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Merge pull request #28 from p2p-ld/hdf5-3_12
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close hdf5 files, use hdfpy 3.12
This commit is contained in:
GitHub
commit
69dbe39557
5 changed files with 71 additions and 58 deletions
1
.gitignore
vendored
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@ -162,3 +162,4 @@ cython_debug/
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ndarray.pyi
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prof/
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__tmp__
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@ -4,7 +4,15 @@
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### 1.6.*
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#### 1.6.2 - 24-09-35
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#### 1.6.3 - 24-09-26
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**Bugfix**
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- h5py v3.12.0 was actually fine, but we did need to change the way that
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the hdf5 tests work to not hold the file open during the test. Easy enough change.
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the version cap has been removed from h5py (which is optional anyway,
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so any version could be installed separately)
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#### 1.6.2 - 24-09-25
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Very minor bugfix and CI release
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89
pdm.lock
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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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[[package]]
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@ -1978,29 +1987,29 @@ files = [
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{file = "ruff-0.6.8-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:677e03c00f37c66cea033274295a983c7c546edea5043d0c798833adf4cf4c6f"},
|
||||
{file = "ruff-0.6.8-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:9f1476236b3eacfacfc0f66aa9e6cd39f2a624cb73ea99189556015f27c0bdeb"},
|
||||
{file = "ruff-0.6.8-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:6f5a2f17c7d32991169195d52a04c95b256378bbf0de8cb98478351eb70d526f"},
|
||||
{file = "ruff-0.6.8-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:5fd0d4b7b1457c49e435ee1e437900ced9b35cb8dc5178921dfb7d98d65a08d0"},
|
||||
{file = "ruff-0.6.8-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:f8034b19b993e9601f2ddf2c517451e17a6ab5cdb1c13fdff50c1442a7171d87"},
|
||||
{file = "ruff-0.6.8-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:6cfb227b932ba8ef6e56c9f875d987973cd5e35bc5d05f5abf045af78ad8e098"},
|
||||
{file = "ruff-0.6.8-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6ef0411eccfc3909269fed47c61ffebdcb84a04504bafa6b6df9b85c27e813b0"},
|
||||
{file = "ruff-0.6.8-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:007dee844738c3d2e6c24ab5bc7d43c99ba3e1943bd2d95d598582e9c1b27750"},
|
||||
{file = "ruff-0.6.8-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:ce60058d3cdd8490e5e5471ef086b3f1e90ab872b548814e35930e21d848c9ce"},
|
||||
{file = "ruff-0.6.8-py3-none-musllinux_1_2_i686.whl", hash = "sha256:1085c455d1b3fdb8021ad534379c60353b81ba079712bce7a900e834859182fa"},
|
||||
{file = "ruff-0.6.8-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:70edf6a93b19481affd287d696d9e311388d808671bc209fb8907b46a8c3af44"},
|
||||
{file = "ruff-0.6.8-py3-none-win32.whl", hash = "sha256:792213f7be25316f9b46b854df80a77e0da87ec66691e8f012f887b4a671ab5a"},
|
||||
{file = "ruff-0.6.8-py3-none-win_amd64.whl", hash = "sha256:ec0517dc0f37cad14a5319ba7bba6e7e339d03fbf967a6d69b0907d61be7a263"},
|
||||
{file = "ruff-0.6.8-py3-none-win_arm64.whl", hash = "sha256:8d3bb2e3fbb9875172119021a13eed38849e762499e3cfde9588e4b4d70968dc"},
|
||||
{file = "ruff-0.6.8.tar.gz", hash = "sha256:a5bf44b1aa0adaf6d9d20f86162b34f7c593bfedabc51239953e446aefc8ce18"},
|
||||
]
|
||||
|
||||
[[package]]
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
[project]
|
||||
name = "numpydantic"
|
||||
version = "1.6.2"
|
||||
version = "1.6.3"
|
||||
description = "Type and shape validation and serialization for arbitrary array types in pydantic models"
|
||||
authors = [
|
||||
{name = "sneakers-the-rat", email = "sneakers-the-rat@protonmail.com"},
|
||||
|
|
@ -53,8 +53,7 @@ dask = [
|
|||
"dask>=2024.4.0",
|
||||
]
|
||||
hdf5 = [
|
||||
"h5py>=3.10.0,<3.12.0;sys_platform!='darwin'",
|
||||
"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