backport hatch to 1.9.x (#2727)

.gitignore

@@ -27,6 +27,7 @@
 
 # Python build files
 __pycache__/
+/scanpy/_version.py
 /dist/
 /build/
 /scanpy.egg-info/

pyproject.toml

@@ -1,17 +1,12 @@
 [build-system]
-build-backend = "flit_core.buildapi"
-requires = [
-    "flit_core >=3.4,<4",
-    "setuptools_scm",
-    "tomli",
-    "importlib_metadata>=0.7; python_version < '3.8'",
-]
+build-backend = "hatchling.build"
+requires = ["hatchling", "hatch-vcs"]
 
 [project]
 name = "scanpy"
 description = "Single-Cell Analysis in Python."
 requires-python = ">=3.8"
-license = {file = "LICENSE"}
+license = "BSD-3-clause"
 authors = [
     {name = "Alex Wolf"},
     {name = "Philipp Angerer"},
@@ -31,7 +26,7 @@ maintainers = [
     {name = "Philipp Angerer", email = "[email protected]"},
     {name = "Alex Wolf", email = "[email protected]"},
 ]
-readme = {file = "README.md", content-type="text/markdown"}
+readme = "README.md"
 classifiers = [
     "License :: OSI Approved :: BSD License",
     "Development Status :: 5 - Production/Stable",
@@ -135,11 +130,12 @@ scrublet = ["scrublet"]  # Doublet detection
 rapids = ["cudf>=0.9", "cuml>=0.9", "cugraph>=0.9"]  # GPU accelerated calculation of neighbors
 dask = ["dask[array]!=2.17.0"]  # Use the Dask parallelization engine
 
-[tool.flit.sdist]
-exclude = [
-    "scanpy/tests",
-    "setup.py",
-]
+[tool.hatch.build]
+exclude = ["scanpy/tests"]
+[tool.hatch.version]
+source = "vcs"
+[tool.hatch.build.hooks.vcs]
+version-file = "scanpy/_version.py"
 
 [tool.pytest.ini_options]
 addopts = [

scanpy/__init__.py

@@ -1,42 +1,52 @@
 """Single-Cell Analysis in Python."""
 
-from ._metadata import __version__, within_flit
-
-if not within_flit():  # see function docstring on why this is there
-    from ._utils import check_versions
-
-    check_versions()
-    del check_versions, within_flit
-
-    # the actual API
-    # (start with settings as several tools are using it)
-    from ._settings import settings, Verbosity
-    from . import tools as tl
-    from . import preprocessing as pp
-    from . import plotting as pl
-    from . import datasets, logging, queries, external, get, metrics, experimental
-
-    from anndata import AnnData, concat
-    from anndata import (
-        read_h5ad,
-        read_csv,
-        read_excel,
-        read_hdf,
-        read_loom,
-        read_mtx,
-        read_text,
-        read_umi_tools,
-    )
-    from .readwrite import read, read_10x_h5, read_10x_mtx, write, read_visium
-    from .neighbors import Neighbors
-
-    set_figure_params = settings.set_figure_params
-
-    # has to be done at the end, after everything has been imported
-    import sys
-
-    sys.modules.update({f'{__name__}.{m}': globals()[m] for m in ['tl', 'pp', 'pl']})
-    from ._utils import annotate_doc_types
-
-    annotate_doc_types(sys.modules[__name__], 'scanpy')
-    del sys, annotate_doc_types
+try:  # See https://github.com/maresb/hatch-vcs-footgun-example
+    from setuptools_scm import get_version
+
+    __version__ = get_version(root="..", relative_to=__file__)
+    del get_version
+except (ImportError, LookupError):
+    try:
+        from ._version import __version__
+    except ModuleNotFoundError:
+        raise RuntimeError(
+            "scanpy is not correctly installed. Please install it, e.g. with pip."
+        )
+
+from ._utils import check_versions
+
+check_versions()
+del check_versions
+
+# the actual API
+# (start with settings as several tools are using it)
+from ._settings import settings, Verbosity
+from . import tools as tl
+from . import preprocessing as pp
+from . import plotting as pl
+from . import datasets, logging, queries, external, get, metrics, experimental
+
+from anndata import AnnData, concat
+from anndata import (
+    read_h5ad,
+    read_csv,
+    read_excel,
+    read_hdf,
+    read_loom,
+    read_mtx,
+    read_text,
+    read_umi_tools,
+)
+from .readwrite import read, read_10x_h5, read_10x_mtx, write, read_visium
+from .neighbors import Neighbors
+
+set_figure_params = settings.set_figure_params
+
+# has to be done at the end, after everything has been imported
+import sys
+
+sys.modules.update({f"{__name__}.{m}": globals()[m] for m in ["tl", "pp", "pl"]})
+from ._utils import annotate_doc_types
+
+annotate_doc_types(sys.modules[__name__], "scanpy")
+del sys, annotate_doc_types