Add wrappers for opening datasets and data variables

.vscode/settings.json

@@ -11,6 +11,7 @@
     "python.linting.flake8Enabled": true,
     "python.linting.flake8Args": ["--config=setup.cfg"],
     "python.linting.mypyEnabled": true,
+    "python.linting.mypyArgs": ["--config=setup.cfg"],
     "python.pythonPath": "/opt/miniconda3/envs/xcdat_dev/bin/python",
     "python.testing.unittestEnabled": false,
     "python.testing.nosetestsEnabled": false,

CONTRIBUTING.rst

@@ -183,14 +183,14 @@ Local Development
     plugins: anyio-2.2.0, cov-2.11.1
     collected 3 items
 
-    tests/test_utils.py ..
+    tests/test_dataset.py ..
     tests/test_xcdat.py .
 
     ---------- coverage: platform darwin, python 3.8.8-final-0 -----------
     Name                Stmts   Miss  Cover
     ---------------------------------------
     xcdat/__init__.py       3      0   100%
-    xcdat/utils.py         18      0   100%
+    xcdat/dataset.py       18      0   100%
     xcdat/xcdat.py          0      0   100%
     ---------------------------------------
     TOTAL                  21      0   100%

conda-env/dev.yml

@@ -9,11 +9,10 @@ dependencies:
     - python=3.8.8
     - pip=21.0.1
     - typing_extensions=3.7.4 # Required to make use of Python >=3.8 backported types
-    - cartopy=0.18.0
-    - matplotlib=3.3.4
     - netcdf4=1.5.6
     - xarray=0.17.0
     - cf_xarray=0.6.0
+    - dask=2021.7.0
     # Additional
     # ==================
     - bump2version==1.0.1

conda-env/readthedocs.yml

@@ -9,10 +9,10 @@ dependencies:
     - python=3.8.8
     - pip=21.0.1
     - typing_extensions=3.7.4 # Required to make use of Python >=3.8 backported types
-    - cartopy=0.18.0
-    - matplotlib=3.3.4
     - netcdf4=1.5.6
     - xarray=0.17.0
+    - dask=2021.7.0
+    - cf_xarray=0.6.0
     # Documentation
     # ==================
     - sphinx=3.5.1

conda-recipe/meta.yaml

@@ -21,19 +21,18 @@ requirements:
   run:
     - python
     - typing_extensions
-    - cartopy
-    - matplotlib
     - netcdf4
     - xarray
-    - typing_extensions
+    - dask
     - cf_xarray
 
 test:
   imports:
     - xcdat
-    - xcdat.logs
-    - xcdat.coord
-    - xcdat.utils
+    - xcdat.bounds
+    - xcdat.dataset
+    - xcdat.logger
+    - xcdat.variable
 
 about:
     home: https://github.com/tomvothecoder/xcdat

docs/api.rst

@@ -4,6 +4,7 @@ API Reference
 .. autosummary::
    :toctree: generated/
 
-   xcdat.coord
-   xcdat.log
-   xcdat.utils
+   xcdat.bounds
+   xcdat.dataset
+   xcdat.logger
+   xcdat.variable

setup.py

@@ -13,7 +13,7 @@
     history = history_file.read()
 
 # https://packaging.python.org/discussions/install-requires-vs-requirements/#install-requires
-requirements: List[str] = []
+requirements: List[str] = ["xarray", "pandas", "numpy"]
 
 setup_requirements = [
     "pytest-runner",

tests/fixtures.py

@@ -0,0 +1,188 @@
+"""This module stores reusable test fixtures."""
+from datetime import datetime
+
+import numpy as np
+import xarray as xr
+
+# If the fixture is an xarray object, make sure to use .copy() to create a
+# shallow copy of the object. Otherwise, you might run into unintentional
+# side-effects caused by reference assignment.
+# https://xarray.pydata.org/en/stable/generated/xarray.DataArray.copy.html
+
+# Dataset coordinates
+time = xr.DataArray(
+    data=[
+        datetime(2000, 1, 1),
+        datetime(2000, 2, 1),
+        datetime(2000, 3, 1),
+        datetime(2000, 4, 1),
+        datetime(2000, 5, 1),
+        datetime(2000, 6, 1),
+        datetime(2000, 7, 1),
+        datetime(2000, 8, 1),
+        datetime(2000, 9, 1),
+        datetime(2000, 10, 1),
+        datetime(2000, 11, 1),
+        datetime(2000, 12, 1),
+    ],
+    dims=["time"],
+)
+time_non_cf_compliant = xr.DataArray(
+    data=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
+    dims=["time"],
+    attrs={"units": "months since 2000-01-01"},
+)
+
+lat = xr.DataArray(
+    data=np.array([-90, -88.75, 88.75, 90]),
+    dims=["lat"],
+    attrs={"units": "degrees_north", "axis": "Y"},
+)
+lon = xr.DataArray(
+    data=np.array([0, 1.875, 356.25, 358.125]),
+    dims=["lon"],
+    attrs={"units": "degrees_east", "axis": "X"},
+)
+
+# Dataset data variables (bounds)
+time_bnds = xr.DataArray(
+    name="time_bnds",
+    data=[
+        [datetime(1999, 12, 16, 12), datetime(2000, 1, 16, 12)],
+        [datetime(2000, 1, 16, 12), datetime(2000, 2, 15, 12)],
+        [datetime(2000, 2, 15, 12), datetime(2000, 3, 16, 12)],
+        [datetime(2000, 3, 16, 12), datetime(2000, 4, 16)],
+        [datetime(2000, 4, 16), datetime(2000, 5, 16, 12)],
+        [datetime(2000, 5, 16, 12), datetime(2000, 6, 16)],
+        [datetime(2000, 6, 16), datetime(2000, 7, 16, 12)],
+        [datetime(2000, 7, 16, 12), datetime(2000, 8, 16, 12)],
+        [datetime(2000, 8, 16, 12), datetime(2000, 9, 16)],
+        [datetime(2000, 9, 16), datetime(2000, 10, 16, 12)],
+        [datetime(2000, 10, 16, 12), datetime(2000, 11, 16)],
+        [datetime(2000, 11, 16), datetime(2000, 12, 16)],
+    ],
+    coords={"time": time},
+    dims=["time", "bnds"],
+    attrs={"is_generated": "True"},
+)
+
+time_bnds_non_cf_compliant = xr.DataArray(
+    name="time_bnds",
+    data=[
+        [datetime(1999, 12, 16, 12), datetime(2000, 1, 16, 12)],
+        [datetime(2000, 1, 16, 12), datetime(2000, 2, 15, 12)],
+        [datetime(2000, 2, 15, 12), datetime(2000, 3, 16, 12)],
+        [datetime(2000, 3, 16, 12), datetime(2000, 4, 16)],
+        [datetime(2000, 4, 16), datetime(2000, 5, 16, 12)],
+        [datetime(2000, 5, 16, 12), datetime(2000, 6, 16)],
+        [datetime(2000, 6, 16), datetime(2000, 7, 16, 12)],
+        [datetime(2000, 7, 16, 12), datetime(2000, 8, 16, 12)],
+        [datetime(2000, 8, 16, 12), datetime(2000, 9, 16)],
+        [datetime(2000, 9, 16), datetime(2000, 10, 16, 12)],
+        [datetime(2000, 10, 16, 12), datetime(2000, 11, 16)],
+        [datetime(2000, 11, 16), datetime(2000, 12, 16)],
+    ],
+    coords={"time": time.data},
+    dims=["time", "bnds"],
+    attrs={"is_generated": "True"},
+)
+lat_bnds = xr.DataArray(
+    name="lat_bnds",
+    data=np.array([[-90, -89.375], [-89.375, 0.0], [0.0, 89.375], [89.375, 90]]),
+    coords={"lat": lat.data},
+    dims=["lat", "bnds"],
+    attrs={"units": "degrees_north", "axis": "Y", "is_generated": "True"},
+)
+lon_bnds = xr.DataArray(
+    name="lon_bnds",
+    data=np.array(
+        [
+            [-0.9375, 0.9375],
+            [0.9375, 179.0625],
+            [179.0625, 357.1875],
+            [357.1875, 359.0625],
+        ]
+    ),
+    coords={"lon": lon.data},
+    dims=["lon", "bnds"],
+    attrs={"units": "degrees_east", "axis": "X", "is_generated": "True"},
+)
+
+# Dataset data variables (variables)
+ts = xr.DataArray(
+    name="ts",
+    data=np.ones((12, 4, 4)),
+    coords={"time": time, "lat": lat, "lon": lon},
+    dims=["time", "lat", "lon"],
+)
+ts_non_cf_compliant = xr.DataArray(
+    name="ts",
+    data=np.ones((12, 4, 4)),
+    coords={"time": time_non_cf_compliant, "lat": lat, "lon": lon},
+    dims=["time", "lat", "lon"],
+)
+
+ts_with_bnds = xr.DataArray(
+    name="ts",
+    data=np.ones((2, 12, 4, 4)),
+    coords={
+        "bnds": np.array([0, 1]),
+        "time": time.assign_attrs(bounds="time_bnds"),
+        "lat": lat.assign_attrs(bounds="lat_bnds"),
+        "lon": lon.assign_attrs(bounds="lon_bnds"),
+        "lat_bnds": lat_bnds,
+        "lon_bnds": lon_bnds,
+        "time_bnds": time_bnds,
+    },
+    dims=[
+        "bnds",
+        "time",
+        "lat",
+        "lon",
+    ],
+)
+
+
+def generate_dataset(cf_compliant=True, has_bounds: bool = True) -> xr.Dataset:
+    """Generates a dataset using coordinate and data variable fixtures.
+
+    NOTE: Using ``.assign()`` to add data variables to an existing dataset will
+    remove attributes from existing coordinates. The workaround is to update a
+    data_vars dict then create the dataset. https://github.com/pydata/xarray/issues/2245
+
+    Parameters
+    ----------
+    cf_compliant : bool, optional
+        CF compliant time units, by default True
+    has_bounds : bool, optional
+        Include bounds for coordinates, by default True
+
+    Returns
+    -------
+    xr.Dataset
+        Test dataset.
+    """
+    data_vars = {}
+    coords = {
+        "lat": lat.copy(),
+        "lon": lon.copy(),
+    }
+
+    if cf_compliant:
+        coords.update({"time": time.copy()})
+        data_vars.update({"ts": ts.copy()})
+    else:
+        coords.update({"time": time_non_cf_compliant.copy()})
+        data_vars.update({"ts": ts_non_cf_compliant.copy()})
+
+    if has_bounds:
+        data_vars.update(
+            {
+                "time_bnds": time_bnds.copy(),
+                "lat_bnds": lat_bnds.copy(),
+                "lon_bnds": lon_bnds.copy(),
+            }
+        )
+
+    ds = xr.Dataset(data_vars=data_vars, coords=coords)
+    return ds