qc.utils import mapdates
+from ioos_qc.utils import add_flag_metadata, great_circle_distance, mapdates
 
-L = logging.getLogger(__name__)  # noqa
+L = logging.getLogger(__name__)
 
 
-@add_flag_metadata(stanard_name='pressure_increasing_test_quality_flag',
-                   long_name='Pressure Increasing Test Quality Flag')
+@add_flag_metadata(stanard_name="pressure_increasing_test_quality_flag",
+                   long_name="Pressure Increasing Test Quality Flag")
 def pressure_increasing_test(inp):
-    """
-    Returns an array of flag values where each input is flagged with SUSPECT if
+    """Returns an array of flag values where each input is flagged with SUSPECT if
     it does not monotonically increase
 
     Ref: ARGO QC Manual: 8. Pressure increasing test
 
     Args:
+    ----
         inp: Pressure values as a numeric numpy array or a list of numbers.
+
     Returns:
+    -------
         A masked array of flag values equal in size to that of the input.
+
     """
     delta = np.diff(inp)
-    flags = np.ones_like(inp, dtype='uint8') * QartodFlags.GOOD
+    flags = np.ones_like(inp, dtype="uint8") * QartodFlags.GOOD
 
     # Correct for downcast vs upcast by flipping the sign if it's decreasing
     sign = np.sign(np.mean(delta))
@@ -44,13 +44,13 @@ def pressure_increasing_test(inp):
     return flags
 
 
-@add_flag_metadata(standard_name='speed_test_quality_flag',
-                   long_name='Speed Test Quality Flag')
+@add_flag_metadata(standard_name="speed_test_quality_flag",
+                   long_name="Speed Test Quality Flag")
 def speed_test(lon: Sequence[N],
                lat: Sequence[N],
                tinp: Sequence[N],
                suspect_threshold: float,
-               fail_threshold: float
+               fail_threshold: float,
                ) -> np.ma.core.MaskedArray:
     """Checks that the calculated speed between two points is within reasonable bounds.
 
@@ -67,6 +67,7 @@ def speed_test(lon: Sequence[N],
     Ref: ARGO QC Manual: 5. Impossible speed test
 
     Args:
+    ----
         lon: Longitudes as a numeric numpy array or a list of numbers.
         lat: Latitudes as a numeric numpy array or a list of numbers.
         tinp: Time data as a sequence of datetime objects compatible with pandas DatetimeIndex.
@@ -79,17 +80,18 @@ def speed_test(lon: Sequence[N],
            Speeds exceeding this will be flagged as FAIL.
 
     Returns:
+    -------
         A masked array of flag values equal in size to that of the input.
-    """
 
+    """
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")
         lat = np.ma.masked_invalid(np.array(lat).astype(np.float64))
         lon = np.ma.masked_invalid(np.array(lon).astype(np.float64))
         tinp = mapdates(tinp)
 
     if lon.shape != lat.shape or lon.shape != tinp.shape:
-        raise ValueError(f'Lon ({lon.shape}) and lat ({lat.shape}) and tinp ({tinp.shape}) must be the same shape')
+        raise ValueError(f"Lon ({lon.shape}) and lat ({lat.shape}) and tinp ({tinp.shape}) must be the same shape")
 
     # Save original shape
     original_shape = lon.shape
@@ -102,7 +104,7 @@ def speed_test(lon: Sequence[N],
         return np.ma.masked_array([])
 
     # Start with everything as passing
-    flag_arr = QartodFlags.GOOD * np.ma.ones(lon.size, dtype='uint8')
+    flag_arr = QartodFlags.GOOD * np.ma.ones(lon.size, dtype="uint8")
 
     # If either lon or lat are masked we just set the flag to MISSING
     mloc = lon.mask & lat.mask
@@ -117,13 +119,13 @@ def speed_test(lon: Sequence[N],
     dist = great_circle_distance(lat, lon)
 
     # calculate speed in m/s
-    speed = np.ma.zeros(tinp.size, dtype='float')
-    speed[1:] = np.abs(dist[1:] / np.diff(tinp).astype('timedelta64[s]').astype(float))
+    speed = np.ma.zeros(tinp.size, dtype="float")
+    speed[1:] = np.abs(dist[1:] / np.diff(tinp).astype("timedelta64[s]").astype(float))
 
-    with np.errstate(invalid='ignore'):
+    with np.errstate(invalid="ignore"):
         flag_arr[speed > suspect_threshold] = QartodFlags.SUSPECT
 
-    with np.errstate(invalid='ignore'):
+    with np.errstate(invalid="ignore"):
         flag_arr[speed > fail_threshold] = QartodFlags.FAIL
 
     # first value is unknown, since we have no speed data for the first point

ioos_qc/axds.py

@@ -1,29 +1,24 @@
 #!/usr/bin/env python
-# coding=utf-8
 """Tests based on the IOOS QARTOD manuals."""
 import logging
-from typing import Tuple, Sequence
 from collections import namedtuple
+from typing import Sequence, Tuple
 
 import numpy as np
 
-from ioos_qc.utils import (
-    isnan,
-    add_flag_metadata,
-    mapdates
-)
 from ioos_qc.qartod import QartodFlags
+from ioos_qc.utils import add_flag_metadata, isnan, mapdates
 
-L = logging.getLogger(__name__)  # noqa
+L = logging.getLogger(__name__)
 
 FLAGS = QartodFlags  # Default name for all check modules
 NOTEVAL_VALUE = QartodFlags.UNKNOWN
 
-span = namedtuple('Span', 'minv maxv')
+span = namedtuple("Span", "minv maxv")
 
 
-@add_flag_metadata(standard_name='gross_range_test_quality_flag',
-                   long_name='Gross Range Test Quality Flag')
+@add_flag_metadata(standard_name="gross_range_test_quality_flag",
+                   long_name="Gross Range Test Quality Flag")
 def valid_range_test(inp : Sequence[any],
                      valid_span : Tuple[any, any],
                      dtype : np.dtype = None,
@@ -41,6 +36,7 @@ def valid_range_test(inp : Sequence[any],
     behavior you can use the parameters `start_inclusive` and `end_inclusive`.
 
     Args:
+    ----
         inp (Sequence[any]): Data as a sequence of objects compatible with the fail_span objects
         fail_span (Tuple[any, any]): 2-tuple range which to flag outside data as FAIL. Objects
             should be of equal format to that of the inp parameter as they will be checked for
@@ -53,17 +49,18 @@ def valid_range_test(inp : Sequence[any],
             exclusive (False).
 
     Returns:
+    -------
         np.ma.core.MaskedArray: A masked array of flag values equal in size to that of the input.
-    """
 
+    """
     # Numpy array inputs
-    if dtype is None and hasattr(inp, 'dtype'):
+    if dtype is None and hasattr(inp, "dtype"):
         dtype = inp.dtype
     # Pandas column inputs
     # This is required because we don't want to restrict a user from using a pd.Series
     # directly with this function. If the data was coming from a Store, it would
     # always be a numpy array.
-    elif dtype is None and hasattr(inp, 'values') and hasattr(inp.values, 'dtype'):
+    elif dtype is None and hasattr(inp, "values") and hasattr(inp.values, "dtype"):
         dtype = inp.values.dtype
 
     # Save original shape
@@ -92,18 +89,18 @@ def valid_range_test(inp : Sequence[any],
     inp = inp.flatten()
 
     # Start with everything as passing (1)
-    flag_arr = np.ma.ones(inp.size, dtype='uint8')
+    flag_arr = np.ma.ones(inp.size, dtype="uint8")
 
     # Set fail on either side of the bounds, inclusive and exclusive
     if not isnan(valid_span[0]):
-        with np.errstate(invalid='ignore'):
+        with np.errstate(invalid="ignore"):
             if start_inclusive is True:
                 flag_arr[inp < valid_span[0]] = QartodFlags.FAIL
             else:
                 flag_arr[inp <= valid_span[0]] = QartodFlags.FAIL
 
     if not isnan(valid_span[1]):
-        with np.errstate(invalid='ignore'):
+        with np.errstate(invalid="ignore"):
             if end_inclusive is True:
                 flag_arr[inp > valid_span[1]] = QartodFlags.FAIL
             else: