Reduce DeprecationWarnings in Testing

.github/workflows/pypi.yaml

@@ -15,10 +15,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools setuptools-scm wheel twine check-manifest
+          python -m pip install build twine check-manifest
       - name: Build tarball and wheels
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
           python -m pip wheel . -w dist --no-deps
       - name: Test the artifacts
         run: |
@@ -39,10 +39,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools setuptools-scm wheel twine check-manifest
+          python -m pip install build twine check-manifest
       - name: Build tarball and wheels
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
           python -m pip wheel . -w dist --no-deps
       - name: Test the artifacts
         run: |

docs/contrib.rst

@@ -34,9 +34,9 @@ in working on an issue, please comment on the issue to let us know you are
 working on it. This will help us avoid duplicate work.
 
 The code for ``geocat-comp`` is hosted on GitHub. If you do not have one, you
-will need to create a `free GitHub account <https://github.com/signup/free>`__.
+will need to create a `free GitHub account <https://github.com/signup>`__.
 The `GitHub Quickstart Guide
-<https://docs.github.com/en/get-started/quickstart>`__ is a great place to get
+<https://docs.github.com/en/get-started/start-your-journey>`__ is a great place to get
 started with git and GitHub.
 
 **************
@@ -63,7 +63,7 @@ you used to do in NCL? See our `feature request template
 to get started.
 
 You can also use our `Feature Request Form
-<https://forms.gle/6DTo3ELLri4DAGfG8>`__ to submit a feature request.
+<https://docs.google.com/forms/d/e/1FAIpQLSeWuogl8Z671et3DdrmglenBPKGFmHVHkpSamTQeoPGuytLZw/viewform>`__ to submit a feature request.
 
 
 ***********************
@@ -130,7 +130,7 @@ repository.
     cd geocat-comp git remote add upstream https://github.com/NCAR/geocat-comp.git
 
 For more information, see the `GitHub quickstart section on forking a repository
-<https://docs.github.com/en/get-started/quickstart/fork-a-repo>`__.
+<https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo>`__.
 
 Create a development environment
 --------------------------------
@@ -301,7 +301,7 @@ need to modify to incorporate your code into the package. These include:
 Write and run tests
 -------------------
 
-``geocat-comp`` uses `pytest <https://pytest.org/>`__ for unit tests, so we
+``geocat-comp`` uses `pytest <https://docs.pytest.org/en/8.0.x/>`__ for unit tests, so we
 encourage you to write new tests using ``pytest`` as well.
 
 To run the tests locally, use the following command from the root of the

docs/examples/calendar_average.ipynb

@@ -36,7 +36,7 @@
     "\n",
     "We will get the data from the [geocat-datafiles](https://github.com/NCAR/geocat-datafiles) package. This package contains example data used in many of the examples for geocat packages.\n",
     "\n",
-    "Then, we use xarray's [open_dataset](http://xarray.pydata.org/en/stable/generated/xarray.open_dataset.html) function to read the data into an xarray dataset, choose a single model from the ensemble run, and extract its surface temperature data into `temp`"
+    "Then, we use xarray's [open_dataset](https://docs.xarray.dev/en/stable/generated/xarray.open_dataset.html) function to read the data into an xarray dataset, choose a single model from the ensemble run, and extract its surface temperature data into `temp`"
    ]
   },
   {

docs/getting_started/overview.rst

@@ -17,7 +17,7 @@ a plethora of scientific analysis packages designed for general use or for niche
 for learning Python basics and for data analysis workflows. Python also enables scalability through parallel computation
 which was never possible with NCL, enabling geoscientists to tackle analysis workflows on large volumes of data.
 
-GeoCAT-comp draws from well-established analysis packages like `NumPy <https://numpy.org/>`__, `Xarray <https://docs.xarray.dev/>`__,
+GeoCAT-comp draws from well-established analysis packages like `NumPy <https://numpy.org/>`__, `Xarray <https://docs.xarray.dev/en/stable/>`__,
 `SciPy <https://scipy.org/>`__, and `MetPy <https://unidata.github.io/MetPy/>`__ to recreate and expand upon NCL
 functions in pure Python. With so many tools being used under the hood, GeoCAT-comp users have access to geoscience
 specific computational tools without needing extensive working knowledge of `Pangeo <https://pangeo.io/>`__ stack.
@@ -42,4 +42,4 @@ GeoCAT-f2py
 While our goal is to recreate NCL functions in pure Python, translating some NCL routines is challenging and time
 consuming. To ensure GeoCAT users have access to those functions while we work on full Python versions, the Fortran code
 they are based upon is wrapped in Python in the GeoCAT-f2py package. Information about
-GeoCAT-f2py can be found on the `package's homepage <https://geocat-f2py.readthedocs.io/>`__.
+GeoCAT-f2py can be found on the `package's homepage <https://geocat-f2py.readthedocs.io/en/latest/>`__.

docs/installation.rst

@@ -13,7 +13,7 @@ Installing GeoCAT-comp via Conda in a New Environment
 -----------------------------------------------------
 
 The easiest way to install GeoCAT-comp is using
-`Conda <http://conda.pydata.org/docs/>`__::
+`Conda <https://docs.conda.io/projects/conda/en/latest/>`__::
 
     conda create -n geocat -c conda-forge geocat-comp
 

docs/release-notes.rst

@@ -5,6 +5,14 @@
 Release Notes
 =============
 
+v2024.04.0 (Unreleased)
+-----------------------
+Upcoming release
+
+Internal Changes
+^^^^^^^^^^^^^^^^
+* Reduce DeprecationWarnings in testing by `Cora Schneck`_ in (:pr:`582`)
+
 v2024.03.0 (March 29, 2024)
 ---------------------------
 This release includes a bug fix for ``delta_pressure``.
@@ -138,7 +146,7 @@ Contributor's Guide to the documentation.
 New Features
 ^^^^^^^^^^^^
 * User-defined seasonal boundaries, ``custom_seasons``, enabled for
-  ``climatology_average`` by `Julia Kent`_ in (:pr:`441`)
+  ``climatology_average`` by `Julia Kent`_ in (:pr:`411`)
 
 Bug Fixes
 ^^^^^^^^^
@@ -183,7 +191,7 @@ Breaking Changes
 
 Bug Fixes
 ^^^^^^^^^
-* Fix bug in ``_temp_extrapolate`` used by ``interp_hybrid_to_pressure`` by `Katelyn FitzGerald`_ in (:pr:`422`)
+* Fix bug in ``_temp_extrapolate`` used by ``interp_hybrid_to_pressure`` by `Katelyn FitzGerald`_ in (:pr:`424`)
 
 
 v2023.05.0 (4 May 2023)

docs/user_api/index.rst

@@ -40,7 +40,7 @@ Gradient
    gradient
 
 Interpolation
-^^^^^^^^^^^^
+^^^^^^^^^^^^^
 .. currentmodule:: geocat.comp.interpolation
 .. autosummary::
    :nosignatures:

geocat/comp/climatologies.py

@@ -86,7 +86,7 @@ def _calculate_center_of_time_bounds(
 
     Notes
     -----
-    See `xarray.cftime_range <http://xarray.pydata.org/en/stable/generated/xarray.cftime_range.html>`__ for accepted values for `freq` and `calendar`.
+    See `xarray.cftime_range <https://docs.xarray.dev/en/stable/generated/xarray.cftime_range.html>`__ for accepted values for `freq` and `calendar`.
     """
 
     time_bounds = xr.cftime_range(start, end, freq=freq, calendar=calendar)

geocat/comp/interpolation.py

@@ -136,7 +136,7 @@ def _vertical_remap(func_interpolate, new_levels, xcoords, data, interp_axis=0):
 def _temp_extrapolate(data, lev_dim, lev, p_sfc, ps, phi_sfc):
     r"""This helper function extrapolates temperature below ground using the
     ECMWF formulation described in `Vertical Interpolation and Truncation of
-    Model-Coordinate Data <http://dx.doi.org/10.5065/D6HX19NH>`__ by Trenberth,
+    Model-Coordinate Data <https://opensky.ucar.edu/islandora/object/technotes:168>`__ by Trenberth,
     Berry, & Buja [NCAR/TN-396, 1993]. Specifically equation 16 is used:
 
     .. math::
@@ -191,7 +191,7 @@ def _temp_extrapolate(data, lev_dim, lev, p_sfc, ps, phi_sfc):
 def _geo_height_extrapolate(t_bot, lev, p_sfc, ps, phi_sfc):
     r"""This helper function extrapolates geopotential height below ground using
     the ECMWF formulation described in `Vertical Interpolation and Truncation
-    of Model-Coordinate Data <http://dx.doi.org/10.5065/D6HX19NH>`__ by
+    of Model-Coordinate Data <https://opensky.ucar.edu/islandora/object/technotes:168>`__ by
     Trenberth, Berry, & Buja [NCAR/TN-396, 1993]. Specifically equation 15 is
     used:
 

test/test_dask.py

@@ -45,6 +45,7 @@ def test_dewtemp_dask(self):
         assert isinstance((out - 273.15).data, dask.array.Array)
         assert np.allclose(out - 273.15, dt_2, atol=0.1)
 
+    @pytest.mark.filterwarnings("ignore:invalid value encountered in sqrt")
     def test_heat_index_dask(self):
 
         ncl_gt_1 = [

test/test_meteorology.py

@@ -96,6 +96,9 @@ def test_alt_coef(self) -> None:
                            self.ncl_gt_2,
                            atol=0.005)
 
+    @pytest.mark.filterwarnings(
+        "ignore:invalid value encountered in sqrt"
+    )  # ignores RuntimeWarning sqrt is negative, np.sqrt produces nan
     def test_xarray_alt_coef(self) -> None:
         assert np.allclose(heat_index(xr.DataArray(self.t2),
                                       xr.DataArray(self.rh2), True),
@@ -110,6 +113,9 @@ def test_list_input(self) -> None:
                            self.ncl_gt_1,
                            atol=0.005)
 
+    @pytest.mark.filterwarnings(
+        "ignore:invalid value encountered in sqrt"
+    )  # ignores RuntimeWarning sqrt is negative, np.sqrt produces nan
     def test_xarray_input(self) -> None:
         t = xr.DataArray(self.t1)
         rh = xr.DataArray(self.rh1)