Move to src / tests layout (#3092)

Author: flying-sheep

.gitignore

@@ -13,9 +13,9 @@
 # tests
 /*cache/
 /test-data/
-/scanpy/tests/test*.h5ad
-/scanpy/tests/**/*actual.png
-/scanpy/tests/**/*failed-diff.png
+/tests/test*.h5ad
+/tests/**/*actual.png
+/tests/**/*failed-diff.png
 
 # Environment management
 /hatch.toml
@@ -28,7 +28,7 @@
 
 # Python build files
 __pycache__/
-/scanpy/_version.py
+/src/scanpy/_version.py
 /dist/
 /*-env/
 /env-*/

.pre-commit-config.yaml

@@ -23,9 +23,9 @@ repos:
     rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
-        exclude: scanpy/tests/_data
+        exclude: tests/_data
     -   id: end-of-file-fixer
-        exclude: scanpy/tests/_data
+        exclude: tests/_data
     -   id: check-added-large-files
     -   id: check-case-conflict
     -   id: check-toml

pyproject.toml

@@ -85,7 +85,7 @@ scanpy = "scanpy.cli:console_main"
 
 [project.optional-dependencies]
 test-min = [
-    "pytest>=7.4.2,!=8.1.*",
+    "pytest>=8.2",
     "pytest-nunit",
     "pytest-mock",
     "pytest-cov",
@@ -153,26 +153,23 @@ rapids = ["cudf>=0.9", "cuml>=0.9", "cugraph>=0.9"]  # GPU accelerated calculati
 dask = ["dask[array]>=2022.09.2"]  # Use the Dask parallelization engine
 dask-ml = ["dask-ml", "scanpy[dask]"]  # Dask-ML for sklearn-like API
 
-[tool.hatch.build]
-exclude = ["scanpy/tests"]
 [tool.hatch.build.targets.wheel]
-# TODO: move scanpy to src/
-only-include = ["src/testing", "scanpy"]
-sources = ["src", "."]
+packages = ["src/testing", "src/scanpy"]
 [tool.hatch.version]
 source = "vcs"
 [tool.hatch.build.hooks.vcs]
-version-file = "scanpy/_version.py"
+version-file = "src/scanpy/_version.py"
 
 [tool.pytest.ini_options]
 addopts = [
     "--import-mode=importlib",
     "--strict-markers",
     "--doctest-modules",
     "-ptesting.scanpy._pytest",
+    "--pyargs",
 ]
-testpaths = ["scanpy"]
-norecursedirs = ["scanpy/tests/_images"]
+testpaths = ["./tests", "scanpy"]
+norecursedirs = ["tests/_images"]
 xfail_strict = true
 nunit_attach_on = "fail"
 markers = [
@@ -206,7 +203,7 @@ filterwarnings = [
 [tool.coverage.run]
 data_file = "test-data/coverage"
 source_pkgs = ["scanpy"]
-omit = ["scanpy/tests/*", "src/testing/*"]
+omit = ["tests/*", "src/testing/*"]
 [tool.coverage.xml]
 output = "test-data/coverage.xml"
 [tool.coverage.paths]
@@ -219,6 +216,9 @@ exclude_also = [
     "@numba.njit.*",
 ]
 
+[tool.ruff]
+src = ["src"]
+
 [tool.ruff.format]
 docstring-code-format = true
 
@@ -247,7 +247,7 @@ ignore = [
 ]
 [tool.ruff.lint.per-file-ignores]
 # Do not assign a lambda expression, use a def
-"scanpy/tools/_rank_genes_groups.py" = ["E731"]
+"src/scanpy/tools/_rank_genes_groups.py" = ["E731"]
 [tool.ruff.lint.isort]
 known-first-party = ["scanpy", "testing.scanpy"]
 required-imports = ["from __future__ import annotations"]

scanpy/__init__.py renamed to src/scanpy/__init__.py

@@ -7,7 +7,7 @@
 try:  # See https://github.com/maresb/hatch-vcs-footgun-example
     from setuptools_scm import get_version
 
-    __version__ = get_version(root="..", relative_to=__file__)
+    __version__ = get_version(root="../..", relative_to=__file__)
     del get_version
 except (ImportError, LookupError):
     try: