From cfb429c1f3dcf3ac2437692c0431123f19dacd0c Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Fri, 10 Apr 2026 10:03:51 +0200 Subject: [PATCH 1/2] Apply latest templates --- .copier-answers.yml | 6 +- .github/workflows/pypi-test.yml | 24 +- .github/workflows/test.yml | 44 +- .github/workflows/tutorial-tests.yml | 4 - docs/docs/installation-and-setup/index.md | 32 +- pixi.lock | 9884 ++++++++++----------- pixi.toml | 28 +- pyproject.toml | 15 +- tests/functional/test_dummy.py | 8 + 9 files changed, 4887 insertions(+), 5158 deletions(-) create mode 100644 tests/functional/test_dummy.py diff --git a/.copier-answers.yml b/.copier-answers.yml index c3886bcb..5743335a 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,6 +1,6 @@ # WARNING: Do not edit this file manually. # Any changes will be overwritten by Copier. -_commit: v0.10.1-38-g85fbe04 +_commit: v0.10.1-41-g508666e _src_path: gh:easyscience/templates app_docs_url: https://easyscience.github.io/dynamics-app app_doi: 10.5281/zenodo.18877180 @@ -12,8 +12,8 @@ home_repo_name: dynamics lib_docs_url: https://easyscience.github.io/dynamics-lib lib_doi: 10.5281/zenodo.18877180 lib_package_name: easydynamics -lib_python_max: '3.12' -lib_python_min: '3.11' +lib_python_max: '3.14' +lib_python_min: '3.12' lib_repo_name: dynamics-lib project_contact_email: henrik.jacobsen@ess.eu project_copyright_years: 2025-2026 diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml index 117d24d6..a0617446 100644 --- a/.github/workflows/pypi-test.yml +++ b/.github/workflows/pypi-test.yml @@ -45,30 +45,30 @@ jobs: - name: Init pixi project run: pixi init easydynamics - - name: Add Python 3.12 from Conda + - name: Set the minimum system requirements working-directory: easydynamics - run: pixi add "python=3.12" + run: pixi project system-requirements add macos 14.0 - - name: Add other Conda dependencies - working-directory: easydynamics - run: pixi add gsl - - - name: Add easydynamics from PyPI + - name: Add Python 3.14 from Conda working-directory: easydynamics - run: pixi add --pypi "easydynamics" + run: pixi add "python=3.14" - - name: Add dev dependencies from PyPI + - name: Add other Conda dependencies working-directory: easydynamics - run: pixi add --pypi pytest pytest-xdist + run: pixi add gsl - - name: Add Pixi task as a shortcut + - name: Add easydynamics (with dev dependencies) from PyPI working-directory: easydynamics - run: pixi task add easydynamics "python -m easydynamics" + run: pixi add --pypi "easydynamics[dev]" - name: Run unit tests to verify the installation working-directory: easydynamics run: pixi run python -m pytest ../tests/unit/ --color=yes -v + - name: Run functional tests to verify the installation + working-directory: easydynamics + run: pixi run python -m pytest ../tests/functional/ --color=yes -v + - name: Run integration tests to verify the installation working-directory: easydynamics run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index ce03715c..774edf78 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -44,8 +44,8 @@ concurrency: # Set the environment variables to be used in all jobs defined in this workflow env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} - PY_VERSIONS: '3.11 3.12' - PIXI_ENVS: 'py-311-env py-312-env' + PY_VERSIONS: '3.12 3.14' + PIXI_ENVS: 'py-312-env py-314-env' jobs: # Job 1: Set up environment variables @@ -96,12 +96,27 @@ jobs: echo echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" - env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env echo "Running tests in environment: $env" pixi run --environment $env unit-tests done + - name: Run functional tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + echo "Running tests in environment: $env" + pixi run --environment $env functional-tests + done + - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }} shell: bash run: | @@ -111,7 +126,7 @@ jobs: echo echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" - env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env echo "Running tests in environment: $env" pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }} @@ -236,7 +251,26 @@ jobs: cd easydynamics_py$py_ver echo "Running tests" - pixi run python -m pytest ../tests/unit/ --color=yes --cov= --cov-report= + pixi run python -m pytest ../tests/unit/ --color=yes -v + + echo "Exiting pixi project directory" + cd .. + done + + - name: Run functional tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Entering pixi project directory easydynamics_py$py_ver" + cd easydynamics_py$py_ver + + echo "Running tests" + pixi run python -m pytest ../tests/functional/ --color=yes -v echo "Exiting pixi project directory" cd .. diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml index 4c9244d0..e976e267 100644 --- a/.github/workflows/tutorial-tests.yml +++ b/.github/workflows/tutorial-tests.yml @@ -45,10 +45,6 @@ jobs: - name: Set up pixi uses: ./.github/actions/setup-pixi - - name: Test tutorials as python scripts - shell: bash - run: pixi run script-tests - - name: Prepare notebooks shell: bash run: pixi run notebook-prepare diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md index 6c928741..243d81f8 100644 --- a/docs/docs/installation-and-setup/index.md +++ b/docs/docs/installation-and-setup/index.md @@ -5,7 +5,7 @@ icon: material/cog-box # :material-cog-box: Installation & Setup **EasyDynamics** is a cross-platform Python library compatible with -**Python 3.11** through **3.12**. +**Python 3.12** through **3.14**. To install and set up EasyDynamics, we recommend using [**Pixi**](https://pixi.prefix.dev), a modern package manager for @@ -62,9 +62,9 @@ This section describes the simplest way to set up EasyDynamics using pixi init easydynamics cd easydynamics ``` -- Set the Python version for the Pixi environment (e.g., 3.12): +- Set the Python version for the Pixi environment (e.g., 3.14): ```txt - pixi add python=3.12 + pixi add python=3.14 ``` - Add EasyDynamics to the Pixi environment from PyPI: ```txt @@ -231,26 +231,36 @@ first. This can be done individually via the :material-download: - Navigate to your existing Pixi project, created as described in the [Installing with Pixi](#installing-with-pixi) section. -- Launch the Jupyter Lab server: +- Add JupyterLab and the Pixi kernel for Jupyter: ```txt - pixi run jupyter lab + pixi add --pypi jupyterlab pixi-kernel + ``` +- Download the EasyDynamics tutorials to the `tutorials/` directory. +- Start JupyterLab in the `tutorials/` directory to access the + notebooks: + ```txt + pixi run jupyter lab tutorials/ ``` - Your web browser should open automatically. Click on one of the - `*.ipynb` files downloaded previously and select the `Python (Pixi)` - kernel to get started. + `*.ipynb` files and select the `Python (Pixi)` kernel to get started. ### Classical Run Tutorials Locally +- Install Jupyter Notebook and IPython kernel: + ```txt + pip install notebook ipykernel + ``` - Add the virtual environment as a Jupyter kernel: ```txt python -m ipykernel install --user --name=venv --display-name "EasyDynamics Python kernel" ``` -- Launch the Jupyter Notebook server: +- Download the EasyDynamics tutorials to the `tutorials/` directory. +- Launch the Jupyter Notebook server (opens browser automatically at + `http://localhost:8888/`): ```txt - jupyter notebook + jupyter notebook tutorials/ ``` -- Your web browser should open automatically. Click on one of the - `*.ipynb` files downloaded previously and select the +- Open one of the `*.ipynb` files and select the `EasyDynamics Python kernel` to get started. ### Run Tutorials via Google Colab diff --git a/pixi.lock b/pixi.lock index acd7cbf3..efafa5aa 100644 --- a/pixi.lock +++ b/pixi.lock @@ -10,15 +10,74 @@ environments: packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.13.0-pyhcf101f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py314h5bd0f2a_2.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda + - 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vc >=14.3,<15 + - vc14_runtime >=14.44.35208 + - ucrt >=10.0.20348.0 + - libzlib >=1.3.1,<2.0a0 + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 388453 + timestamp: 1764777142545 diff --git a/pixi.toml b/pixi.toml index ac6a7e02..c711a178 100644 --- a/pixi.toml +++ b/pixi.toml @@ -29,7 +29,7 @@ PYTHONPATH = "${PIXI_PROJECT_ROOT}/src;%PYTHONPATH%" [workspace] # Supported platforms for the lock file (pixi.lock) -platforms = ['win-64', 'linux-64', 'osx-64', 'osx-arm64'] +platforms = ['win-64', 'linux-64', 'osx-arm64'] # Channels for fetching packages channels = ['conda-forge'] @@ -53,17 +53,20 @@ macos = '14.0' # Default feature configuration [dependencies] -nodejs = '*' # Required for Prettier (non-Python formatting) +nodejs = '*' # Required for Prettier (non-Python formatting) +jupyterlab = '*' # Jupyter notebooks +pixi-kernel = '*' # Pixi Jupyter kernel [pypi-dependencies] # == [feature.default.pypi-dependencies] -easydynamics = { path = ".", editable = true, extras = ['dev'] } +#pip = '*' # Native package installer +easydynamics = { path = '.', editable = true, extras = ['dev'] } # Specific features: Set specific Python versions [feature.py-min.dependencies] -python = '3.11.*' -[feature.py-max.dependencies] python = '3.12.*' +[feature.py-max.dependencies] +python = '3.14.*' ############## # ENVIRONMENTS @@ -73,12 +76,12 @@ python = '3.12.*' # The `default` feature is always included in all environments. # Additional features can be specified per environment. -py-311-env = { features = ['default', 'py-min'] } -py-312-env = { features = ['default', 'py-max'] } +py-312-env = { features = ['py-min'] } +py-314-env = { features = ['py-max'] } # The `default` environment is always created and includes the `default` feature. # It does not need to be specified explicitly unless non-default features are included. -default = { features = ['default', 'py-max'] } +default = { features = ['py-max'] } ####### # TASKS @@ -91,9 +94,9 @@ default = { features = ['default', 'py-max'] } ################## unit-tests = 'python -m pytest tests/unit/ --color=yes -v' +functional-tests = 'python -m pytest tests/functional/ --color=yes -v' integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v' -script-tests = 'python -m pytest tools/test_scripts.py --color=yes -n auto -v' -notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=600 --color=yes -n auto -v' +notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --color=yes -n auto -v' test = { depends-on = ['unit-tests'] } @@ -150,6 +153,7 @@ raw-metrics-json = 'radon raw -s -j src/' ############# unit-tests-coverage = 'pixi run unit-tests --cov=src/easydynamics --cov-report=term-missing' +functional-tests-coverage = 'pixi run functional-tests --cov=src/easydynamics --cov-report=term-missing' integration-tests-coverage = 'pixi run integration-tests --cov=src/easydynamics --cov-report=term-missing' docstring-coverage = 'interrogate -c pyproject.toml src/easydynamics' @@ -165,8 +169,8 @@ cov = { depends-on = [ notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb' notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb' -notebook-tweak = 'python tools/tweak_notebooks.py tutorials/' -notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=600 --overwrite --color=yes -n auto -v' +notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/' +notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v' notebook-prepare = { depends-on = [ #'notebook-convert', diff --git a/pyproject.toml b/pyproject.toml index 9e75a4a7..17452cd7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,10 +17,11 @@ classifiers = [ 'Operating System :: OS Independent', 'Programming Language :: Python :: 3 :: Only', 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.11', 'Programming Language :: Python :: 3.12', + 'Programming Language :: Python :: 3.13', + 'Programming Language :: Python :: 3.14', ] -requires-python = '>=3.11' +requires-python = '>=3.12' dependencies = [ 'easyscience', # The base library of the EasyScience framework 'pooch', # Data downloader @@ -47,7 +48,6 @@ dev = [ 'pytest', # Testing 'pytest-cov', # Test coverage 'pytest-xdist', # Enable parallel testing - 'pytest-forked', # Isolate tests in subprocesses 'ruff', # Linting and formatting code 'radon', # Code complexity and maintainability 'validate-pyproject[all]', # Validate pyproject.toml @@ -256,7 +256,8 @@ select = [ # Ignore specific rules globally ignore = [ 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ - # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/ ] @@ -303,6 +304,12 @@ max-doc-length = 99 [tool.ruff.lint.pydocstyle] convention = 'numpy' +[tool.ruff.lint.pylint] +# Ruff counts `self`/`cls` in max-args; traditional pylint does not. +# Setting 6 here matches pylint's default of 5 (excluding self). +max-args = 6 +max-positional-args = 6 + ############################# # Configuration for pydoclint ############################# diff --git a/tests/functional/test_dummy.py b/tests/functional/test_dummy.py new file mode 100644 index 00000000..b45b191f --- /dev/null +++ b/tests/functional/test_dummy.py @@ -0,0 +1,8 @@ +# SPDX-FileCopyrightText: 2025-2026 EasyDynamics contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_dummy(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected From 974458f1a274e1712ac92f18c855b2eda97935c8 Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Fri, 10 Apr 2026 10:14:28 +0200 Subject: [PATCH 2/2] Remove unnecessary Conda dependency addition from CI configuration --- .github/workflows/pypi-test.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml index a0617446..7224f1e4 100644 --- a/.github/workflows/pypi-test.yml +++ b/.github/workflows/pypi-test.yml @@ -53,10 +53,6 @@ jobs: working-directory: easydynamics run: pixi add "python=3.14" - - name: Add other Conda dependencies - working-directory: easydynamics - run: pixi add gsl - - name: Add easydynamics (with dev dependencies) from PyPI working-directory: easydynamics run: pixi add --pypi "easydynamics[dev]"