mirror of
https://github.com/p2p-ld/numpydantic.git
synced 2024-12-04 20:44:29 +00:00
close hdf5 files, use hdfpy 3.12
This commit is contained in:
parent
99e07925e6
commit
8f7d48fc56
GPG key ID:
6DCB96EF1E4D232D
4 changed files with 61 additions and 56 deletions
3
.gitignore
vendored
3
.gitignore
vendored
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@ -161,4 +161,5 @@ cython_debug/
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.pdm-python
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ndarray.pyi
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prof/
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prof/
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__tmp__
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89
pdm.lock
89
pdm.lock
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@ -5,7 +5,7 @@
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groups = ["default", "arrays", "dask", "dev", "docs", "hdf5", "tests", "video", "zarr"]
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strategy = ["cross_platform", "inherit_metadata"]
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lock_version = "4.5.0"
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content_hash = "sha256:dee4ba1fabeacedf80f85b145bcb2ef83a2005cac6454f9672eb9a873cadd70b"
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content_hash = "sha256:cc2b0fb32896c6df0ad747ddb5dee89af22f5c4c4643ee7a52db47fef30da936"
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[[metadata.targets]]
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requires_python = "~=3.9"
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@ -731,31 +731,40 @@ files = [
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[[package]]
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name = "h5py"
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version = "3.11.0"
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requires_python = ">=3.8"
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version = "3.12.1"
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requires_python = ">=3.9"
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summary = "Read and write HDF5 files from Python"
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groups = ["arrays", "dev", "docs", "hdf5", "tests"]
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dependencies = [
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"numpy>=1.17.3",
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"numpy>=1.19.3",
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]
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{file = "h5py-3.12.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:84342bffd1f82d4f036433e7039e241a243531a1d3acd7341b35ae58cdab05bf"},
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{file = "h5py-3.12.1-cp39-cp39-win_amd64.whl", hash = "sha256:62be1fc0ef195891949b2c627ec06bc8e837ff62d5b911b6e42e38e0f20a897d"},
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{file = "h5py-3.12.1.tar.gz", hash = "sha256:326d70b53d31baa61f00b8aa5f95c2fcb9621a3ee8365d770c551a13dbbcbfdf"},
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]
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[[package]]
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@ -1978,29 +1987,29 @@ files = [
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[[package]]
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name = "ruff"
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version = "0.6.7"
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version = "0.6.8"
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requires_python = ">=3.7"
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summary = "An extremely fast Python linter and code formatter, written in Rust."
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groups = ["dev"]
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files = [
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]
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[[package]]
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@ -53,8 +53,7 @@ dask = [
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"dask>=2024.4.0",
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]
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hdf5 = [
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"h5py>=3.10.0,<3.12.0;sys_platform!='darwin'",
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"h5py>=3.10.0;sys_platform=='darwin'",
|
||||
"h5py>=3.10.0",
|
||||
]
|
||||
video = [
|
||||
"opencv-python>=4.9.0.80",
|
||||
|
|
|
|||
|
|
@ -104,18 +104,11 @@ def model_blank() -> Type[BaseModel]:
|
|||
return BlankModel
|
||||
|
||||
|
||||
@pytest.fixture(scope="function")
|
||||
def hdf5_file(tmp_output_dir_func) -> h5py.File:
|
||||
h5f_file = tmp_output_dir_func / "h5f.h5"
|
||||
h5f = h5py.File(h5f_file, "w")
|
||||
yield h5f
|
||||
h5f.close()
|
||||
|
||||
|
||||
@pytest.fixture(scope="function")
|
||||
def hdf5_array(
|
||||
hdf5_file, request
|
||||
request, tmp_output_dir_func
|
||||
) -> Callable[[Tuple[int, ...], Union[np.dtype, type]], H5ArrayPath]:
|
||||
hdf5_file = tmp_output_dir_func / "h5f.h5"
|
||||
|
||||
def _hdf5_array(
|
||||
shape: Tuple[int, ...] = (10, 10),
|
||||
|
|
@ -132,8 +125,8 @@ def hdf5_array(
|
|||
data.fill(datetime.now(timezone.utc).isoformat().encode("utf-8"))
|
||||
else:
|
||||
data = np.random.random(shape).astype(dtype)
|
||||
_ = hdf5_file.create_dataset(array_path, data=data)
|
||||
return H5ArrayPath(Path(hdf5_file.filename), array_path)
|
||||
|
||||
h5path = H5ArrayPath(hdf5_file, array_path)
|
||||
else:
|
||||
if dtype is str:
|
||||
dt = np.dtype([("data", np.dtype("S10")), ("extra", "i8")])
|
||||
|
|
@ -148,8 +141,11 @@ def hdf5_array(
|
|||
else:
|
||||
dt = np.dtype([("data", dtype), ("extra", "i8")])
|
||||
data = np.zeros(shape, dtype=dt)
|
||||
_ = hdf5_file.create_dataset(array_path, data=data)
|
||||
return H5ArrayPath(Path(hdf5_file.filename), array_path, "data")
|
||||
h5path = H5ArrayPath(hdf5_file, array_path, "data")
|
||||
|
||||
with h5py.File(hdf5_file, "w") as h5f:
|
||||
_ = h5f.create_dataset(array_path, data=data)
|
||||
return h5path
|
||||
|
||||
return _hdf5_array
|
||||
|
||||
|
|
|
|||
Loading…
Reference in a new issue