Merge pull request #714 from bioimage-io/dev

Housekeeping setup.py -> pyproject.toml and black -> ruff

Author: FynnBe

.github/workflows/build.yml

@@ -41,10 +41,10 @@ jobs:
           key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}"
       - name: Check autogenerated imports
         run: python scripts/generate_version_submodule_imports.py check
-      - run: black --check .
-        if: matrix.is-dev-version
       - run: ruff check
         if: matrix.is-dev-version
+      - run: ruff format
+        if: matrix.is-dev-version
       - name: Run Pyright
         if: matrix.is-dev-version
         run: |
@@ -184,11 +184,13 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          pip install --upgrade pip
-          pip install wheel
-          pip install -e .[tests]
+          python -m pip install --upgrade pip
+          pip --version
+          pip install --upgrade build
+          pip install .
+          pip install pytest
       - name: Test with pytest
-        run: pytest
+        run: pytest --disable-pytest-warnings
       - name: Check version submodule imports
         run: python scripts/generate_version_submodule_imports.py check
       - name: Check if there is a parent commit
@@ -203,7 +205,7 @@ jobs:
         with:
           create-tag: false
           version-command: |
-            bash -o pipefail -c "cat bioimageio/spec/VERSION | jq -r '.version'"
+            python -c "from pathlib import Path;print(Path('bioimageio/spec/__init__.py').read_text().split('__version__ = \"')[1].split('\"')[0])"
 
       - name: Push tag
         id: tag-version
@@ -215,7 +217,7 @@ jobs:
 
       - name: Build package
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
 
       - name: Publish package on PyPI
         if: steps.tag-version.outputs.new_tag

.pre-commit-config.yaml

@@ -1,13 +1,10 @@
 repos:
-  - repo: https://github.com/ambv/black
-    rev: 25.1.0
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.12.8
     hooks:
       - id: ruff-check
         args: [--fix, --show-fixes]
+      - id: ruff-format
   - repo: local
     hooks:
       - id: pyright

MANIFEST.in

@@ -1,4 +1,3 @@
-include bioimageio/spec/VERSION
 include README.md
 include LICENSE
 include bioimageio/spec/static/spdx_licenses.json

README.md

@@ -3,7 +3,7 @@
 [![conda-version](https://anaconda.org/conda-forge/bioimageio.spec/badges/version.svg)](https://anaconda.org/conda-forge/bioimageio.spec/)
 [![downloads](https://static.pepy.tech/badge/bioimageio.spec)](https://pepy.tech/project/bioimageio.spec)
 [![conda-forge downloads](https://img.shields.io/conda/dn/conda-forge/bioimageio.spec.svg?label=conda-forge)](https://anaconda.org/conda-forge/bioimageio.spec/)
-![code style](https://img.shields.io/badge/code%20style-black-000000.svg)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![coverage](https://bioimage-io.github.io/spec-bioimage-io/coverage/coverage-badge.svg)](https://bioimage-io.github.io/spec-bioimage-io/coverage/index.html)
 
 # Specifications for bioimage.io
@@ -123,4 +123,4 @@ To keep the bioimageio.spec Python package version in sync with the (model) desc
 
 ## Δ Changelog
 
-The changelog of the bioimageio.spec Python package and the changes to the resource description format it implements can be found [here](https://github.com/bioimage-io/spec-bioimage-io/blob/main/changelog.md).
+The changelog of the bioimageio.spec Python package and the changes to the resource description format it implements can be found in [changelog.md](https://github.com/bioimage-io/spec-bioimage-io/blob/main/changelog.md).

bioimageio/spec/VERSION

@@ -2,6 +2,9 @@
 .. include:: ../../README.md
 """
 
+__version__ = "0.5.5.0"
+
+
 from . import (
     application,
     common,
@@ -24,7 +27,6 @@
 from ._get_conda_env import BioimageioCondaEnv, get_conda_env
 from ._internal import settings
 from ._internal.common_nodes import InvalidDescr
-from ._internal.constants import VERSION
 from ._internal.validation_context import ValidationContext, get_validation_context
 from ._io import (
     load_dataset_description,
@@ -50,8 +52,6 @@
 from .pretty_validation_errors import enable_pretty_validation_errors_in_ipynb
 from .summary import ValidationSummary
 
-__version__ = VERSION
-
 __all__ = [
     "__version__",
     "AnyApplicationDescr",

bioimageio/spec/__init__.py

@@ -160,8 +160,11 @@ def _get_default_pytorch_env(
 
     # avoid `undefined symbol: iJIT_NotifyEvent` from `torch/lib/libtorch_cpu.so`
     # see https://github.com/pytorch/pytorch/issues/123097
-    if pytorch_version < Version(
-        "2.1.0"  # TODO: check if this is the correct cutoff where the fix is not longer needed
+    if (
+        pytorch_version
+        < Version(
+            "2.1.0"  # TODO: check if this is the correct cutoff where the fix is not longer needed
+        )
     ):
         deps.append("mkl ==2024.0.0")
 

bioimageio/spec/_get_conda_env.py

@@ -205,9 +205,9 @@ def __pydantic_init_subclass__(cls, **kwargs: Any):
                 cls.implemented_format_version_tuple = (0, 0, 0)
             else:
                 fv_tuple = get_format_version_tuple(cls.implemented_format_version)
-                assert (
-                    fv_tuple is not None
-                ), f"failed to cast '{cls.implemented_format_version}' to tuple"
+                assert fv_tuple is not None, (
+                    f"failed to cast '{cls.implemented_format_version}' to tuple"
+                )
                 cls.implemented_format_version_tuple = fv_tuple
 
     @classmethod

bioimageio/spec/_internal/common_nodes.py

@@ -6,11 +6,6 @@
 
 from .utils import files
 
-with files("bioimageio.spec").joinpath("VERSION").open("r", encoding="utf-8") as f:
-    VERSION: str = json.load(f)["version"]
-    assert isinstance(VERSION, str), VERSION
-
-
 DOI_REGEX = (  # lax DOI regex validating the first 7 DOI characters only
     r"^10\.[0-9]{4}.+$"
 )
@@ -20,8 +15,10 @@
 Or you can generate a SHA256 checksum with Python's `hashlib`,
 [here is a codesnippet](https://gist.github.com/FynnBe/e64460463df89439cff218bbf59c1100)."""
 
-with files("bioimageio.spec").joinpath("static/tag_categories.json").open(
-    "r", encoding="utf-8"
+with (
+    files("bioimageio.spec")
+    .joinpath("static/tag_categories.json")
+    .open("r", encoding="utf-8")
 ) as f:
     TAG_CATEGORIES: Mapping[str, Mapping[str, Sequence[str]]] = json.load(f)
 

bioimageio/spec/_internal/constants.py

@@ -21,6 +21,6 @@ def set_github_warning(title: str, message: str):
     # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#setting-a-warning-message
     print(
         f"::warning file={frameinfo.filename},"
-        + f"line={frameinfo.lineno},endLine={frameinfo.lineno+1},"
+        + f"line={frameinfo.lineno},endLine={frameinfo.lineno + 1},"
         + f"title={title}::{message}"
     )