diff --git a/.gitattributes b/.gitattributes index 00a7b00..e16b0d3 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,3 @@ .git_archival.txt export-subst +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.github/renovate.json b/.github/renovate.json new file mode 100644 index 0000000..ad7ef10 --- /dev/null +++ b/.github/renovate.json @@ -0,0 +1,32 @@ +{ + "$schema": "https://docs.renovatebot.com/renovate-schema.json", + "extends": ["config:recommended"], + "dependencyDashboard": true, + "schedule": ["on monday"], + "managers": [ + { + "managerType": "pixi", + "fileMatch": ["(^|/)pyproject\\.toml$"], + "lockFileMaintenance": true + } + ], + "lockFileMaintenance": { + "enabled": true, + "schedule": ["on the first day of the month"], + "automerge": true + }, + "packageRules": [ + { + "matchManagers": ["pixi"], + "matchUpdateTypes": ["lockFileMaintenance"], + "commitMessagePrefix": "chore(pixi):", + "labels": ["dependencies", "pixi"] + }, + { + "matchManagers": ["github-actions"], + "commitMessagePrefix": "chore(ci):", + "labels": ["dependencies", "github-actions"], + "pinDigests": false + } + ] +} diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/ci.yml similarity index 54% rename from .github/workflows/unit_tests.yml rename to .github/workflows/ci.yml index 3339e08..34350a0 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/ci.yml @@ -2,12 +2,12 @@ name: unit-tests on: pull_request: push: - schedule: - - cron: "0 7 * * 1" # Run every Monday at 7:00 UTC + branches: + - "main" -defaults: - run: - shell: bash -el {0} +concurrency: + group: branch-${{ github.head_ref }} + cancel-in-progress: true jobs: unit-test: @@ -18,15 +18,10 @@ jobs: steps: - name: Checkout uses: actions/checkout@v3 - - name: Setup Conda and parcels - uses: ./.github/actions/install-plasticparcels - with: - environment-file: environment.yml - environment-name: py3_parcels + - name: Setup pixi + uses: prefix-dev/setup-pixi@v0.8.5 - name: Unit test - run: | - coverage run -m pytest -v -s tests - coverage xml + run: pixi run tests with-coverage - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v4.0.1 with: diff --git a/.gitignore b/.gitignore index fbddf57..1aa28fe 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,9 @@ docs/_build/* .vscode _version_setup.py +# pixi environments +.pixi/* +!.pixi/config.toml + +# coverage +coverage.xml \ No newline at end of file diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ac52fdc..c62305a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,14 +1,18 @@ version: 2 build: - os: ubuntu-22.04 + os: ubuntu-lts-latest tools: - python: mambaforge-22.9 + # just so RTD stops complaining + python: "latest" jobs: - pre_build: - - pip install . # Need access to version information - + create_environment: + - asdf plugin add pixi + - asdf install pixi latest + - asdf global pixi latest + install: + - pixi install --frozen + build: + html: + - pixi run sphinx-build -T -b html docs $READTHEDOCS_OUTPUT/html sphinx: configuration: docs/conf.py - -conda: - environment: docs/environment_docs.yml diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..d52b2ce --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,38 @@ +# Contributing + +Contributions are welcome, though please for opinionated changes discuss +them first in an issue before making a pull request. + +## Developer instructions + +We use Pixi for our development workflow (a modern alternative to Conda). + +- [install Pixi](https://pixi.prefix.dev/latest/installation/) +- fork and clone the repository, and `cd` into the repository +- run `pixi task list` (which will show you the available commands for the repository - such as building the documentation, or running tests) +- run the command you would like using `pixi run ...` (e.g, `pixi run tests`) + +You can also enter the environment for the repository by doing `pixi shell` (this is equivalent to `conda activate ...`). + +The installation of the virtual environment will be done automatically by Pixi when running `pixi run` or `pixi shell` - this environment is visible in the `./pixi` folder under the repo root. + +The `.pixi` folder and the `pixi.lock` file should not be editted by hand. The `pixi.lock` file should be committed. + + +## Maintainer instructions + +### About the `pixi.lock` + +This repo has a committed `pixi.lock` (meaning that the tree of dependencies used in development is static). +This results in perfectly reproducibility between dev machines and CI. + +This, however, means that releases of dependencies (e.g., deprecations in Parcels or Xarray) may unknowingly break Plasticparcels. +To mitigate this - there is a Renovate Bot (i.e., an alternative to Dependabot) that will upgrade the Pixi lock on a regular basis and automerge if CI passes. +If CI fails, there is a change upstream that Plasticparcels needs a code adjustment to deal with. + +### Release checklist + +- Make sure CI is passing on the latest version of `main` +- Go to GitHub, draft new release. Enter name of version and "create new tag" if it doesn't already exist. Click "Generate Release Notes". Currate release notes as needed. Look at a previous version release to match the format (title, header, section organisation etc.) +- Go to [conda-forge/plasticparcels-feedstock](https://github.com/conda-forge/plasticparcels-feedstock), create a new issue (select the "Bot Commands" issue from the menu) with title `@conda-forge-admin, please update version`. This will prompt a build, otherwise there can be a delay in the build. + - Approve PR and merge on green \ No newline at end of file diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..c67baf9 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,4343 @@ +version: 7 +platforms: +- name: linux-64 + virtual-packages: + - __unix=0=0 + - __linux=4.18 + - __glibc=2.28 + - __archspec=0=x86_64 +- name: osx-arm64 + virtual-packages: + - __unix=0=0 + - __osx=13.0 + - __archspec=0=m1 +- name: win-64 + virtual-packages: + - __win=10.0 + - __archspec=0=x86_64 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda + - 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Alpha", - "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", @@ -28,9 +27,25 @@ dependencies = [ "parcels >= 3.0.2, < 4", "shapely", "geopandas", - "pytest", ] +[dependency-groups] +dev = [ + "pytest>=8.3.5", + "pytest-cov", + "ipython", +] +docs = [ + "numpydoc", + "nbsphinx", + "sphinx", + "pandoc", + "pydata-sphinx-theme", + "sphinx-autobuild", + "myst-parser", +] + + [project.urls] homepage = "https://parcels-code.org/" repository = "https://github.com/Parcels-code/plasticparcels/" @@ -91,3 +106,34 @@ ignore = [ [tool.ruff.lint.pydocstyle] convention = "numpy" + +[tool.pixi.workspace] +channels = ["conda-forge"] +platforms = ["osx-arm64", "win-64", "linux-64"] +exclude-newer = "7d" + +[tool.pixi.pypi-dependencies] +plasticparcels = { path = ".", editable = true } + +[tool.pixi.dependencies] +# Pin Python <3.14: numcodecs' bundled c-blosc uses `typedef _Bool bool` which +# is illegal in C23 (the default standard in newer GCC). This breaks source +# builds on linux with Python 3.14+. Test removing this pin upgrading to v4 of Parcels (as that uses Zarr v3, and a different numcodecs) +python = ">=3.12,<3.14" + +[tool.pixi.feature.dev.dependencies] +proj = "*" + +[tool.pixi.feature.dev.tasks.tests] +cmd = "pytest {{ '--cov=plasticparcels --cov-report=xml' if coverage=='with-coverage' else '' }}" +description = "Run the tests" +args = [{ arg = "coverage", default = 'no-coverage', choices = ["with-coverage", "no-coverage"] }] + + +[tool.pixi.feature.docs.tasks] +docs-build = {cmd = "make html", cwd = "docs", description = "Biuld the docs."} + + +[tool.pixi.environments] +default = ["dev", "docs"] + diff --git a/tests/test_kernels.py b/tests/test_kernels.py index 89b644f..ad4fbd7 100644 --- a/tests/test_kernels.py +++ b/tests/test_kernels.py @@ -237,7 +237,6 @@ def test_mixing(): pset = make_standard_particleset(fieldset, settings) pset_mixing = make_standard_particleset(fieldset, settings) - pset.execute(kernels, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt']) pset_mixing.execute(kernels_mixing, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])