update pyproject.toml for src-layout

Author: FynnBe

pyproject.toml

@@ -74,7 +74,7 @@ requires = ["pip", "setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
-include = ["bioimageio"]
+where = ["src/"]
 
 [tool.setuptools.dynamic]
 version = { attr = "bioimageio.core.__version__" }
@@ -95,7 +95,7 @@ exclude = [
     "scripts/pdoc/patched.py",
     "tests/old_*",
 ]
-include = ["bioimageio", "scripts", "tests"]
+include = ["src", "scripts", "tests"]
 pythonPlatform = "All"
 pythonVersion = "3.9"
 reportDuplicateImport = "error"
@@ -121,8 +121,8 @@ typeCheckingMode = "strict"
 useLibraryCodeForTypes = true
 
 [tool.pytest.ini_options]
-addopts = "--doctest-modules --failed-first --ignore dogfood --ignore bioimageio/core/backends --ignore bioimageio/core/weight_converters"
-testpaths = ["bioimageio/core", "tests"]
+addopts = "--doctest-modules --failed-first --ignore dogfood --ignore src/bioimageio/core/backends --ignore src/bioimageio/core/weight_converters"
+testpaths = ["src", "tests"]
 
 [tool.ruff]
 line-length = 88