diff --git a/.github/workflows/constraints.txt b/.github/workflows/constraints.txt index fac95554..f28989f5 100644 --- a/.github/workflows/constraints.txt +++ b/.github/workflows/constraints.txt @@ -1,5 +1,5 @@ -pip==23.3.1 +pip==23.3.2 nox==2023.4.22 nox-poetry==1.0.3 -poetry==1.6.1 -virtualenv==20.24.6 +poetry==1.7.1 +virtualenv==20.25.0 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 36a349d2..98b43b52 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -17,7 +17,7 @@ jobs: fetch-depth: 2 - name: Set up Python - uses: actions/setup-python@v4.7.1 + uses: actions/setup-python@v5.0.0 with: python-version: "3.9" @@ -57,18 +57,18 @@ jobs: - name: Publish package on PyPI if: steps.check-version.outputs.tag - uses: pypa/gh-action-pypi-publish@v1.8.10 + uses: pypa/gh-action-pypi-publish@v1.8.11 with: user: __token__ password: ${{ secrets.PYPI_TOKEN }} - name: Publish package on TestPyPI if: "! steps.check-version.outputs.tag" - uses: pypa/gh-action-pypi-publish@v1.8.10 + uses: pypa/gh-action-pypi-publish@v1.8.11 with: user: __token__ password: ${{ secrets.TEST_PYPI_TOKEN }} - repository_url: https://test.pypi.org/legacy/ + repository-url: https://test.pypi.org/legacy/ - name: Publish the release notes uses: release-drafter/release-drafter@v5.25.0 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 3efbc2b0..204e6f7a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -13,18 +13,21 @@ jobs: include: - { python-version: 3.9, os: ubuntu-latest, session: "pre-commit" } - { python-version: 3.9, os: ubuntu-latest, session: "safety" } + - { python-version: "3.12", os: ubuntu-latest, session: "mypy" } - { python-version: "3.11", os: ubuntu-latest, session: "mypy" } - { python-version: "3.10", os: ubuntu-latest, session: "mypy" } - { python-version: 3.9, os: ubuntu-latest, session: "mypy" } - { python-version: 3.8, os: ubuntu-latest, session: "mypy" } + - { python-version: "3.12", os: ubuntu-latest, session: "tests" } - { python-version: "3.11", os: ubuntu-latest, session: "tests" } - { python-version: "3.10", os: ubuntu-latest, session: "tests" } - { python-version: 3.9, os: ubuntu-latest, session: "tests" } - { python-version: 3.8, os: ubuntu-latest, session: "tests" } - - { python-version: "3.10", os: windows-latest, session: "tests" } - - { python-version: "3.10", os: macos-latest, session: "tests" } - - { python-version: 3.9, os: ubuntu-latest, session: "typeguard" } - - { python-version: "3.10", os: ubuntu-latest, session: "docs-build" } + - { python-version: "3.12", os: windows-latest, session: "tests" } + - { python-version: "3.12", os: macos-latest, session: "tests" } + # since ray is still not available wiht 3.12 + - { python-version: "3.11", os: ubuntu-latest, session: "typeguard" } + - { python-version: "3.12", os: ubuntu-latest, session: "docs-build" } env: NOXSESSION: ${{ matrix.session }} @@ -38,7 +41,7 @@ jobs: run: sudo apt-get install pandoc - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4.7.1 + uses: actions/setup-python@v5.0.0 with: python-version: ${{ matrix.python-version }} @@ -49,7 +52,7 @@ jobs: - name: Install Poetry run: | - pip install --constraint=.github/workflows/constraints.txt poetry + pip install --constraint=.github/workflows/constraints.txt poetry poetry-plugin-export poetry --version - name: Install Nox @@ -75,7 +78,7 @@ jobs: os.environ["GITHUB_OUTPUT"] = "result={}".format(result) - name: Restore pre-commit cache - uses: actions/cache@v3.3.2 + uses: actions/cache@v4.0.0 if: matrix.session == 'pre-commit' with: path: ~/.cache/pre-commit @@ -88,15 +91,15 @@ jobs: nox --force-color --python=${{ matrix.python-version }} - name: Upload coverage data - if: always() && matrix.session == 'tests' - uses: "actions/upload-artifact@v3.1.3" + if: matrix.session == 'tests' + uses: "actions/upload-artifact@v4.3.0" with: - name: coverage-data + name: coverage-data.${{ matrix.python-version }}.${{ matrix.os }} path: ".coverage.*" - name: Upload documentation if: matrix.session == 'docs-build' - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.0 with: name: docs path: docs/_build @@ -109,7 +112,7 @@ jobs: uses: actions/checkout@v4.1.1 - name: Set up Python 3.9 - uses: actions/setup-python@v4.7.1 + uses: actions/setup-python@v5.0.0 with: python-version: 3.9 @@ -120,7 +123,7 @@ jobs: - name: Install Poetry run: | - pip install --constraint=.github/workflows/constraints.txt poetry + pip install --constraint=.github/workflows/constraints.txt poetry poetry-plugin-export poetry --version - name: Install Nox @@ -129,9 +132,9 @@ jobs: nox --version - name: Download coverage data - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.1 with: - name: coverage-data + name: coverage-data.3.11.ubuntu-latest - name: Combine coverage data and display human readable report run: | @@ -142,4 +145,4 @@ jobs: nox --force-color --session=coverage -- xml - name: Upload coverage report - uses: codecov/codecov-action@v3.1.4 + uses: codecov/codecov-action@v4.0.1 diff --git a/README.rst b/README.rst index 766cb902..76f8c5ad 100644 --- a/README.rst +++ b/README.rst @@ -58,7 +58,7 @@ Requirements ------------ Python >= 3.8 is supported. -The software is tested against Python 3.8-3.11 in Ubuntu, and 3.10 in MacOS and Windows environments, +The software is tested against Python 3.8-3.12 in Ubuntu, and 3.12 in MacOS and Windows environments, but the other combinations should also be fine. Please `file an issue`_ if you encounter any problem. Installation diff --git a/docs/examples/bright_spots.ipynb b/docs/examples/bright_spots.ipynb index 4282abc1..8e2c78ba 100644 --- a/docs/examples/bright_spots.ipynb +++ b/docs/examples/bright_spots.ipynb @@ -217,7 +217,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.11" + "version": "3.1.0" }, "vscode": { "interpreter": { diff --git a/noxfile.py b/noxfile.py index b98d6460..8696b9b0 100644 --- a/noxfile.py +++ b/noxfile.py @@ -20,7 +20,7 @@ package = "laptrack" -python_versions = ["3.11", "3.10", "3.9", "3.8"] +python_versions = ["3.12", "3.11", "3.10", "3.9", "3.8"] safety_ignore = [44717, 44715, 44716, 51457] # ignore numpy 1.21 CVEs and py 1.11.0 nox.needs_version = ">= 2021.6.6" nox.options.sessions = ( @@ -84,7 +84,12 @@ def mypy(session: Session) -> None: def tests(session: Session) -> None: """Run the test suite.""" session.install(".") - session.install("coverage[toml]", "pytest", "pytest-datadir", "pygments", "ray") + session.install("coverage[toml]", "pytest", "pytest-datadir", "pygments") + try: + session.install("ray") + except nox.command.CommandFailed: + session.warn("Ray not installed, skipping ray tests") + try: session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs) finally: @@ -113,7 +118,7 @@ def typeguard(session: Session) -> None: session.run("pytest", f"--typeguard-packages={package}", *session.posargs) -@session(name="docs-build", python="3.10") +@session(name="docs-build", python=python_versions[0]) def docs_build(session: Session) -> None: """Build the documentation.""" args = session.posargs or ["docs", "docs/_build"] @@ -126,7 +131,7 @@ def docs_build(session: Session) -> None: session.run("sphinx-build", *args) -@session(python="3.10") +@session(python=python_versions[0]) def docs(session: Session) -> None: """Build and serve the documentation with live reloading on file changes.""" args = session.posargs or ["--open-browser", "docs", "docs/_build"] diff --git a/poetry.lock b/poetry.lock index 49e91b0d..40f6774b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,24 +13,25 @@ files = [ [[package]] name = "anyio" -version = "4.0.0" +version = "4.2.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, - {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, + {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, + {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (>=0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "appnope" @@ -117,34 +118,40 @@ tests = ["pytest"] [[package]] name = "arrow" -version = "1.2.3" +version = "1.3.0" description = "Better dates & times for Python" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, + {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, + {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, ] [package.dependencies] python-dateutil = ">=2.7.0" +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "asttokens" -version = "2.4.0" +version = "2.4.1" description = "Annotate AST trees with source code positions" optional = false python-versions = "*" files = [ - {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"}, - {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"}, + {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, + {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, ] [package.dependencies] six = ">=1.12.0" [package.extras] -test = ["astroid", "pytest"] +astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] +test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] [[package]] name = "async-lru" @@ -172,21 +179,22 @@ files = [ [[package]] name = "attrs" -version = "23.1.0" +version = "23.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, - 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(==2.10.3)", "pybind11 (==2.7.1)", "scikit-build (==0.11.1)", "scikit-build (==0.16.1)"] -tests-strict = ["codecov (==2.0.15)", "pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==6.2.5)", "pytest-cov (==3.0.0)", "typing (==3.7.4)"] +tests-strict = ["pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==6.2.5)", "pytest-cov (==3.0.0)", "typing (==3.7.4)"] [[package]] name = "xmltodict" @@ -4038,5 +4229,5 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" -python-versions = "^3.8,<3.12" -content-hash = "149e953fece55952b4fda44ce47ef2dac91a83504b432a7991d3b1e908d7734f" +python-versions = "^3.8,<3.13" +content-hash = "9c59b59f129ec2673f36e3c843cb33b2efb0654357f584f064aff471b75dbb1e" diff --git a/pyproject.toml b/pyproject.toml index 240c1247..be8125d4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,7 @@ classifiers = [ "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", "License :: OSI Approved :: BSD License", ] @@ -25,10 +26,16 @@ classifiers = [ Changelog = "https://github.com/yfukai/laptrack/releases" [tool.poetry.dependencies] -python = "^3.8,<3.12" +python = "^3.8,<3.13" click = "^8.0.1" -numpy = "^1.21.0" -scipy = "^1.8.0" +numpy = [ + { version = "^1.26", python = ">=3.9" }, + { version = "^1.24", python = "<3.9" } +] +scipy = [ + { version = "^1.12.0", python = ">=3.12" }, + { version = "^1.8.0", python = "<3.12" } +] networkx = "^2.6.1" pandas = "^1.3.1" typing-extensions = "^4.1.0" diff --git a/tests/test_overlap_tracking.py b/tests/test_overlap_tracking.py index d0745624..1af0ad3f 100644 --- a/tests/test_overlap_tracking.py +++ b/tests/test_overlap_tracking.py @@ -31,6 +31,10 @@ def test_overlap_tracking( track_overlap_coefs, splitting_overlap_coefs, ) -> None: + + if parallel_backend == "ray": + pytest.importorskip("ray") + if dataset == "mouse_epidermis": labels = fetch(dataset) else: diff --git a/tests/test_tracking.py b/tests/test_tracking.py index b1cd2363..01f9da8e 100644 --- a/tests/test_tracking.py +++ b/tests/test_tracking.py @@ -104,6 +104,10 @@ def testdata(request, shared_datadir: str): @pytest.mark.parametrize("parallel_backend", ["serial", "ray"]) def test_reproducing_trackmate(testdata, parallel_backend) -> None: + + if parallel_backend == "ray": + pytest.importorskip("ray") + params, coords, edges_set = testdata params["parallel_backend"] = parallel_backend lt = LapTrack(**params)