Simplify conda environments and move configs to pyproject.toml

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
           - id: check-yaml
 
     - repo: https://github.com/psf/black
-      rev: 23.1.0
+      rev: 23.3.0
       hooks:
           - id: black
 
@@ -30,15 +30,15 @@ repos:
             additional_dependencies: [flake8-isort]
 
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.1.1
+      rev: v1.4.0
       hooks:
           - id: mypy
-            args: ["--config=setup.cfg"]
+            args: ["--config=pyproject.toml"]
             additional_dependencies:
                 [
-                    dask==2023.3.2,
-                    numpy==1.23.5,
-                    pandas==1.5.3,
-                    xarray==2023.3.0,
-                    types-python-dateutil==2.8.19,
+                    dask,
+                    numpy>=1.23.0,
+                    pandas,
+                    xarray>=2023.2.0,
+                    types-python-dateutil,
                 ]

.readthedocs.yml

@@ -6,9 +6,9 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
-  tools:
-    python: "mambaforge-4.10"
+    os: "ubuntu-20.04"
+    tools:
+        python: "mambaforge-4.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -19,4 +19,4 @@ formats:
     - pdf
 
 conda:
-    environment: conda-env/readthedocs.yml
+    environment: conda-env/dev.yml

conda-env/ci.yml

@@ -1,28 +1,25 @@
-# Conda xcdat CI/CD environment (used in GH Actions)
+# Conda xcdat CI/CD environment (used in GH Actions).
 name: xcdat_ci
 channels:
     - conda-forge
     - defaults
 dependencies:
-    # ==================
-    # Base
-    # ==================
-    - python >=3.8
-    - pip
+    # Base - required for building the package.
+    # =========================================
+    - python >=3.9
     - cf_xarray
     - cftime
     - dask
-    - esmpy
     - lxml
     - netcdf4
-    - numpy
+    - numpy >=1.23.0 # This version of numpy includes support for Python 3.11.
     - pandas
     - python-dateutil
-    - xarray
-    # Constrained because 0.6.3 breaks with import ESMF
-    # Source: https://github.com/pangeo-data/xESMF/issues/212
-    - xesmf >0.6.3
+    - xarray >=2022.02.0 # This version of Xarray drops support for Python 3.9.
     - xgcm
+    # Optional - enables additional features.
+    # =========================================
+    - xesmf >=0.7.0 # Constrained because https://github.com/pangeo-data/xESMF/issues/212.
     # Quality Assurance
     # ==================
     - types-python-dateutil

conda-env/dev.yml

@@ -4,58 +4,50 @@ channels:
     - conda-forge
     - defaults
 dependencies:
-    # ==================
-    # Base
-    # ==================
-    # NOTE: If versions are updated, also `additional_dependencies` list for mypy in `.pre-commit-config.yaml`
-    - python=3.10.10
-    - pip=23.0.1
-    - cf_xarray=0.8.0
-    - cftime=1.6.2
-    - dask=2023.3.2
-    - lxml=4.9.2
-    - netcdf4=1.6.3
-    - numpy=1.23.5
-    - pandas=1.5.3
-    - python-dateutil=2.8.2
-    - xarray=2023.4.2
-    - xgcm=0.8.0
-    # ==================
-    # Optional
-    # ==================
-    - xesmf=0.7.0
-    - matplotlib-base=3.7.1
+    # Base - required for building the package.
+    # =========================================
+    - python >=3.9
+    - cf_xarray
+    - cftime
+    - dask
+    - lxml
+    - netcdf4
+    - numpy >=1.23.0 # This version of numpy includes support for Python 3.11.
+    - pandas
+    - python-dateutil
+    - xarray >=2022.02.0 # This version of Xarray drops support for Python 3.9.
+    - xgcm
+    # Optional - enables additional features.
+    # =========================================
+    - xesmf >=0.7.0 # Constrained because https://github.com/pangeo-data/xESMF/issues/212.
+    - matplotlib-base >=3.7.0
     - nc-time-axis=1.4.1
-    # ==================
     # Documentation
     # ==================
-    - sphinx=5.3.0
-    - sphinx-autosummary-accessors=2022.4.0
-    - sphinx-book-theme=1.0.1
-    - sphinx-copybutton=0.5.1
-    - nbsphinx=0.9.1
-    - pandoc=3.1.1
-    - ipython=8.11.0 # Required for nbsphinx syntax highlighting
+    - sphinx >=5.0.0
+    - sphinx-autosummary-accessors
+    - sphinx-book-theme
+    - sphinx-copybutton
+    - nbsphinx
+    - pandoc
+    - ipython >=8.0.0 # Required for nbsphinx syntax highlighting
     - gsw-xarray=0.3.0 # Required for vertical regridding example
-    # ==================
     # Quality Assurance
     # ==================
-    # NOTE: If versions are updated, also update 'rev' in `.pre-commit.config.yaml`
-    - black=23.1.0
+    - types-python-dateutil
+    # NOTE: If the tools below are updated, also update their 'rev' in `.pre-commit.config.yaml`
+    - black=23.3.0
     - flake8=6.0.0
     - flake8-isort=6.0.0
     - isort=5.12.0
-    - mypy=1.1.1
+    - mypy=1.4.0
     - pre-commit=3.2.0
-    - types-python-dateutil=2.8.19
-    # ==================
     # Testing
     # ==================
-    - pytest=7.2.2
-    - pytest-cov=4.0.0
-    # ==================
+    - pytest
+    - pytest-cov
     # Developer Tools
     # ==================
-    - jupyterlab=3.6.2
-    - tbump=6.9.0
+    - jupyterlab
+    - tbump
 prefix: /opt/miniconda3/envs/xcdat_dev

docs/getting-started.rst

@@ -12,63 +12,62 @@ Prerequisites
    - We highly recommend visiting the `xarray tutorial`_ and `xarray documentation`_
      pages if you aren't familiar with ``xarray``.
 
-2. xCDAT is distributed through conda, which is available through Anaconda and Miniconda.
+2. xCDAT is distributed available on Anaconda. We recommend installing `mamba`_, which
+   is a drop-in replacement of ``conda``.
 
-   We recommend following these steps to install Miniconda:
+   We recommend following these steps to install Mambaforge (Linux example):
 
    .. code-block:: console
 
-      wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-      bash Miniconda3-latest-Linux-x86_64.sh
+      wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
 
-   Then follow the instructions for installation. To have conda added to
-   your path you will need to type ``yes`` in response to ``"Do you wish the
-   installer to initialize Miniconda3 by running conda init?"`` (we recommend
-   that you do this). Note that this will modify your shell profile (e.g.,
-   ``~/.bashrc``) to add ``conda`` to your path.
+      bash ./Mambaforge-Linux-x86_64.sh
 
-   Note: After installation completes you may need to type ``bash`` to
-   restart your shell (if you use bash). Alternatively, you can log out and
-   log back in.
+   When you see: ::
 
+      by running conda init? [yes|no]
+      [no] >>> yes
+
+   respond with ``yes`` so ``conda`` and ``mamba`` commands are available on
+   initializing a new bash terminal.
+
+.. _mamba: https://mamba.readthedocs.io/en/latest/index.html
 .. _xarray tutorial: https://tutorial.xarray.dev/intro.html
 .. _xarray documentation: https://docs.xarray.dev/en/stable/getting-started-guide/index.html
 
 Installation
 ------------
 
-1. Create a conda environment from scratch with ``xcdat`` (`conda create`_)
+1. Create a mamba environment from scratch with ``xcdat`` (`mamba create`_)
 
-   We recommend using the Conda environment creation procedure to install ``xcdat``.
-   The advantage with following this approach is that Conda will attempt to resolve
-   dependencies (e.g. ``python >= 3.8``) for compatibility.
+   We recommend using the mamba environment creation procedure to install ``xcdat``.
+   The advantage with following this approach is that mamba will attempt to resolve
+   dependencies (e.g. ``python >= 3.9``) for compatibility.
 
-   To create an ``xcdat`` conda environment with ``xesmf`` (a recommended dependency),
-   run:
+   To create an ``xcdat`` environment with ``xesmf`` (a recommended dependency), run:
 
    .. code-block:: console
 
-       >>> conda create -n <ENV_NAME> -c conda-forge xcdat xesmf
-       >>> conda activate <ENV_NAME>
+       >>> mamba create -n <ENV_NAME> -c conda-forge xcdat xesmf
+       >>> mamba activate <ENV_NAME>
 
    Note that ``xesmf`` is an optional dependency, which is required for using ``xesmf``
    based horizontal regridding APIs in ``xcdat``. ``xesmf`` is not currently supported
-   on `osx-arm64`_ or `windows`_ because ``esmpy`` is not yet available on these
-   platforms. Windows users can try `WSL2`_ as a workaround.
+   on `windows`_ because ``esmpy`` is not yet available on these platforms. Windows
+   users can try `WSL2`_ as a workaround.
 
 .. _windows: https://github.com/conda-forge/esmf-feedstock/issues/64
-.. _osx-arm64: https://github.com/conda-forge/esmf-feedstock/issues/74
 .. _WSL2: https://docs.microsoft.com/en-us/windows/wsl/install
 
-2. Install ``xcdat`` in an existing conda environment (`conda install`_)
+2. Install ``xcdat`` in an existing mamba environment (`mamba install`_)
 
-   You can also install ``xcdat`` in an existing Conda environment, granted that Conda
+   You can also install ``xcdat`` in an existing mamba environment, granted that mamba
    is able to resolve the compatible dependencies.
 
    .. code-block:: console
 
-       >>> conda activate <ENV_NAME>
-       >>> conda install -c conda-forge xcdat xesmf
+       >>> mamba activate <ENV_NAME>
+       >>> mamba install -c conda-forge xcdat xesmf
 
    Note: As above, ``xesmf`` is an optional dependency.
 
@@ -80,5 +79,5 @@ Installation
    - ``matplotlib``: a library for creating visualizations in Python.
    - ``cartopy``: an add-on package for ``matplotlib`` and specialized for geospatial data processing.
 
-.. _conda create: https://docs.conda.io/projects/conda/en/latest/commands/create.html?highlight=create
-.. _conda install: https://docs.conda.io/projects/conda/en/latest/commands/install.html?highlight=install
+.. _mamba create: https://fig.io/manual/mamba/create
+.. _mamba install: https://fig.io/manual/mamba/install

pyproject.toml

@@ -21,3 +21,28 @@ exclude = '''
   )/
 )
 '''
+
+[tool.isort]
+# Docs: https://pycqa.github.io/isort/docs/configuration/options.html#example-pyprojecttoml_4
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+line_length = 88
+
+[tool.pytest.ini_options]
+# Docs: https://docs.pytest.org/en/7.2.x/reference/customize.html#configuration
+junit_family = "xunit2"
+addopts = "--cov=xcdat --cov-report term --cov-report html:tests_coverage_reports/htmlcov --cov-report xml:tests_coverage_reports/coverage.xml -s"
+python_files = ["tests.py", "test_*.py"]
+# These markers are defined in `xarray.tests` and must be included to avoid warnings when importing from this module.
+markers = ["flaky", "network"]
+
+[tool.mypy]
+# Docs: https://mypy.readthedocs.io/en/stable/config_file.html
+python_version = 3.10
+check_untyped_defs = true
+ignore_missing_imports = true
+warn_unused_ignores = true
+warn_redundant_casts = true
+warn_unused_configs = true