Workflow optimisations

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: xclim Testing Suite
+name: Testing
 
 on:
  push:
@@ -69,15 +69,13 @@ jobs:
  python -m tox -e lint
 
  test-preliminary:
- name: Python${{ matrix.python-version }} (${{ matrix.tox-env }}, ${{ matrix.os }})
+ name: Python${{ matrix.python-version }} (ubuntu-latest)
  needs: lint
- runs-on: ${{ matrix.os }}
+ runs-on: ubuntu-latest
  strategy:
  matrix:
- include:
- - tox-env: "py39-coverage"
- python-version: "3.9"
- os: ubuntu-latest
+ python-version:
+ - "3.9"
  steps:
  - name: Harden Runner
  uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
@@ -102,54 +100,58 @@ jobs:
  python -m pip install --require-hashes -r CI/requirements_ci.txt
  - name: Test with tox
  run: |
- python -m tox -e ${{ matrix.tox-env }}
+ python -m tox -- -m 'not slow'
  env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
  test-pypi:
  needs: lint
- name: Python${{ matrix.python-version }} (${{ matrix.tox-env }}, ${{ matrix.os }})
+ name: Python${{ matrix.python-version }} (${{ matrix.os }}, ${{ matrix.tox-env }})
  if: |
  contains(github.event.pull_request.labels.*.name, 'approved') ||
  (github.event.review.state == 'approved') ||
  (github.event_name == 'push')
  runs-on: ${{ matrix.os }}
+ timeout-minutes: 20
  strategy:
  matrix:
  include:
- # Windows builds
- - tox-env: py39-coverage-prefetch
- python-version: "3.9"
+ # Linux builds
+ - os: ubuntu-latest
  markers: -m 'not slow'
- os: windows-latest
- # macOS builds
- - tox-env: py310-coverage-extras-lmoments-numpy
  python-version: "3.10"
+ tox-env: standard
+ - os: ubuntu-latest
  markers: -m 'not slow'
- os: macos-latest
- # Linux builds
- - tox-env: py39-coverage-offline-prefetch
- python-version: "3.9"
- markers: -m 'not slow and not requires_internet'
- os: ubuntu-latest
- - tox-env: py310-coverage-lmoments # No markers -- includes slow tests
- python-version: "3.10"
- os: ubuntu-latest
- - tox-env: py311-coverage-extras-sbck-numpy
  python-version: "3.11"
+ tox-env: standard
+ - os: ubuntu-latest
  markers: -m 'not slow'
- os: ubuntu-latest
- - tox-env: py312-coverage-extras-lmoments
  python-version: "3.12"
+ tox-env: standard
+ # Windows builds
+ - os: windows-latest
  markers: -m 'not slow'
- os: ubuntu-latest
+ python-version: "3.9"
+ tox-env: py39-coverage-prefetch # Test data prefetch is needed for Windows
+ # macOS builds
+ - os: macos-latest
+ python-version: "3.10"
+ markers: '' # Slow tests
+ tox-env: py310-coverage-extras
  # Specialized tests
- - tox-env: notebooks
+ - os: ubuntu-latest
+ markers: -m 'not requires_internet and not slow'
+ python-version: "3.9"
+ tox-env: py39-coverage-offline-prefetch
+ - os: ubuntu-latest
+ markers: ''
  python-version: "3.10"
- os: ubuntu-latest
- - tox-env: doctests
+ tox-env: notebooks
+ - os: ubuntu-latest
+ markers: ''
  python-version: "3.12"
- os: ubuntu-latest
+ tox-env: doctests
  steps:
  - name: Harden Runner
  uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
@@ -168,9 +170,10 @@ jobs:
  ppa.launchpadcontent.net:443
  pypi.org:443
  raw.githubusercontent.com:443
- - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
- - name: Install Eigen3
- if: contains(matrix.tox-env, 'sbck')
+ - name: Checkout Repository
+ uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+ - name: Install Eigen3 (SBCK)
+ if: ${{ matrix.python-version == '3.11' }}
  run: |
  sudo apt-get update
  sudo apt-get install libeigen3-dev
@@ -182,26 +185,36 @@ jobs:
  run: |
  python -m pip install --require-hashes -r CI/requirements_ci.txt
  - name: Test with tox
+ if: ${{ matrix.tox-env == 'standard' }}
+ run: |
+ python -m tox -- ${{ matrix.markers }};
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ COVERALLS_FLAG_NAME: run-${{ matrix.python-version }}-${{ matrix.os }}-${{ matrix.tox-env }}
+ COVERALLS_PARALLEL: true
+ COVERALLS_SERVICE_NAME: github
+ - name: Test with tox (specialized tests)
+ if: ${{ matrix.tox-env != 'standard' }}
  run: |
- python -m tox -e ${{ matrix.tox-env }} -- ${{ matrix.markers }}
+ python -m tox -e ${{ matrix.tox-env }} -- ${{ matrix.markers }};
  env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- COVERALLS_FLAG_NAME: run-{{ matrix.tox-env }}-{{ matrix.os }}
+ COVERALLS_FLAG_NAME: run-${{ matrix.python-version }}-${{ matrix.os }}-${{ matrix.tox-env }}
  COVERALLS_PARALLEL: true
  COVERALLS_SERVICE_NAME: github
 
  test-conda:
  needs: lint
- name: Python${{ matrix.python-version }} (Conda, ${{ matrix.os }})
+ name: Python${{ matrix.python-version }} (${{ matrix.os }}, conda)
  if: |
  contains(github.event.pull_request.labels.*.name, 'approved') ||
  (github.event.review.state == 'approved') ||
  (github.event_name == 'push')
  runs-on: ${{ matrix.os }}
  strategy:
  matrix:
- os: [ubuntu-latest]
- python-version: ["3.9", "3.12"]
+ os: [ ubuntu-latest ]
+ python-version: [ "3.9", "3.12" ]
  defaults:
  run:
  shell: bash -l {0}
@@ -232,15 +245,15 @@ jobs:
  environment-file: environment.yml
  create-args: >-
  python=${{ matrix.python-version }}
- - name: Conda and Mamba versions
+ - name: Micromamba version
  run: |
  echo "micromamba: $(micromamba --version)"
  - name: Install xclim
  run: |
  python -m pip install --no-user --editable .
  - name: Check versions
  run: |
- conda list
+ micromamba list
  xclim show_version_info
  python -m pip check || true
  - name: Test with pytest
@@ -263,7 +276,7 @@ jobs:
  coveralls
  env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- COVERALLS_FLAG_NAME: run-{{ matrix.tox-env }}-opt-slow
+ COVERALLS_FLAG_NAME: run-{{ matrix.python-version }}-conda
  COVERALLS_PARALLEL: true
  COVERALLS_SERVICE_NAME: github
 

.github/workflows/upstream.yml

@@ -24,7 +24,6 @@ jobs:
  name: test-upstream-dev (Python${{ matrix.python-version }})
  runs-on: ubuntu-latest
  permissions:
- contents: read
  issues: write
  if: |
  (github.event_name == 'schedule') ||
@@ -65,25 +64,24 @@ jobs:
  cache-environment: true
  environment-file: environment.yml
  create-args: >-
- conda
  eigen
  pybind11
  python=${{ matrix.python-version }}
  pytest-reportlog
- - name: Conda and Mamba versions
+ - name: Micromamba version
  run: |
- conda --version
  echo "micromamba: $(micromamba --version)"
  - name: Install upstream versions and SBCK
  run: |
- python -m pip install --require-hashes -r CI/requirements_upstream.txt
+ # git-based dependencies cannot be installed from hashes
+ python -m pip install -r CI/requirements_upstream.txt
  python -m pip install "sbck @ git+https://github.com/yrobink/SBCK-python.git@master"
  - name: Install xclim
  run: |
  python -m pip install --no-user --no-deps --editable .
  - name: Check versions
  run: |
- conda list
+ micromamba list
  xclim show_version_info
  python -m pip check || true
  - name: Run Tests

CHANGELOG.rst

@@ -32,6 +32,8 @@ CI changes
 * `pip-tools` (`pip-compile`) has been used to generate a lock file with hashes for the CI dependencies. (:pull:`1841`).
 * The ``main.yml`` workflow has been updated to use simpler trigger logic. (:pull:`1841`).
 * A workflow bug has been fixed that was causing multiple duplicate comments to be made on Pull Requests originating from forks. (:pull:`1841`).
+* The ``upstream.yml`` workflow was adapted to not install upstream Python dependencies using hashes (impossible to install directly from GitHub sources using --require-hashes). (:pull:`1859`).
+* The `tox-gh` configuration has been set to handle the environment configurations on GitHub Workflows. The tox.ini file is also a bit more organized/consistent. (:pull:`1859`).
 
 v0.51.0 (2024-07-04)
 --------------------

CONTRIBUTING.rst

@@ -61,8 +61,8 @@ General notes for implementing new bias-adjustment methods:
 
 * Method are implemented as classes in ``xclim/sdba/adjustment.py``.
 * If the algorithm gets complicated and would generate many dask tasks, it should be implemented as functions wrapped by :py:func:`~xclim.sdba.map_blocks` or :py:func:`~xclim.sdba.map_groups` in ``xclim/sdba/_adjustment.py``.
-* xclim doesn't implement monolithic multi-parameter methods, but rather smaller modular functions to construct post-processing workflows.
-* If you are working on numba-accelerated function that use ``@guvectorize``, consider disabling caching during the development phase and reactivating it once all changes are ready for review. This is done by commenting ``cache=True`` in the decorator.
+* `xclim` doesn't implement monolithic multi-parameter methods, but rather smaller modular functions to construct post-processing workflows.
+* If you are working on numba-accelerated function that uses ``@guvectorize``, consider disabling caching during the development phase and reactivating it once all changes are ready for review. This is done by commenting ``cache=True`` in the decorator.
 
 Report Bugs
 ~~~~~~~~~~~
@@ -83,7 +83,7 @@ Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wa
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-xclim could always use more documentation, whether as part of the official xclim docs, in docstrings, or even on the web in blog posts, articles, and such.
+xclim could always use more documentation, whether as part of the official `xclim` docs, in docstrings, or even on the web in blog posts, articles, and such.
 
 To reference documents (article, presentation, thesis, etc) in the documentation or in a docstring, xclim uses `sphinxcontrib-bibtex`_.
 Metadata of the documents is stored as BibTeX entries in the ``docs/references.bib`` file.
@@ -162,25 +162,26 @@ Ready to contribute? Here's how to set up `xclim` for local development.
 
  Alternatively, one can use ``$ tox`` to run very specific testing configurations, as GitHub Workflows would do when a Pull Request is submitted and new commits are pushed::
 
- $ tox -e py39 # run tests on Python 3.9
- $ tox -e py310-upstream-doctest # run tests on Python 3.10, including doctests, with upstream dependencies
- $ tox -e py311 -- -m "not slow # run tests on Python 3.11, excluding "slow" marked tests
- $ tox -e py312-numba -- -m "not slow # run tests on Python 3.12, installing upstream `numba`, excluding "slow" marked tests
- $ tox -e notebooks_doctests # run tests using the base Python on doctests and evaluate all notebooks
- $ tox -e offline # run tests using the base Python, excluding tests requiring internet access
+ $ tox -e py39-coverage # run tests on Python 3.9, reporting code coverage
+ $ tox -e py310-upstream # run tests on Python 3.10, with upstream dependencies
+ $ tox -e py311-prefetch-offline -- -m "not slow" # run tests on Python 3.11, force download of testing, ensure tests are all offline, exclude "slow" marked tests
+ $ tox -e py312-lmoments -- -m "not slow" # run tests on Python 3.12, installing lmoments3, excluding "slow" marked tests
+ $ tox -e notebooks,doctests # run the notebook-based tests, then run the doctests
 
- $ tox -m test # run all builds listed above
+ $ tox -m test # run the standard tests used in GitHub Workflows
 
  .. warning::
+
  Starting from `xclim` v0.46.0, when running tests with `tox`, any `pytest` markers passed to `pyXX` builds (e.g. `-m "not slow"`) must be passed to `tox` directly. This can be done as follows::
 
  $ tox -e py310 -- -m "not slow"
 
  The exceptions to this rule are:
- `notebooks_doctests`: this configuration does not pass test  markers to its `pytest` call.
+ `notebooks` and `doctests`: these configurations do not pass test markers to its `pytest` call.
  `offline`: this configuration runs by default with the `-m "not requires_internet"` test marker. Be aware that running `tox` and manually setting a `pytest` marker will override this default.
 
  .. note::
+
  `xclim` tests are organized to support the `pytest-xdist`_ plugin for distributed testing across workers or CPUs.
  In order to benefit from multiple processes, add the flag `--numprocesses=auto` or `-n auto` to your `pytest` calls.
 

environment.yml

@@ -72,8 +72,8 @@ dependencies:
  - sphinx-mdinclude
  - sphinxcontrib-bibtex
  - tokenize-rt
- - tox >=4.15.1
-#  - tox-conda # Will be added when a tox@v4.0+ compatible plugin is released.
+ - tox >=4.16.0
+ # - tox-conda # Will be added when a tox@v4.0+ compatible plugin is released.
  - vulture # ==2.11 # The conda-forge version is out of date.
  - xdoctest >=1.1.5
  - yamllint

pyproject.toml

@@ -85,9 +85,8 @@ dev = [
  "pytest-xdist[psutil] >=3.2",
  "ruff >=0.4.10",
  "tokenize-rt",
- "tox >=4.15.1",
+ "tox >=4.16.0",
  # "tox-conda", # Will be added when a tox@v4.0+ compatible plugin is released.
- "tox-gh >=1.3.1",
  "vulture ==2.11",
  "xdoctest >=1.1.5",
  "yamllint ==1.35.1"

tox.ini

@@ -1,26 +1,29 @@
 [tox]
-min_version = 4.15.1
+min_version = 4.16.0
 env_list =
  lint
  docs
  notebooks
  doctests
- py39-upstream-doctest
- py310-doctest
- py311-lmoments
+ py39
+ py310-extras-numpy
+ py311-extras-sbck
+ py312-extras-lmoments
 labels =
- test = py39, py310-upstream-doctest, py311, notebooks_doctests, offline-prefetch
+ static = lint
+ test = py39, py310-extras-numpy, py311-extras-sbck, py312-extras-lmoments
+ special = docs, notebooks, doctests
 requires =
  pip >= 24.0
  flit >=3.9
 opts = -vv
 
 [gh]
 python =
- 3.12 = doctests
- 3.11 = py311-coverage-lmoments-sbck, offline-coverage-prefetch
- 3.10 = py310-coverage-lmoments, notebooks
- 3.9 = py39-coverage-sbck, lint, docs
+ 3.9 = py39-coverage
+ 3.10 = py310-coverage-extras-numpy
+ 3.11 = py311-coverage-extras-sbck
+ 3.12 = py312-coverage-extras-lmoments
 
 [testenv:lint]
 description = Run code quality compliance tests under {basepython}
@@ -120,6 +123,7 @@ deps =
 install_command = python -m pip install --no-user {opts} {packages}
 download = True
 commands_pre =
+ sbck: python -c 'print("The sbck dependency requires the \"libeigen3-dev\" package to be installed on the system.")'
  sbck: python -m pip install sbck
  python -m pip list
  xclim show_version_info