Merge pull request #830 from dopplershift/cleanup

Miscellaneous Cleanups

.gitignore

@@ -52,3 +52,4 @@ nosetests.xml
 
 # Translations
 *.mo
+docs/sg_execution_times.rst

CONTRIBUTING.md

@@ -83,7 +83,7 @@ Add tests for your change(s). Make the tests pass:
 
     py.test
 
-Commit the changes you made. Chris Beams has written a [guide](https://chris.beams.io/posts/git-commit/) on how to write good commit messages.
+Commit the changes you made. Chris Beams has written a [guide](https://cbea.ms/git-commit/) on how to write good commit messages.
 
 Push to your fork and [submit a pull request][pr].
 
@@ -111,8 +111,8 @@ Some things that will increase the chance that your pull request is accepted:
 * Follow [PEP8][pep8] for style. (The `flake8` utility can help with this.)
 * Write a [good commit message][commit].
 
-Pull requests will automatically have tests run by Travis. This includes
-running both the unit tests as well as the `flake8` code linter.
+Pull requests will automatically have tests run by GitHub Actions. This includes
+running both the unit tests as well as the `flake8` and `ruff` code linters.
 
 [pep8]: https://pep8.org
 [commit]: https://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html

README.rst

@@ -5,7 +5,7 @@ Siphon
 
 |Docs| |PyPI| |Conda|
 
-|Travis| |AppVeyor| |CodeCov|
+|CodeCov|
 
 |Codacy|
 

docs/conf.py

@@ -58,8 +58,15 @@
                        'numpy': ('https://numpy.org/doc/stable/', None),
                        'matplotlib': ('https://matplotlib.org/stable/', None),
                        'requests': ('https://requests.kennethreitz.org/en/latest/', None),
+                       'pandas': ('https://pandas.pydata.org/docs/', None),
                        }
 
+nitpicky = True
+nitpick_ignore = [
+    ('py:class', 'optional'), ('py:class', 'file-like object'), ('py:class', 'iterator')
+]
+nitpick_ignore_regex = [('py:class', r'.*[cC]allable'),]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -304,3 +311,10 @@
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
+
+# Dictionary of URL redirects allowed
+linkcheck_allowed_redirects = {
+    r'https://doi.org/.*': r'https://.*',
+    r'https://gitter.im/Unidata/siphon': r'https://app.gitter.im/.*siphon.*',
+    r'https://codecov.io/github/Unidata/siphon': r'https://app.codecov.io/github/Unidata/siphon',
+}

docs/developerguide.rst

@@ -83,7 +83,7 @@ Code Style
 ----------
 
 Siphon uses the Python code style outlined in `PEP8
-<https://www.python.org/dev/peps/pep-0008/>`_. For better or worse, this is what the majority
+<https://peps.python.org/pep-0008/>`_. For better or worse, this is what the majority
 of the Python world uses. The one deviation is that line length limit is 95 characters. 80 is a
 good target, but some times longer lines are needed.
 
@@ -107,7 +107,7 @@ generated from docstrings, written using the
 There are also examples in the ``examples/`` directory.
 
 The documentation is hosted on `GitHub Pages <https://unidata.github.io/siphon>`_. The docs are
-built automatically from ``main`` with every build on Travis-CI; every merged PR will
+built automatically from ``main`` with every build on GitHub Actions; every merged PR will
 have the built docs upload to GitHub Pages. As part of the build, the documentation is also
 checked with ``doc8``. To see what the docs will look like, you also need to install the
 ``sphinx-rtd-theme`` package.
@@ -116,12 +116,19 @@ checked with ``doc8``. To see what the docs will look like, you also need to ins
 Other Tools
 -----------
 
-Continuous integration is performed by `Travis CI <https://www.travis-ci.org/Unidata/siphon>`_.
-This service runs the unit tests on all support versions, as well as runs against the minimum
-package versions. ``flake8`` is also run against the code to check formatting. Travis is also
-used to build the documentation and to run the examples to ensure they stay working.
-
-Test coverage is monitored by `Codecov.io <https://codecov.io/github/Unidata/siphon>`_.
+Continuous integration is performed by
+`GitHub Actions <https://github.com/Unidata/siphon/actions>`_.
+This integration runs the unit tests on Linux for all supported versions of Python, as well
+as runs against the minimum package versions, using PyPI packages. This also runs against
+a (non-exhaustive) matrix of python versions on macOS and Windows. In addition to these tests,
+GitHub actions also builds the documentation and runs the examples across multiple platforms
+and Python versions, as well as checks for any broken web links. ``flake8`` (along with a
+variety of plugins found in ``ci/linting.txt``) and ``ruff`` are also run against the code to
+check formatting using another job on GitHub Actions. As part of this linting job, the docs
+are also checked using the ``doc8`` tool, and spelling is checked using ``codespell``.
+Configurations for these are in a variety of files in ``.github/workflows``.
+
+Test coverage is monitored by `codecov.io <https://codecov.io/github/Unidata/siphon>`_.
 
 ---------
 Releasing

examples/Radar_Server_Level_3.py

@@ -8,7 +8,7 @@
 
 Use Siphon to get NEXRAD Level 3 data from a TDS.
 """
-from datetime import datetime
+from datetime import datetime, timezone
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -38,7 +38,7 @@
 # N0B, which is reflectivity data for the lowest tilt. We see that when the query
 # is represented as a string, it shows the encoded URL.
 query = rs.query()
-query.stations('CYS').time(datetime.utcnow()).variables('N0B')
+query.stations('CYS').time(datetime.now(timezone.utc)).variables('N0B')
 
 ###########################################
 # We can use the RadarServer instance to check our query, to make

examples/ncss/NCSS_Cartopy_Example.py

@@ -11,7 +11,7 @@
 This example uses Siphon's NCSS class to provide temperature data
 for contouring a basic map using CartoPy.
 """
-from datetime import datetime
+from datetime import datetime, timezone
 
 import cartopy.crs as ccrs
 import cartopy.feature as cfeature
@@ -49,13 +49,13 @@
 # will return all surface temperatures for points in our bounding box for a single time,
 # nearest to that requested. Note the string representation of the query is a properly encoded
 # query string.
-query.lonlat_box(north=43, south=35, east=-100, west=-111).time(datetime.utcnow())
+query.lonlat_box(north=43, south=35, east=-100, west=-111).time(datetime.now(timezone.utc))
 query.accept('netcdf4')
 query.variables('Temperature_surface')
 
 ###########################################
 # We now request data from the server using this query. The `NCSS` class handles parsing
-# this NetCDF data (using the `netCDF4` module). If we print out the variable names, we see
+# this NetCDF data (using the ``netCDF4`` module). If we print out the variable names, we see
 # our requested variable, as well as the coordinate variables (needed to properly reference
 # the data).
 data = ncss.get_data(query)

examples/ncss/NCSS_Example.py

@@ -8,7 +8,7 @@
 
 Use Siphon to query the NetCDF Subset Service (NCSS).
 """
-from datetime import datetime
+from datetime import datetime, timezone
 
 import matplotlib.pyplot as plt
 
@@ -38,13 +38,13 @@
 # 'Temperature_isobaric' and 'Relative_humidity_isobaric'. This request will return all
 # vertical levels for a single point and single time. Note the string representation of
 # the query is a properly encoded query string.
-query.lonlat_point(-105, 40).time(datetime.utcnow())
+query.lonlat_point(-105, 40).time(datetime.now(timezone.utc))
 query.accept('netcdf4')
 query.variables('Temperature_isobaric', 'Relative_humidity_isobaric')
 
 ###########################################
 # We now request data from the server using this query. The `NCSS` class handles parsing
-# this NetCDF data (using the `netCDF4` module). If we print out the variable names,
+# this NetCDF data (using the ``netCDF4`` module). If we print out the variable names,
 # we see our requested variables, as well as a few others (more metadata information)
 data = ncss.get_data(query)
 list(data.variables)

examples/ncss/NCSS_Timeseries_Examples.py

@@ -8,7 +8,7 @@
 
 Use Siphon to query the NetCDF Subset Service for a timeseries.
 """
-from datetime import datetime, timedelta
+from datetime import datetime, timedelta, timezone
 
 import matplotlib.pyplot as plt
 from netCDF4 import num2date
@@ -39,13 +39,13 @@
 # 'Temperature_isobaric', at the vertical level of 100000 Pa (approximately surface).
 # This request will return all times in the range for a single point. Note the string
 # representation of the query is a properly encoded query string.
-now = datetime.utcnow()
+now = datetime.now(timezone.utc)
 query.lonlat_point(-105, 40).vertical_level(100000).time_range(now, now + timedelta(days=7))
 query.variables('Temperature_isobaric').accept('netcdf')
 
 ###########################################
 # We now request data from the server using this query. The `NCSS` class handles parsing
-# this NetCDF data (using the `netCDF4` module). If we print out the variable names, we
+# this NetCDF data (using the ``netCDF4`` module). If we print out the variable names, we
 # see our requested variables, as well as a few others (more metadata information)
 data = ncss.get_data(query)
 list(data.variables)
@@ -57,7 +57,7 @@
 
 ###########################################
 # The time values are in hours relative to the start of the entire model collection.
-# Fortunately, the `netCDF4` module has a helper function to convert these numbers into
+# Fortunately, the ``netCDF4`` module has a helper function to convert these numbers into
 # Python `datetime` objects. We can see the first 5 element output by the function look
 # reasonable.
 time_vals = num2date(time[:].squeeze(), time.units, only_use_cftime_datetimes=False)

pyproject.toml

@@ -52,7 +52,7 @@ test = [
     "siphon[extras]"
 ]
 extras = [
-    "xarray>=2022.3.0"
+    "xarray>=2022.6.0"
 ]
 
 [project.urls]
@@ -87,6 +87,11 @@ combine_star = true
 [tool.pytest.ini_options]
 norecursedirs = "build docs .idea"
 doctest_optionflags = "NORMALIZE_WHITESPACE"
+xfail_strict = true
+filterwarnings = [
+    "error",
+    "ignore:numpy.ndarray size changed:RuntimeWarning",
+]
 
 [tool.ruff]
 line-length = 95

src/siphon/catalog.py

@@ -101,6 +101,7 @@ def filter_time_nearest(self, time, regex=None, strptime=None):
 
         Returns
         -------
+        Dataset
             The value with a time closest to that desired
 
         """
@@ -137,6 +138,7 @@ def filter_time_range(self, start, end, regex=None, strptime=None):
 
         Returns
         -------
+        List[Dataset]
             All values corresponding to times within the specified range
 
         """
@@ -611,7 +613,7 @@ def remote_open(self, mode='b', encoding='ascii', errors='ignore'):
 
         Parameters
         ----------
-        mode : 'b' or 't', optional
+        mode : `'b'` or `'t'`, optional
             Mode with which to open the remote data; 'b' for binary, 't' for text. Defaults
             to 'b'.
 
@@ -625,7 +627,8 @@ def remote_open(self, mode='b', encoding='ascii', errors='ignore'):
 
         Returns
         -------
-        A random access, file-like object
+        fobj : file-like object
+            A random access, file-like object for reading data
 
         """
         fobj = self.access_with_service('HTTPServer')

src/siphon/http_util.py

@@ -96,7 +96,7 @@ def urlopen(self, url, decompress=False, **kwargs):
         url : str
             The URL to request
 
-        kwargs : arbitrary keyword arguments
+        kwargs
             Additional keyword arguments to pass to :meth:`requests.Session.get`.
 
         Returns
@@ -140,14 +140,14 @@ class DataQuery:
 
     This object provides a clear API to formulate a query for data, including
     a spatial query, a time query, and possibly some variables or other parameters.
-    These objects provide a dictionary-like interface, (:meth:`items` and :meth:`__iter__`)
+    These objects provide a dictionary-like interface, (``items`` and ``__iter__``)
     sufficient to be passed to functions expecting a dictionary representing a URL query.
     Instances of this object can also be turned into a string, which will yield a
     properly escaped string for a URL.
     """
 
     def __init__(self):
-        """Construct an empty :class:`DataQuery`."""
+        """Construct an empty class representing a query for data."""
         self.var = set()
         self.time_query = OrderedDict()
         self.spatial_query = OrderedDict()
@@ -163,7 +163,7 @@ def variables(self, *var_names):
 
         Parameters
         ----------
-        var_names : one or more strings
+        var_names : str
             One or more names of variables to request. Use 'all' to request all.
 
         Returns
@@ -183,7 +183,7 @@ def add_query_parameter(self, **kwargs):
 
         Parameters
         ----------
-        kwargs : one or more strings passed as keyword arguments
+        kwargs
             Names and values of parameters to add to the query
 
         Returns
@@ -471,7 +471,7 @@ def get(self, path, params=None):
 
         Raises
         ------
-        HTTPError
+        `~requests.HTTPError`
             If the server returns anything other than a 200 (OK) code
 
         See Also
@@ -506,7 +506,7 @@ def validate_query(self, query):
 
         Parameters
         ----------
-        query : DataQuery (or subclass)
+        query : DataQuery
 
         Returns
         -------

src/siphon/ncss.py

@@ -49,7 +49,7 @@ class NCSS(HTTPEndPoint):
     """
 
     # Need staticmethod to keep this from becoming a bound method, where self
-    # is passed implicitly
+    # is passed implicitly. Needed to avoid warning about duplicated docstring.
     unit_handler = staticmethod(lambda *a, **kw: default_unit_handler(*a, **kw))
 
     def _get_metadata(self):

src/siphon/radarserver.py

@@ -30,7 +30,7 @@ def stations(self, *stns):
 
         Parameters
         ----------
-        stns : one or more strings
+        stns : str
             One or more names of variables to request
 
         Returns
@@ -192,7 +192,7 @@ def get_radarserver_datasets(server):
 
     Parameters
     ----------
-    server : string
+    server : str
         The base URL to the THREDDS server
 
     Returns

src/siphon/simplewebservice/acis.py

@@ -37,11 +37,12 @@ def acis_request(method, params):
 
     Returns
     -------
-    A dictionary of data based on the JSON parameters
+    dict[str, Any]
+        A dictionary of data based on the JSON parameters
 
     Raises
     ------
-    :class: `ACIS_API_Exception`
+    `AcisApiException`
         When the API is unable to establish a connection or returns
         unparsable data.