Relaxing dependencies and moving to Hatch and Pixi (#130)

* added hatch pyproject.toml

* add pixi

* added cuda support

* organized pyproject

* added cuda feature

* fixed python mip

* updated pydantic and other minor packages

* added uv to CI and reduce upper version restriction

* added env

* Fix pydantic.v1 integration with fastapi; fix ome-zarr broken package

* updated pydantic

* bump higra version to 6.9

* removed [api] from github workflow

* higra version bump to 6.10

* updating runners

* bump python version

* fix python versions

* bumped version and skipping server test on macos

* Avoid server being killed while trying to remove dir

---------

Co-authored-by: Ilan F. S. Theodoro <[email protected]>

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/workflows/test_pull_request.yml

@@ -14,22 +14,22 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest]
-        python: ["3.9", "3.10"]
+        python: ["3.10", "3.12"]
         backend: [pyqt5]
         include:
-          - python: 3.9
+          - python: 3.11
             platform: windows-latest
             backend: pyqt5
-          - python: 3.9
-            platform: macos-latest
+          - python: 3.11
+            platform: macos-13  # latest not-arm version
             backend: pyside2
-          - python: 3.9
+          - python: 3.11
             platform: ubuntu-latest
             backend: pyqt6
-          - python: 3.9
+          - python: 3.11
             platform: ubuntu-latest
             backend: pyside2
-          - python: 3.9  # only this run execute coverage
+          - python: 3.11 # only this run execute coverage
             platform: ubuntu-latest
             backend: pyside6
             coverage: true
@@ -51,10 +51,13 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
-          cache: 'pip'
 
       - uses: tlambert03/setup-qt-libs@v1
 
+      - uses: yezz123/setup-uv@v4
+        with:
+          uv-venv: "ultrack-env"
+
       # strategy borrowed from vispy for installing opengl libs on windows
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
@@ -67,9 +70,8 @@ jobs:
       # of python dependendencies into a virtualenv.  see tox.ini for more
       - name: Install dependencies
         run: |
-          pip install --upgrade pip
-          pip install setuptools tox tox-gh-actions
-          pip install ".[api]"
+          uv pip install setuptools tox tox-gh-actions
+          uv pip install ".[test]"
 
       # here we pass off control of environment creation and running of tests to tox
       # tox-gh-actions, installed above, helps to convert environment variables into

.gitignore

@@ -175,3 +175,6 @@ docs/source/examples
 metadata.toml
 data.db
 *.lock
+# pixi environments
+.pixi
+*.egg-info

MANIFEST.in

@@ -1,3 +1,4 @@
 include README.md
 include LICENSE
-recursive-include ultrack/widgets/ultrackwidget/resources *.json
+recursive-include ultrack/widgets/ultrackwidget/resources *.json
+exclude examples/**

pyproject.toml

@@ -1,9 +1,159 @@
 [build-system]
-requires = ["setuptools>=42", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
+[project]
+name = "ultrack"
+dynamic = ["version"]
+description = "Large-scale multi-hypotheses cell tracking"
+readme = "README.md"
+license = ""
+requires-python = ">=3.9,<3.13"
+authors = [
+    { name = "Jordao Bragantini", email = "[email protected]" },
+]
+dependencies = [
+    "blosc2 >=2.2.0",
+    "click >=8.1.3",
+    "cloudpickle >=3.0.0",
+    "edt >=2.3.2",
+    "fastapi >= 0.109.2",
+    "gurobipy >=9.0.0",
+    "higra >= 0.6.10",
+    "httpx >= 0.26.0",
+    "imagecodecs >=2023.3.16",
+    "imageio >=2.28.0",
+    "magicgui >=0.7.2",
+    "mip >=1.16rc0",
+    "napari >=0.4.18",
+    "numba >=0.57.0",
+    "ome-zarr >= 0.9.0",
+    "pandas >=2.0.1",
+    "pillow >=10.0.0",
+    "psycopg2-binary >=2.9.6",
+    "psygnal >=0.9.0",
+    "pydantic >= 2",
+    "pydot >= 2.0.0",
+    "qtawesome >= 1.3.1",
+    "rich >=13.3.5",
+    "scikit-image >=0.21.0",
+    "seaborn >=0.13.0",
+    "SQLAlchemy >=2.0.0",
+    "toml >=0.10.2",
+    "torch >=2.0.1",
+    "urllib3",
+    "uvicorn >= 0.27.0.post1",
+    "websocket >= 0.2.1",
+    "websockets >= 12.0",
+    "zarr >=2.15.0,<3.0.0",
+    "pyqt5 >=5.15.4",
+]
+
+[project.optional-dependencies]
+docs = [
+    "autodoc_pydantic >= 2.0.0",
+    "furo",
+    "myst-parser >= 2.0.0",
+    "nbsphinx >= 0.9.3",
+    "sphinx-click >=5.0.1,<6.0.0",
+    "sphinx-copybutton",
+    "sphinx-gallery == 0.15.0",
+    "sphinxcontrib-applehelp == 1.0.8",
+]
+test = [
+    "asv >=0.5.1",
+    "pre-commit >=3.2.2",
+    "pytest >=7.3.1",
+    "pytest-qt >=4.2.0",
+    "pytrackmate @ git+https://github.com/hadim/pytrackmate.git",
+    "napari[testing] > 0.4.18",
+]
+
+[project.scripts]
+ultrack = "ultrack.cli.main:main"
+
+[project.entry-points."napari.manifest"]
+ultrack = "ultrack:napari.yaml"
+
+# pixi config
+[tool.pixi.project]
+channels = ["conda-forge", "nvidia", "pytorch", "numba", "gurobi"]
+platforms = ["linux-64", "win-64", "osx-64"]
+
+[tool.pixi.dependencies]
+click = ">=8.1.3"
+cloudpickle = ">=3.0.0"
+edt = ">=2.3.2"
+fastapi = ">= 0.109.2"
+gurobi = ">=9.0.0"
+higra = ">= 0.6.10"
+httpx = ">= 0.26.0"
+imagecodecs = ">=2023.3.16"
+imageio = ">=2.28.0"
+magicgui = ">=0.7.2"
+# mip = ">=1.16.0"  # TODO: change to python-mip for OSX is released and when available in conda-forge
+napari = ">=0.4.18"
+numba = {version = ">=0.57.0", channel = "numba"}
+ome-zarr = ">= 0.9"
+pandas = ">=2.0.1"
+pillow = ">=10.0.0"
+psycopg2-binary = ">=2.9.6"
+psygnal = ">=0.9.0"
+pydantic = ">=2"
+pydot = ">= 2.0.0"
+qtawesome = ">= 1.3.1"
+rich = ">=13.3.5"
+scikit-image = ">=0.21.0"
+seaborn = ">=0.13.0"
+SQLAlchemy = ">=2.0.0"
+toml = ">=0.10.2"
+pytorch = {version = ">=2.0.1", channel = "pytorch"}
+urllib3 = "*"
+uvicorn = ">= 0.27.0.post1"
+websocket = ">= 0.2.1"
+websockets = ">= 12.0"
+zarr = ">=2.15.0,<3.0.0"
+pyqt = ">=5.15.4"
+
+[tool.pixi.feature.cuda]
+channels = ["conda-forge", "rapidsai"]
+platforms = ["linux-64"] # TODO: waiting for cucim to be available for windows , "win-64"]
+
+[tool.pixi.feature.cuda.dependencies]
+cupy = "*"
+cucim = "*"
+pytorch-cuda = "*"
+
+[tool.pixi.feature.cuda.system-requirements]
+cuda = "11"
 
 [tool.pytest.ini_options]
 filterwarnings = [
     "ignore::DeprecationWarning:pkg_resources.*:",
 ]
+
+[tool.pixi.pypi-dependencies]
+ultrack = { path = ".", editable = true }
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+cuda = { features = ["cuda"] }
+docs = { features = ["docs"], solve-group = "default" }
+test = { features = ["test"], solve-group = "default" }
+
+[tool.pixi.tasks]
+
+# Hatch config
+[tool.hatch.version]
+path = "ultrack/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+only-include = [
+    "/ultrack",
+]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+# TODO:
+# - add `test` and `docs` feature to `pixi` config

tox.ini

@@ -34,8 +34,6 @@ deps =
     pytest-cov
     pytest-qt
     pyqt5
-    poetry
-    testing.postgresql
     git+https://github.com/hadim/pytrackmate.git
 commands =
     pytest -v --color=yes --cov=ultrack --cov-report=xml --durations=15 --ignore=ultrack/widgets

ultrack/__init__.py

@@ -10,9 +10,7 @@
 # ignoring small float32/64 zero flush warning
 warnings.filterwarnings("ignore", message="The value of the smallest subnormal for")
 
-from importlib.metadata import version as _version
-
-__version__ = _version(__name__)
+__version__ = "0.6.0"
 
 from ultrack.config.config import MainConfig, load_config
 from ultrack.core.export.ctc import to_ctc

ultrack/api/_test/test_api.py

@@ -103,7 +103,7 @@ def test_config():
     default_config = MainConfig()
     default_config.data_config = None
 
-    assert MainConfig.parse_raw(response.text) == default_config
+    assert response.json() == default_config.dict()
 
 
 def test_manual_segment(experiment_instance: Experiment):

ultrack/api/app.py

@@ -174,7 +174,7 @@ async def root() -> Dict[str, str]:
 
 
 @app.get("/config/default")
-async def get_default_config() -> MainConfig:
+async def get_default_config() -> Dict:
     """Gets the default ultrack configuration.
 
     Returns
@@ -184,7 +184,7 @@ async def get_default_config() -> MainConfig:
     """
     config = MainConfig()
     config.data_config = None
-    return config
+    return config.dict()
 
 
 @app.get("/config/available")
@@ -201,7 +201,7 @@ async def get_available_configs() -> Dict:
 
     experiment = {
         "name": "Unnamed Experiment",
-        "config": default_config,
+        "config": default_config.dict(),
     }
 
     auto_detect_config = {