From abc517a44936ea02d347200ca7b74f08ed89e0a8 Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Fri, 2 Feb 2024 11:04:44 +0900 Subject: [PATCH 01/13] updated coverage upload --- .github/workflows/release.yml | 2 +- .github/workflows/tests.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index f6612f6..98b43b5 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -68,7 +68,7 @@ jobs: 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 27322f7..417ff8b 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -89,7 +89,7 @@ jobs: - name: Upload coverage data if: always() && matrix.session == 'tests' - uses: "actions/upload-artifact@v3.1.3" + uses: "actions/upload-artifact@v4.3.0" with: name: coverage-data path: ".coverage.*" From 54cbb63b3ec04f2f8e3df9e1de0319d313fe66bf Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Fri, 2 Feb 2024 21:58:56 +0900 Subject: [PATCH 02/13] update python dep --- .github/workflows/tests.yml | 16 +++++++++------- noxfile.py | 2 +- pyproject.toml | 3 ++- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 417ff8b..573bfc3 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -13,18 +13,20 @@ 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" } + - { python-version: "3.12", os: ubuntu-latest, session: "typeguard" } + - { python-version: "3.12", os: ubuntu-latest, session: "docs-build" } env: NOXSESSION: ${{ matrix.session }} @@ -88,10 +90,10 @@ jobs: nox --force-color --python=${{ matrix.python-version }} - name: Upload coverage data - if: always() && matrix.session == 'tests' + 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 @@ -131,7 +133,7 @@ jobs: - name: Download coverage data uses: actions/download-artifact@v4.1.0 with: - name: coverage-data + name: coverage-data.3.11.ubuntu-latest - name: Combine coverage data and display human readable report run: | diff --git a/noxfile.py b/noxfile.py index b98d646..97135b9 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 = ( diff --git a/pyproject.toml b/pyproject.toml index 240c124..8bf6674 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", ] @@ -25,7 +26,7 @@ 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" From c92666115b21b838c7ff59379930f1cdd0063d14 Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Fri, 2 Feb 2024 22:03:39 +0900 Subject: [PATCH 03/13] updated poetry version --- poetry.lock | 1078 ++++++++++++++++++++++++++++----------------------- 1 file changed, 587 insertions(+), 491 deletions(-) diff --git a/poetry.lock b/poetry.lock index c6faf41..2bcd1c5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,19 +13,20 @@ files = [ [[package]] name = "anyio" -version = "4.1.0" +version = "4.2.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.1.0-py3-none-any.whl", hash = "sha256:56a415fbc462291813a94528a779597226619c8e78af7de0507333f700011e5f"}, - {file = "anyio-4.1.0.tar.gz", hash = "sha256:5a0bec7085176715be77df87fc66d6c9d70626bd752fcc85f57cdbee5b3760da"}, + {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)", "sphinx-rtd-theme"] @@ -178,21 +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"}, - {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, + {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, + {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, ] [package.extras] cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[docs,tests]", "pre-commit"] +dev = ["attrs[tests]", "pre-commit"] docs = ["furo", "myst-parser", "sphinx", 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further --- noxfile.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/noxfile.py b/noxfile.py index 97135b9..e9c2dab 100644 --- a/noxfile.py +++ b/noxfile.py @@ -113,7 +113,7 @@ 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 +126,7 @@ 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"] From c47838ee4db7d396fadb2fa741370cb69cd70754 Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Fri, 2 Feb 2024 23:41:26 +0900 Subject: [PATCH 08/13] readme --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index beec938..861eae3 100644 --- a/README.rst +++ b/README.rst @@ -55,7 +55,7 @@ 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 From a6f55cca268109a9097a3b3906be12560bc18c0f Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Fri, 2 Feb 2024 23:51:38 +0900 Subject: [PATCH 09/13] added poetry-plugin-export install --- .github/workflows/tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 573bfc3..b5010e7 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -51,7 +51,7 @@ 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 @@ -122,7 +122,7 @@ 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 From 6dc959aa5e2cf868ba4fd7a18982c3d73b982faa Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Sat, 3 Feb 2024 21:30:21 +0900 Subject: [PATCH 10/13] iskipping ray for unavailble version --- docs/examples/bright_spots.ipynb | 2 +- noxfile.py | 7 ++++++- tests/test_overlap_tracking.py | 9 ++++++++- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/docs/examples/bright_spots.ipynb b/docs/examples/bright_spots.ipynb index 4282abc..8e2c78b 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 e9c2dab..8696b9b 100644 --- a/noxfile.py +++ b/noxfile.py @@ -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: diff --git a/tests/test_overlap_tracking.py b/tests/test_overlap_tracking.py index d074562..5ca463c 100644 --- a/tests/test_overlap_tracking.py +++ b/tests/test_overlap_tracking.py @@ -11,11 +11,18 @@ from laptrack.datasets import fetch from laptrack.metric_utils import LabelOverlapOld +try: + import ray # noqa: F401 + + PARALLEL_BACKENDS = ["serial", "ray"] +except ImportError: + PARALLEL_BACKENDS = ["serial"] + @pytest.mark.parametrize( "dataset", ["cell_segmentation", "mouse_epidermis", "HL60_3D_synthesized"] ) -@pytest.mark.parametrize("parallel_backend", ["serial", "ray"]) +@pytest.mark.parametrize("parallel_backend", PARALLEL_BACKENDS) @pytest.mark.parametrize("splitting_cost_cutoff", [False, 0.9]) @pytest.mark.parametrize("merging_cost_cutoff", [False, 0.9]) @pytest.mark.parametrize("track_overlap_coefs", [(2.0, -0.5, -0.5, -0.5, -0.5)]) From 494e8e2806271e02fe4d2c6cbc7ae74fd258d4d7 Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Sat, 3 Feb 2024 22:54:04 +0900 Subject: [PATCH 11/13] skipping ray if not installed --- tests/test_overlap_tracking.py | 13 +++++-------- tests/test_tracking.py | 4 ++++ 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/tests/test_overlap_tracking.py b/tests/test_overlap_tracking.py index 5ca463c..1af0ad3 100644 --- a/tests/test_overlap_tracking.py +++ b/tests/test_overlap_tracking.py @@ -11,18 +11,11 @@ from laptrack.datasets import fetch from laptrack.metric_utils import LabelOverlapOld -try: - import ray # noqa: F401 - - PARALLEL_BACKENDS = ["serial", "ray"] -except ImportError: - PARALLEL_BACKENDS = ["serial"] - @pytest.mark.parametrize( "dataset", ["cell_segmentation", "mouse_epidermis", "HL60_3D_synthesized"] ) -@pytest.mark.parametrize("parallel_backend", PARALLEL_BACKENDS) +@pytest.mark.parametrize("parallel_backend", ["serial", "ray"]) @pytest.mark.parametrize("splitting_cost_cutoff", [False, 0.9]) @pytest.mark.parametrize("merging_cost_cutoff", [False, 0.9]) @pytest.mark.parametrize("track_overlap_coefs", [(2.0, -0.5, -0.5, -0.5, -0.5)]) @@ -38,6 +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 b1cd236..01f9da8 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) From d759175801055d039b1dcfb0f99588d30a428e8f Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Sun, 4 Feb 2024 09:08:22 +0900 Subject: [PATCH 12/13] update typeguard version --- .github/workflows/tests.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b5010e7..de51717 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -25,8 +25,9 @@ jobs: - { python-version: 3.8, os: ubuntu-latest, session: "tests" } - { python-version: "3.12", os: windows-latest, session: "tests" } - { python-version: "3.12", os: macos-latest, session: "tests" } - - { python-version: "3.12", os: ubuntu-latest, session: "typeguard" } - - { python-version: "3.12", os: ubuntu-latest, session: "docs-build" } + # since ray is still not available wiht 3.12 + - { python-version: "3.11", os: ubuntu-latest, session: "typeguard" } + - { python-version: "3.11", os: ubuntu-latest, session: "docs-build" } env: NOXSESSION: ${{ matrix.session }} From eb2cea680f14a74f06bcefc8b2d06fe8636c995e Mon Sep 17 00:00:00 2001 From: Yohsuke Fukai Date: Sun, 4 Feb 2024 09:14:35 +0900 Subject: [PATCH 13/13] doc versino to 3.12 --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index de51717..272b881 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -27,7 +27,7 @@ jobs: - { 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: "3.11", os: ubuntu-latest, session: "docs-build" } + - { python-version: "3.12", os: ubuntu-latest, session: "docs-build" } env: NOXSESSION: ${{ matrix.session }}