Simplify conda environments and move configs to pyproject.toml (#512)

Author: tomvothecoder

.github/workflows/build_workflow.yml

@@ -50,7 +50,7 @@ jobs:
                 shell: bash -l {0}
         strategy:
             matrix:
-                python-version: ["3.8", "3.9", "3.10"]
+                python-version: ["3.9", "3.10", "3.11"]
         steps:
             - id: skip_check
               uses: fkirc/skip-duplicate-actions@master
@@ -98,7 +98,10 @@ jobs:
 
             - if: $${{ steps.skip_check.outputs.should_skip != 'true' || steps.cache.outputs.cache-hit != 'true' }}
               name: Update environment
-              run: mamba env update -n xcdat_ci -f conda-env/ci.yml
+              run: |
+                  mamba env update -n xcdat_ci -f conda-env/ci.yml
+                  # Make sure the Python version in the env matches the current matrix version.
+                  mamba install -c conda-forge python=${{ matrix.python-version }}
 
             - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
               name: Install xcdat

.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

@@ -4,29 +4,24 @@ 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
@@ -37,25 +32,22 @@ dependencies:
     - pandoc=3.1.1
     - ipython=8.11.0 # 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

conda-env/readthedocs.yml

@@ -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

pyproject.toml

@@ -1,5 +1,6 @@
 [flake8]
 # https://pep8.readthedocs.io/en/latest/intro.html#error-codes
+# flake8 dooes not support pyproject.toml yet: https://github.com/PyCQA/flake8/issues/234
 ignore =
     # whitespace before ‘:’
     E203
@@ -23,45 +24,6 @@ exclude =
     *__init__.py
     venv
 
-[isort]
-multi_line_output=3
-include_trailing_comma=True
-force_grid_wrap=0
-use_parentheses=True
-line_length=88
-
-[pycodestyle]
-max-line-length = 119
-exclude =
-    .tox
-    .git
-    */migrations/*
-    */static/CACHE/*
-    docs
-    node_modules
-    .idea
-    .mypy_cache
-    .pytest_cache
-    *__init__.py
-    venv
-
-[mypy]
-python_version = 3.10
-check_untyped_defs = True
-ignore_missing_imports = True
-warn_unused_ignores = True
-warn_redundant_casts = True
-warn_unused_configs = True
-
 [aliases]
 # Define setup.py command aliases here
 test = pytest
-
-[tool:pytest]
-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