Reconfigure Builds and perform more doctests (#1709)

### What kind of change does this PR introduce? * Splits the `notebooks` recipe in the `tox.ini` file * Sets the GitHub Workflows to test the doctests across more builds * Stages the `tox-gh` plugin for eventual integration ### Does this PR introduce a breaking change? Yes, `tox-gh` is now a development dependency and the `"notebooks_doctests"` `tox` recipe has been replaced with `"notebooks"`, while `doctest` has been made into a modifier for typical `tox` runs to also run the documentation examples. ### Other information: https://github.com/tox-dev/tox-gh
Ouranosinc · Apr 17, 2024 · d27b4ed · d27b4ed
2 parents 0edfe42 + 982a656
commit d27b4ed
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -23,7 +23,7 @@ env:
 
 concurrency:
  # For a given workflow, if we push to the same branch, cancel all previous builds on that branch except on main.
- group: ${{ github.workflow }}-${{ github.ref }}
+ group: "${{ github.workflow }}-${{ github.ref }}"
  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 
 permissions:
@@ -57,8 +57,9 @@ jobs:
  uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
  with:
  python-version: ${{ matrix.python-version }}
- - name: Install pylint and tox
- run: pip install pylint tox~=4.0
+ - name: Install pip, pylint, and tox
+ run: |
+ python -m pip install flit pip~=24.0 pylint tox~=4.0
  - name: Run pylint
  run: |
  python -m pylint --rcfile=.pylintrc.toml --disable=import-error --exit-zero xclim
@@ -97,7 +98,7 @@ jobs:
  python-version: ${{ matrix.python-version }}
  - name: Install tox
  run: |
- python -m pip install tox~=4.0
+ python -m pip install flit pip~=24.0 tox~=4.0
  - name: Test with tox
  run: |
  python -m tox -e ${{ matrix.tox-env }}
@@ -118,17 +119,17 @@ jobs:
  matrix:
  include:
  # Windows builds
- - tox-env: py39-prefetch-coverage
+ - tox-env: py39-coverage-prefetch
  python-version: "3.9"
  markers: -m 'not slow'
  os: windows-latest
  # macOS builds
- - tox-env: py310-coverage
+ - tox-env: py310-coverage-lmoments-doctest
  python-version: "3.10"
  markers: -m 'not slow'
  os: macos-latest
  # Linux builds
- - tox-env: py39-coverage-sbck
+ - tox-env: py39-coverage-sbck-doctest
  python-version: "3.9"
  markers: -m 'not slow'
  os: ubuntu-latest
@@ -139,11 +140,11 @@ jobs:
  python-version: "3.11"
  markers: -m 'not slow'
  os: ubuntu-latest
- - tox-env: py312-coverage-numba
+ - tox-env: py312-coverage-lmoments-doctest
  python-version: "3.12"
  markers: -m 'not slow'
  os: ubuntu-latest
- - tox-env: notebooks_doctests
+ - tox-env: notebooks
  python-version: "3.10"
  os: ubuntu-latest
  - tox-env: offline-prefetch
@@ -180,7 +181,7 @@ jobs:
  python-version: ${{ matrix.python-version }}
  - name: Install tox
  run: |
- python -m pip install tox~=4.0
+ python -m pip install flit pip~=24.0 tox~=4.0 tox-gh
  - name: Test with tox
  run: |
  python -m tox -e ${{ matrix.tox-env }} -- ${{ matrix.markers }}
@@ -192,17 +193,16 @@ jobs:
 
  test-conda:
  needs: lint
- name: test-conda-Python${{ matrix.python-version }}
+ name: Python${{ matrix.python-version }} (Conda, ${{ matrix.os }})
  if: |
  contains(github.event.pull_request.labels.*.name, 'approved') ||
  (github.event.review.state == 'approved') ||
  (github.event_name == 'push')
- runs-on: ubuntu-latest
+ runs-on: ${{ matrix.os }}
  strategy:
  matrix:
- include:
- - python-version: "3.9"
- - python-version: "3.12"
+ os: [ubuntu-latest]
+ python-version: ["3.9", "3.12"]
  defaults:
  run:
  shell: bash -l {0}

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -21,7 +21,9 @@ Bug fixes
 Internal changes
 ^^^^^^^^^^^^^^^^
 * Added "doymin" and "doymax" to the possible operations of ``generic.stats``. Fixed a warning issue when ``op`` was "integral". (:pull:`1672`).
-
+* Reorganized GitHub CI build matrices to run the doctests more consistently. (:pull:`1709`).
+* Removed the experimental `numba` and `llvm` dependency installation steps in the `tox.ini` file. Added `numba@main` to the upstream dependencies. (:pull:`1709`).
+* Added the `tox-gh` dependency to the development installation recipe. This will soon be required for running the `tox` test ensemble on GitHub Workflows. (:pull:`1709`).
 
 v0.48.2 (2024-02-26)
 --------------------

diff --git a/pyproject.toml b/pyproject.toml
@@ -83,6 +83,7 @@ dev = [
  "tokenize-rt",
  "tox >=4.0",
  # "tox-conda", # Will be added when a tox@v4.0+ compatible plugin is released.
+ "tox-gh >=1.3.1",
  "xdoctest",
  "yamllint",
  # Documentation and examples

diff --git a/requirements_upstream.txt b/requirements_upstream.txt
@@ -1,4 +1,5 @@
 bottleneck @ git+https://github.com/pydata/bottleneck.git@master
 cftime @ git+https://github.com/Unidata/cftime.git@master
 flox @ git+https://github.com/xarray-contrib/flox.git@main
+numba @ git+https://github.com/numba/numba.git@main
 xarray @ git+https://github.com/pydata/xarray.git@main
diff --git a/tox.ini b/tox.ini
@@ -3,18 +3,26 @@ min_version = 4.0
 env_list =
  lint
  docs
- notebooks_doctests
+ notebooks
  offline-prefetch
  py39-upstream-doctest
- py310
+ py310-doctest
  py311-lmoments
- py312-numba
+ py312-lmoments-doctest
 labels =
  test = py39, py310-upstream-doctest, py311, notebooks_doctests, offline-prefetch
 requires =
- pip >= 23.0
+ pip >= 24.0
+ flit
 opts = -vv
 
+[gh]
+python =
+ 3.12 = py312-coverage-lmoments-doctest
+ 3.11 = py311-coverage-lmoments-sbck-doctest, offline-coverage-prefetch
+ 3.10 = py310-coverage-lmoments-doctest, notebooks
+ 3.9 = py39-coverage-sbck-doctest, lint, docs
+
 [testenv:lint]
 description = Run code quality compliance tests under {basepython}
 skip_install = True
@@ -65,16 +73,15 @@ allowlist_externals =
 ;deps =
 ;extras =
 
-[testenv:notebooks_doctests{-coverage,}]
-description = Run notebooks and doctests with pytest under {basepython}
+[testenv:notebooks{-prefetch,}]
+description = Run notebooks with pytest under {basepython}
 commands =
  pytest --no-cov --nbval --dist=loadscope --rootdir=tests/ --ignore=docs/notebooks/example.ipynb docs/notebooks
- pytest --rootdir=tests/ --xdoctest xclim
+commands_post =
 
 [testenv:offline{-prefetch,}{-coverage,}]
 description = Run tests with pytest under {basepython}, preventing socket connections (except for unix sockets for async support)
 commands:
- prefetch: xclim prefetch_testing_data
  python -c 'print("Running offline tests with positional arguments: --disable-socket --allow-unix-socket --m \"not requires_internet\"")'
  python -c 'print("These can be overwritten with: tox -e offline -- -m \"some other marker statement\"")'
  pytest --disable-socket --allow-unix-socket {posargs:-m 'not requires_internet'}
@@ -99,14 +106,11 @@ passenv =
  XCLIM_*
 extras = dev
 deps =
- # FIXME: Remove when numba 0.59.0 is released
- numba: numba==0.59.0rc1
- numba: llvmlite==0.42.0rc1
  coverage: coveralls
  upstream: -rrequirements_upstream.txt
  sbck: pybind11
  lmoments: lmoments3
- notebooks_doctests: lmoments3
+ notebooks: lmoments3
 install_command = python -m pip install --no-user {opts} {packages}
 download = True
 commands_pre =
@@ -115,11 +119,13 @@ commands_pre =
  xclim show_version_info
  python -m pip check
  xclim --help
+ prefetch: xclim prefetch_testing_data
 commands =
  prefetch: xclim prefetch_testing_data
- doctest: pytest --no-cov --rootdir=tests/ --xdoctest xclim
  pytest {posargs}
+ doctest: pytest --rootdir=tests/ --xdoctest xclim
 commands_post =
  coverage: - coveralls
 allowlist_externals =
  git
+ xclim