Merge branch 'master' into locstream-support

.github/workflows/main.yml

@@ -40,6 +40,8 @@ jobs:
             tox-env: py39
           - python-version: "3.10"
             tox-env: py310
+          - python-version: "3.11"
+            tox-env: py311
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.7.0
+    rev: v3.9.0
     hooks:
     -   id: pyupgrade
         args: [ '--py38-plus' ]

CONTRIBUTING.rst

@@ -145,6 +145,6 @@ Before you submit a pull request, check that it meets these guidelines:
 #. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-#. The pull request should work for Python 3.8, 3.9, and 3.10. Check
+#. The pull request should work for Python 3.8, 3.9, 3.10, and 3.11. Check
    https://github.com/roocs/clisops/actions
    and make sure that the tests pass for all supported Python versions.

HISTORY.rst

@@ -1,14 +1,22 @@
 Version History
 ===============
 
-v.10.0 (unreleased)
--------------------
+v0.10.0 (2023-06-28)
+--------------------
+
+New Features
+^^^^^^^^^^^^
+* Added support for Python 3.11 (#287).
 
 Bug Fixes
 ^^^^^^^^^
-* Fixed bug in `core.subset.shape_bbox_indexer` with the union of invalid geometries. Added regression test. (Issue #280)
-* Added support in `core.subset.shape_bbox_indexer` for Point and MultiPoint geometries. (Issue #283)
-* Fixed `core.subset.subset_bbox` and `core.subset.subset_shape` for datasets with 1D longitude and latitude (ex : Station data).
+* Fixed bug in `core.subset.shape_bbox_indexer` with the union of invalid geometries. Added regression test. (#280)
+* Added support in `core.subset.shape_bbox_indexer` for Point and MultiPoint geometries. (#283)
+* Fixed `core.subset.subset_bbox` and `core.subset.subset_shape` for datasets with 1D longitude and latitude (ex: Station data). (#288)
+
+Other Changes
+^^^^^^^^^^^^^
+* Shapely 2.0 is now faster than pygeos for ``create_mask``. Removed pygeos from extra dependencies and pinned shapely above 2.0. (#289)
 
 v0.9.6 (2023-04-05)
 -------------------
@@ -262,7 +270,6 @@ Other Changes
 * Using file caching to gather ``xclim`` test data.
 * Change made to ``core.subset.subset_bbox._check_desc_coords`` to cope with subsetting when only one latitude or longitude exists in the input dataset
 
-
 v0.5.0 (2020-12-17)
 -------------------
 
@@ -295,7 +302,6 @@ Breaking Changes
 
 New Features
 ^^^^^^^^^^^^
-
 * ``subset_level`` added.
 * PR template.
 * Config file now exists at ``clisops.etc.roocs.ini``. This can be overwritten by setting the environment variable
@@ -313,13 +319,11 @@ New Features
 
 Bug Fixes
 ^^^^^^^^^
-
 * Nudging time values to nearest available in dataset to fix a bug where subsetting failed when the exact date
   did not exist in the dataset.
 
 Other Changes
 ^^^^^^^^^^^^^
-
 * ``cfunits`` dependency removed - not needed.
 * requirements.txt and environment.yml synced.
 * Documentation updated to include API.
@@ -341,15 +345,13 @@ Other Changes
 ^^^^^^^^^^^^^
 * Update testdata and subset module (#34).
 
-
 v0.2.1 (2020-07-08)
 -------------------
 
 Other Changes
 ^^^^^^^^^^^^^
 * Fixed docs version (#25).
 
-
 v0.2.0 (2020-06-19)
 -------------------
 
@@ -365,7 +367,6 @@ Other Changes
 * Now employing PEP8 + Black compatible autoformatting.
 * Pre-commit is now used to launch code formatting inspections for local development.
 
-
 v0.1.0 (2020-04-22)
 -------------------
 

README.rst

@@ -1,25 +1,7 @@
 clisops - climate simulation operations
 =======================================
 
-.. image:: https://img.shields.io/pypi/v/clisops.svg
-   :target: https://pypi.python.org/pypi/clisops
-   :alt: PyPI
-
-.. image:: https://img.shields.io/conda/vn/conda-forge/clisops.svg
-   :target: https://anaconda.org/conda-forge/clisops
-   :alt: Conda Forge
-
-.. image:: https://github.com/roocs/clisops/workflows/build/badge.svg
-   :target: https://github.com/roocs/clisops/actions
-   :alt: Build Status
-
-.. image:: https://coveralls.io/repos/github/roocs/clisops/badge.svg?branch=master
-   :target: https://coveralls.io/github/roocs/clisops?branch=master
-   :alt: Coverage
-
-.. image:: https://readthedocs.org/projects/clisops/badge/?version=latest
-   :target: https://clisops.readthedocs.io/en/latest/?badge=latest
-   :alt: Documentation
+|pypi| |conda| |build| |coveralls| |docs| |black|
 
 The ``clisops`` package (pronounced "clie-sops") provides a python library for running
 *data-reduction* operations on `Xarray <http://xarray.pydata.org/>`_ data sets or files
@@ -56,6 +38,27 @@ This package was created with ``Cookiecutter`` and the ``audreyr/cookiecutter-py
 * Cookiecutter: https://github.com/audreyr/cookiecutter
 * cookiecutter-pypackage: https://github.com/audreyr/cookiecutter-pypackage
 
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+
+.. |pypi| image:: https://img.shields.io/pypi/v/clisops.svg
+   :target: https://pypi.python.org/pypi/clisops
+   :alt: PyPI
+
+.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/clisops.svg
+   :target: https://anaconda.org/conda-forge/clisops
+   :alt: Conda Forge
+
+.. |build| image:: https://github.com/roocs/clisops/workflows/build/badge.svg
+   :target: https://github.com/roocs/clisops/actions
+   :alt: Build Status
+
+.. |coveralls| image:: https://coveralls.io/repos/github/roocs/clisops/badge.svg?branch=master
+   :target: https://coveralls.io/github/roocs/clisops?branch=master
+   :alt: Coverage
+
+.. |docs| image:: https://readthedocs.org/projects/clisops/badge/?version=latest
+   :target: https://clisops.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation
+
+.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/python/black
-   :alt: Python Black
+   :alt: Black

clisops/__version__.py

@@ -4,4 +4,4 @@
 
 __author__ = "Elle Smith"
 __email__ = "eleanor.smith@stfc.ac.uk"
-__version__ = "0.9.6"
+__version__ = "0.10.0"

clisops/core/subset.py

@@ -25,12 +25,6 @@
 
 from clisops.utils.dataset_utils import adjust_date_to_calendar
 
-try:
-    import pygeos  # noqa
-except ImportError:
-    pygeos = None
-
-
 __all__ = [
     "create_mask",
     "create_weight_masks",
@@ -552,35 +546,16 @@ def create_mask(
     if not is_integer_dtype(poly.index.dtype):
         poly = poly.reset_index()
 
-    if pygeos is not None:
-        # Vectorized creation of Point geometries
-        pts = pygeos.points(lon1, lat1)[np.newaxis, ...]
-        # Preparation for optimized computation
-        pygeos.prepare(pts)
-
-        geoms = pygeos.from_shapely(poly.geometry.values)[:, np.newaxis, np.newaxis]
-        pygeos.prepare(geoms)
-    else:
-        geoms = poly.geometry.values
-
-    # Do for all geometries
-    # For the pygeos case, this is slightly slower than going directly 3D,
-    # but keeps memory usage at an acceptable level with large polygon collections.
+    geoms = poly.geometry.values
     mask = np.full(lat1.shape, np.nan)
     for val, geom in zip(poly.index[::-1], geoms[::-1]):
-        if pygeos is not None:
-            # Get "covers" and remove singleton first dim
-            intersection = pygeos.covers(geom, pts)[0, ...]
-        else:
-            # Slow way because of the "touches"
-            contained = vectorized.contains(
-                geom, lon1.flatten(), lat1.flatten()
-            ).reshape(lat1.shape)
-            touched = vectorized.touches(geom, lon1.flatten(), lat1.flatten()).reshape(
-                lat1.shape
-            )
-            intersection = np.logical_or(contained, touched)
-
+        contained = vectorized.contains(geom, lon1.flatten(), lat1.flatten()).reshape(
+            lat1.shape
+        )
+        touched = vectorized.touches(geom, lon1.flatten(), lat1.flatten()).reshape(
+            lat1.shape
+        )
+        intersection = np.logical_or(contained, touched)
         mask[intersection] = val
 
     mask = xarray.DataArray(mask, dims=dims_out, coords=coords_out)

docs/conf.py

@@ -82,7 +82,7 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.9.6"
+version = "0.10.0"
 # The full version, including alpha/beta/rc tags.
 release = version
 

docs/installation.rst

@@ -29,9 +29,6 @@ you through the process.
    on packages (ESMF, ESMpy) unavailable on windows.  It can still be installed on osx/linux through `conda` or
    directly [from source](https://github.com/pangeo-data/xESMF/).
 
-Another optional dependency is [pygeos](https://pygeos.readthedocs.io/en/latest/index.html). If installed,
-the performance of `core.subset.create_mask` and `core.subset.subset_shape` are greatly improved.
-
 From sources
 ------------
 

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.6
+current_version = 0.10.0
 commit = True
 tag = True
 

setup.py

@@ -35,7 +35,7 @@
     "matplotlib",
 ]
 
-extra_requirements = ["xesmf>=0.6.2", "pygeos>=0.9"]
+extra_requirements = ["xesmf>=0.6.2"]
 
 setup(
     version=about["__version__"],
@@ -61,6 +61,7 @@
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Topic :: Security",
         "Topic :: Internet",
         "Topic :: Scientific/Engineering",

tests/core/test_subset.py

@@ -16,27 +16,6 @@
 except ImportError:
     xesmf = None
 
-try:
-    import pygeos
-except ImportError:
-    pygeos = None
-
-
-@pytest.fixture(params=[True, False])
-def toggle_pygeos(request):
-    if request.param:
-        if pygeos is None:
-            pytest.skip("pygeos not installed")
-        else:
-            yield request.param
-    else:
-        # Do not use pygeos
-        mod = subset.pygeos
-        # Monkeypatch core.subset to imitate the absence of pygeos.
-        subset.pygeos = None
-        yield request.param
-        subset.pygeos = mod
-
 
 class TestSubsetTime:
     nc_poslons = get_file("cmip3/tas.sresb1.giss_model_e_r.run1.atm.da.nc")
@@ -849,7 +828,7 @@ def test_small_poly_buffer(self, tmp_netcdf_filename):
         with xr.open_dataset(filename_or_obj=tmp_netcdf_filename) as f:
             assert {"tas", "crs"}.issubset(set(f.data_vars))
 
-    def test_mask_multiregions(self, toggle_pygeos):
+    def test_mask_multiregions(self):
         ds = xr.open_dataset(self.nc_file)
         regions = gpd.read_file(self.multi_regions_geojson)
         regions.set_index("id")
@@ -881,7 +860,7 @@ def test_subset_multiregions(self):
         assert ds_sub.notnull().sum() == 58 + 250 + 22
         assert ds_sub.tas.shape == (12, 14, 128)
 
-    def test_vectorize_touches_polygons(self, toggle_pygeos):
+    def test_vectorize_touches_polygons(self):
         """Check that points touching the polygon are included in subset."""
         # Create simple polygon
         poly = Polygon([[0, 0], [1, 0], [1, 1]])

tox.ini

@@ -1,7 +1,7 @@
 [tox]
 min_version = 4.0
 envlist =
-    py{38,39,310}
+    py{38,39,310,311}
     black
     docs
 requires =