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Remove build hacks #1001

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merged 7 commits into from
Jun 19, 2023
Merged

Remove build hacks #1001

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c025315
Remove build hacks
flying-sheep Jun 12, 2023
b4e8273
Simplify metadata
flying-sheep Jun 12, 2023
5e1ec05
Use proper SPDX identifier
flying-sheep Jun 12, 2023
35ea7c3
re-add dynamic version
flying-sheep Jun 15, 2023
c40ac9b
Merge branch 'main' into simplify-build-metadata
flying-sheep Jun 15, 2023
2f0b2fe
Check version in built package
flying-sheep Jun 15, 2023
287c981
Don’t check that built file is there
flying-sheep Jun 16, 2023
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5 changes: 5 additions & 0 deletions .azure-pipelines.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -101,3 +101,8 @@ jobs:
python -m build --sdist --wheel .
twine check dist/*
displayName: "Build & Twine check"

- script: |
pip install dist/*.whl
python -c 'import anndata; print(anndata.__version__)'
displayName: "Check runtime version"
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -8,6 +8,7 @@ __pycache__/
# Distribution / packaging
/build/
/dist/
/anndata/_version.py
/*.egg-info/
/requirements*.lock
/.python-version
Expand Down
58 changes: 33 additions & 25 deletions anndata/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,29 +1,37 @@
"""Annotated multivariate observation data."""

from ._metadata import __version__, within_flit
try: # See https://github.com/maresb/hatch-vcs-footgun-example
from setuptools_scm import get_version

if not within_flit():
del within_flit
from ._core.anndata import AnnData
from ._core.merge import concat
from ._core.raw import Raw
from ._io import (
read_h5ad,
read_loom,
read_hdf,
read_excel,
read_umi_tools,
read_csv,
read_text,
read_mtx,
read_zarr,
)
from ._warnings import (
OldFormatWarning,
WriteWarning,
ImplicitModificationWarning,
ExperimentalFeatureWarning,
)
__version__ = get_version(root="..", relative_to=__file__)
except (ImportError, LookupError):
try:
from ._version import __version__
except ModuleNotFoundError:
raise RuntimeError(
"anndata is not correctly installed. Please install it, e.g. with pip."
)

# backwards compat / shortcut for default format
from ._io import read_h5ad as read
from ._core.anndata import AnnData
from ._core.merge import concat
from ._core.raw import Raw
from ._io import (
read_h5ad,
read_loom,
read_hdf,
read_excel,
read_umi_tools,
read_csv,
read_text,
read_mtx,
read_zarr,
)
from ._warnings import (
OldFormatWarning,
WriteWarning,
ImplicitModificationWarning,
ExperimentalFeatureWarning,
)

# backwards compat / shortcut for default format
from ._io import read_h5ad as read
46 changes: 0 additions & 46 deletions anndata/_metadata.py
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This file was deleted.

2 changes: 0 additions & 2 deletions benchmarks/asv.conf.json
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Original file line number Diff line number Diff line change
Expand Up @@ -80,8 +80,6 @@
"pandas": [""],
"memory_profiler": [""],
"zarr": [""],
"setuptools_scm": [""],
"flit": [""],
"pytoml": [""],
"pytest": [""],
"pooch": [""],
Expand Down
27 changes: 14 additions & 13 deletions pyproject.toml
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@@ -1,15 +1,12 @@
[build-system]
build-backend = "flit_core.buildapi"
requires = [
"flit_core >=3.4,<4",
"setuptools_scm",
]
build-backend = "hatchling.build"
requires = ["hatchling", "hatch-vcs"]

[project]
name = "anndata"
description = "Annotated data."
requires-python = ">=3.8"
license = {file = "LICENSE"}
license = "BSD-3-Clause"
authors = [
{name = "Philipp Angerer"},
{name = "Alex Wolf"},
Expand All @@ -18,12 +15,11 @@ authors = [
]
maintainers = [
{name = "Isaac Virshup", email = "ivirshup@gmail.com"},
{name = "Philipp Angerer", email = "philipp.angerer@helmholtz-muenchen.de"},
{name = "Philipp Angerer", email = "philipp.angerer@helmholtz-munich.de"},
{name = "Alex Wolf", email = "f.alex.wolf@gmx.de"},
]
readme = {file = "README.md", content-type="text/markdown"}
readme = "README.md"
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I recall this throwing errors if I didn't specify the content-type. Was that flit specific?

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not for many years: pypa/flit#169

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Pretty sure I was running into this more recently than that. But I believe twine check was the one complaining, so it's fine as long as the build check is passing.

classifiers = [
"License :: OSI Approved :: BSD License",
"Environment :: Console",
"Framework :: Jupyter",
"Intended Audience :: Developers",
Expand All @@ -36,11 +32,12 @@ classifiers = [
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Visualization",
]
dependencies = [
"pandas>=1.1.1,!=2.0.1", # pandas <1.1.1 has pandas/issues/35446
"pandas>=1.1.1", # pandas <1.1.1 has pandas/issues/35446
"numpy>=1.16.5", # required by pandas 1.x
"scipy>1.4",
"h5py>=3",
Expand Down Expand Up @@ -92,11 +89,15 @@ test = [
"pytest_memray",
]

[tool.flit.sdist]
[tool.hatch.build]
exclude = [
'anndata/tests/test_*.py',
'anndata/tests/data',
"anndata/tests/test_*.py",
"anndata/tests/data",
]
[tool.hatch.version]
source = "vcs"
[tool.hatch.build.hooks.vcs]
version-file = "anndata/_version.py"
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[tool.coverage.run]
source = ["anndata"]
Expand Down