Bump to v0.4.0 (#384)

- Bump conda env dependencies and remove unused dependencies
- Update GH Actions build workflow with latest dependencies
- Fix `mypy` warnings and errors

Author: tomvothecoder

.github/workflows/build_workflow.yml

@@ -26,20 +26,20 @@ jobs:
 
             - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
               name: Checkout Code Repository
-              uses: actions/checkout@v2
+              uses: actions/checkout@v3
 
             - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-              name: Set up Python 3.9
-              uses: actions/setup-python@v2
+              name: Set up Python 3.10
+              uses: actions/setup-python@v3
               with:
-                  python-version: 3.9
+                  python-version: "3.10"
 
             - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
               # Run all pre-commit hooks on all the files.
               # Getting only staged files can be tricky in case a new PR is opened
               # since the action is run on a branch in detached head state
               name: Install and Run Pre-commit
-              uses: pre-commit/action@v2.0.3
+              uses: pre-commit/action@v3.0.0
 
     build:
         name: Build (Python ${{ matrix.python-version }})
@@ -60,11 +60,11 @@ jobs:
                   do_not_skip: '["push", "workflow_dispatch"]'
 
             - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-              uses: actions/checkout@v2
+              uses: actions/checkout@v3
 
             - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
               name: Cache Conda
-              uses: actions/cache@v2
+              uses: actions/cache@v3
               env:
                   # Increase this value to reset cache if conda-env/ci.yml has not changed in the workflow
                   CACHE_NUMBER: 0
@@ -96,7 +96,7 @@ jobs:
 
             - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
               name: Upload Coverage Report
-              uses: codecov/codecov-action@v1
+              uses: codecov/codecov-action@v3
               with:
                   file: "tests_coverage_reports/coverage.xml"
                   fail_ci_if_error: true

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
           - id: check-yaml
 
     - repo: https://github.com/psf/black
-      rev: 22.6.0
+      rev: 22.10.0
       hooks:
           - id: black
 
@@ -23,22 +23,22 @@ repos:
     # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
     # https://github.com/pre-commit/pre-commit/issues/1206
     - repo: https://github.com/pycqa/flake8
-      rev: 4.0.1
+      rev: 5.0.4
       hooks:
           - id: flake8
             args: ["--config=setup.cfg"]
             additional_dependencies: [flake8-isort]
 
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.971
+      rev: v0.990
       hooks:
           - id: mypy
             args: ["--config=setup.cfg"]
             additional_dependencies:
                 [
-                    dask==2022.7.1,
-                    numpy==1.22.4,
-                    pandas==1.4.3,
-                    xarray==2022.6.0,
+                    dask==2022.10.2,
+                    numpy==1.23.4,
+                    pandas==1.5.1,
+                    xarray==2022.11.0,
                     types-python-dateutil==2.8.19,
                 ]

HISTORY.rst

@@ -2,6 +2,79 @@
 History
 =======
 
+v0.4.0 (9 November 2022)
+--------------------------
+
+This minor release includes a feature update to support datasets that
+have *N* dimensions mapped to *N* coordinates to represent an axis. This
+means ``xcdat`` APIs are able to intelligently select which axis's
+coordinates and bounds to work with if multiple are present within the
+dataset. Decoding time is now a lazy operation, leading to significant
+upfront runtime improvements when opening datasets with
+``decode_times=True``.
+
+A new notebook called “A Gentle Introduction to xCDAT” was added to the
+documentation gallery to help guide new xarray/xcdat users. xCDAT is now
+hosted on Zenodo with a DOI for citations.
+
+There are various bug fixes for bounds, naming of spatial weights, and a
+missing flag for ``xesmf`` that broke curvilinear regridding.
+
+Features
+~~~~~~~~
+
+-  Support for N axis dimensions mapped to N coordinates by
+   `Tom Vo`_ and `Stephen Po-Chedley`_ in
+   https://github.com/xCDAT/xcdat/pull/343
+
+   -  Rename ``get_axis_coord()`` to ``get_dim_coords()`` and
+      ``get_axis_dim()`` to ``get_dim_keys()``
+   -  Update spatial and temporal accessor class methods to refer to the
+      dimension coordinate variable on the data_var being operated on,
+      rather than the parent dataset
+
+-  Decoding times (``decode_time()``) is now a lazy operation, which
+   results in significant runtime improvements by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/343
+
+Bug Fixes
+~~~~~~~~~
+
+-  Fix ``add_bounds()`` not ignoring 0-dim singleton coords by
+   `Tom Vo`_ and `Stephen Po-Chedley`_ in
+   https://github.com/xCDAT/xcdat/pull/343
+-  Fix name of spatial weights with singleton coord by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/379
+-  Fixes ``xesmf`` flag that was missing which broke curvilinear
+   regridding by `Jason Boutte`_ and `Stephen Po-Chedley`_ in
+   https://github.com/xCDAT/xcdat/pull/374
+
+Documentation
+~~~~~~~~~~~~~
+
+-  Add FAQs section for temporal metadata by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/383
+-  Add gentle introduction notebook by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/373
+-  Link repo to Zenodo and upload GitHub releases by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/367
+-  Update project overview, FAQs, and add a link to xarray tutorials by
+   `Tom Vo`_ in https://github.com/xCDAT/xcdat/pull/365
+-  Update feature list, add metadata interpretation to FAQs, and add
+   ``ipython`` syntax highlighting for notebooks by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/362
+
+DevOps
+~~~~~~
+
+-  Update release-drafter template by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/371 and
+   https://github.com/xCDAT/xcdat/pull/370
+-  Automate release notes generation by `Tom Vo`_ in
+   https://github.com/xCDAT/xcdat/pull/368
+
+**Full Changelog**: https://github.com/xCDAT/xcdat/compare/v0.3.3...v0.4.0
+
 v0.3.3 (12 October 2022)
 ------------------------
 

conda-env/ci.yml

@@ -14,7 +14,6 @@ dependencies:
     - dask
     - esmpy
     - netcdf4
-    - numba >=0.55.2 # TODO: Remove this pin once `numba` is properly patched with `numpy` compatability.
     - numpy
     - pandas
     - xarray

conda-env/dev.yml

@@ -8,17 +8,16 @@ dependencies:
     # Base
     # ==================
     # NOTE: If versions are updated, also `additional_dependencies` list for mypy in `.pre-commit-config.yaml`
-    - python=3.9.13 # TODO: Update to >=3.10 once sphinxcontrib-napoleon supports it.
-    - pip=22.2.2
+    - python=3.10.6
+    - pip=22.3.1
     - cf_xarray=0.7.4
-    - cftime=1.6.1
-    - dask=2022.8.0
-    - netcdf4=1.6.0
-    - numba=0.55.2 # TODO: Remove this pin once `numba` is properly patched with `numpy` compatibility.
-    - numpy=1.22.4
-    - pandas=1.4.3
+    - cftime=1.6.2
+    - dask=2022.10.2
+    - netcdf4=1.6.1
+    - numpy=1.23.4
+    - pandas=1.5.1
     - python-dateutil=2.8.2
-    - xarray=2022.6.0
+    - xarray=2022.11.0
     # ==================
     # Optional
     # ==================
@@ -27,32 +26,32 @@ dependencies:
     # Documentation
     # ==================
     - sphinx=4.5.0
-    - sphinxcontrib-napoleon=0.7
     - sphinx-autosummary-accessors=2022.4.0
     - sphinx-book-theme=0.3.3
     - sphinx-copybutton=0.5.0
     - nbsphinx=0.8.9
-    - pandoc=2.19
+    - pandoc=2.19.2
+    - ipython=8.5.0 # Required for nbsphinx syntax highlighting
     # ==================
     # Quality Assurance
     # ==================
     # NOTE: If versions are updated, also update 'rev' in `.pre-commit.config.yaml`
-    - black=22.6.0
+    - black=22.10.0
     - flake8=5.0.4
-    - flake8-isort=4.2.0
+    - flake8-isort=5.0.0
     - isort=5.10.1
-    - mypy=0.971
+    - mypy=0.990
     - pre-commit=2.20.0
     - types-python-dateutil=2.8.19
     # ==================
     # Testing
     # ==================
-    - pytest=7.1.2
-    - pytest-cov=3.0.0
+    - pytest=7.2.0
+    - pytest-cov=4.0.0
     # ==================
     # Developer Tools
     # ==================
-    - matplotlib=3.5.2
-    - jupyterlab=3.4.5
+    - matplotlib=3.6.2
+    - jupyterlab=3.5.0
     - tbump=6.9.0
 prefix: /opt/miniconda3/envs/xcdat_dev

conda-env/dev_min.yml

@@ -7,31 +7,32 @@ dependencies:
     # Base
     # ==================
     # NOTE: If versions are updated, also `additional_dependencies` list for mypy in `.pre-commit-config.yaml`
-    - python=3.9.13 # TODO: Update to >=3.10 once sphinxcontrib-napoleon supports it.
-    - pip=22.2.2
+    - python=3.10.6
+    - pip=22.3.1
     - cf_xarray=0.7.4
-    - cftime=1.6.1
-    - dask=2022.8.0
-    - netcdf4=1.6.0
-    - numba=0.55.2 # TODO: Remove this pin once `numba` is properly patched with `numpy` compatibility.
-    - numpy=1.22.4
-    - pandas=1.4.3
+    - cftime=1.6.2
+    - dask=2022.10.2
+    - netcdf4=1.6.1
+    - numpy=1.23.4
+    - pandas=1.5.1
     - python-dateutil=2.8.2
-    - types-python-dateutil=2.8.19
-    - xarray=2022.6.0
+    - xarray=2022.11.0
     # ==================
     # Optional
     # ==================
     - xesmf=0.6.3
     # ==================
+    # ==================
+    # Quality Assurance
+    # ==================
+    - types-python-dateutil=2.8.19
     # Documentation
     # ==================
     - sphinx=4.5.0
-    - sphinxcontrib-napoleon=0.7
     - sphinx-autosummary-accessors=2022.4.0
     - sphinx-book-theme=0.3.3
     - sphinx-copybutton=0.5.0
     - nbsphinx=0.8.9
     - pandoc=2.19
-    - ipython=8.5.0  # Required for nbsphinx syntax highlighting.
+    - ipython=8.5.0 # Required for nbsphinx syntax highlighting.
 prefix: /opt/miniconda3/envs/xcdat_rtd

conda-env/readthedocs.yml

@@ -37,10 +37,10 @@
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
-    "sphinx_autosummary_accessors",
+    "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
+    "sphinx_autosummary_accessors",
     "sphinx_copybutton",
-    "sphinxcontrib.napoleon",
     "nbsphinx",
 ]
 

docs/conf.py

@@ -46,7 +46,7 @@ exclude =
     venv
 
 [mypy]
-python_version = 3.9
+python_version = 3.10
 check_untyped_defs = True
 ignore_missing_imports = True
 warn_unused_ignores = True

setup.cfg

@@ -35,6 +35,6 @@
     test_suite="tests",
     tests_require=test_requires,
     url="https://github.com/xCDAT/xcdat",
-    version="0.3.3",
+    version="0.4.0",
     zip_safe=False,
 )