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

.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/readthedocs.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

docs/conf.py

@@ -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",
 ]
 

setup.cfg

@@ -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.py

@@ -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,
 )

tbump.toml

@@ -2,7 +2,7 @@
 github_url = "https://github.com/xCDAT/xcdat"
 
 [version]
-current = "0.3.3"
+current = "0.4.0"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

xcdat/__init__.py

@@ -19,4 +19,4 @@
 from xcdat.temporal import TemporalAccessor # noqa: F401
 from xcdat.utils import compare_datasets # noqa: F401
 
-__version__ = "0.3.3"
+__version__ = "0.4.0"