mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-09-19 15:34:28 +00:00
remove dask, nptyping
This commit is contained in:
parent
a309c25c3d
commit
edea802ff1
GPG key ID:
6DCB96EF1E4D232D
7 changed files with 124 additions and 382 deletions
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@ -5,7 +5,7 @@
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groups = ["default", "dev", "plot", "tests"]
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strategy = ["inherit_metadata"]
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lock_version = "4.5.0"
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content_hash = "sha256:6b84e75b424a643bdfbc4cb0d775e6db831b27c7a770097e28dc8eb8bf76b54d"
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content_hash = "sha256:903c3aeebf0fb234263b45213693f0eaee7ac290d22633b1d7a4d5aff51d032b"
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[[metadata.targets]]
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requires_python = ">=3.10,<3.13"
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@ -53,7 +53,7 @@ files = [
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[[package]]
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name = "attrs"
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version = "24.1.0"
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version = "24.2.0"
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requires_python = ">=3.7"
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summary = "Classes Without Boilerplate"
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groups = ["default", "dev", "tests"]
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@ -61,8 +61,8 @@ dependencies = [
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"importlib-metadata; python_version < \"3.8\"",
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]
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files = [
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{file = "attrs-24.1.0-py3-none-any.whl", hash = "sha256:377b47448cb61fea38533f671fba0d0f8a96fd58facd4dc518e3dac9dbea0905"},
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{file = "attrs-24.1.0.tar.gz", hash = "sha256:adbdec84af72d38be7628e353a09b6a6790d15cd71819f6e9d7b0faa8a125745"},
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{file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
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{file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
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]
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[[package]]
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@ -229,17 +229,6 @@ files = [
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{file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
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]
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[[package]]
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name = "cloudpickle"
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version = "3.0.0"
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requires_python = ">=3.8"
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summary = "Pickler class to extend the standard pickle.Pickler functionality"
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groups = ["default"]
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files = [
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{file = "cloudpickle-3.0.0-py3-none-any.whl", hash = "sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7"},
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{file = "cloudpickle-3.0.0.tar.gz", hash = "sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"},
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]
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[[package]]
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name = "colorama"
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version = "0.4.6"
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@ -414,27 +403,6 @@ files = [
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{file = "dash_table-5.0.0.tar.gz", hash = "sha256:18624d693d4c8ef2ddec99a6f167593437a7ea0bf153aa20f318c170c5bc7308"},
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]
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[[package]]
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name = "dask"
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version = "2024.7.1"
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requires_python = ">=3.9"
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summary = "Parallel PyData with Task Scheduling"
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groups = ["default"]
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dependencies = [
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"click>=8.1",
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"cloudpickle>=1.5.0",
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"fsspec>=2021.09.0",
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"importlib-metadata>=4.13.0; python_version < \"3.12\"",
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"packaging>=20.0",
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"partd>=1.4.0",
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"pyyaml>=5.3.1",
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"toolz>=0.10.0",
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]
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files = [
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{file = "dask-2024.7.1-py3-none-any.whl", hash = "sha256:dd046840050376c317de90629db5c6197adda820176cf3e2df10c3219d11951f"},
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{file = "dask-2024.7.1.tar.gz", hash = "sha256:dbaef2d50efee841a9d981a218cfeb50392fc9a95e0403b6d680450e4f50d531"},
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]
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[[package]]
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name = "deprecated"
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version = "1.2.14"
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@ -514,17 +482,6 @@ files = [
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{file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"},
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]
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[[package]]
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name = "fsspec"
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version = "2024.6.1"
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requires_python = ">=3.8"
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summary = "File-system specification"
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groups = ["default"]
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files = [
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{file = "fsspec-2024.6.1-py3-none-any.whl", hash = "sha256:3cb443f8bcd2efb31295a5b9fdb02aee81d8452c80d28f97a6d0959e6cee101e"},
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{file = "fsspec-2024.6.1.tar.gz", hash = "sha256:fad7d7e209dd4c1208e3bbfda706620e0da5142bebbd9c384afb95b07e798e49"},
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]
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[[package]]
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name = "future-fstrings"
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version = "1.2.0"
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@ -651,7 +608,7 @@ name = "importlib-metadata"
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version = "8.2.0"
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requires_python = ">=3.8"
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summary = "Read metadata from Python packages"
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groups = ["default", "dev", "plot", "tests"]
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groups = ["dev", "plot", "tests"]
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dependencies = [
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"typing-extensions>=3.6.4; python_version < \"3.8\"",
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"zipp>=0.5",
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@ -939,17 +896,6 @@ files = [
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{file = "linkml_runtime-1.8.0.tar.gz", hash = "sha256:436381a7bf791e9af4ef0a5adcac86762d451b77670fbdb3ba083d2c177fb5f2"},
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]
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[[package]]
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name = "locket"
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version = "1.0.0"
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requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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summary = "File-based locks for Python on Linux and Windows"
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groups = ["default"]
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files = [
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{file = "locket-1.0.0-py2.py3-none-any.whl", hash = "sha256:b6c819a722f7b6bd955b80781788e4a66a55628b858d347536b7e81325a3a5e3"},
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{file = "locket-1.0.0.tar.gz", hash = "sha256:5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632"},
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]
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[[package]]
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name = "markdown-it-py"
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version = "3.0.0"
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@ -1048,54 +994,44 @@ files = [
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{file = "networkx-3.3.tar.gz", hash = "sha256:0c127d8b2f4865f59ae9cb8aafcd60b5c70f3241ebd66f7defad7c4ab90126c9"},
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[[package]]
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name = "nptyping"
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version = "2.5.0"
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requires_python = ">=3.7"
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summary = "Type hints for NumPy."
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groups = ["default"]
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dependencies = [
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"numpy<2.0.0,>=1.20.0; python_version >= \"3.8\"",
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"numpy==1.21.5; python_version < \"3.8\"",
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"typing-extensions<5.0.0,>=4.0.0; python_version < \"3.10\"",
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files = [
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{file = "nptyping-2.5.0-py3-none-any.whl", hash = "sha256:764e51836faae33a7ae2e928af574cfb701355647accadcc89f2ad793630b7c8"},
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[[package]]
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name = "numpy"
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version = "1.26.4"
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version = "2.0.1"
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requires_python = ">=3.9"
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summary = "Fundamental package for array computing in Python"
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groups = ["default"]
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||||
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||||
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|
||||
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||||
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|
||||
]
|
||||
|
||||
[[package]]
|
||||
|
|
@ -1203,21 +1139,6 @@ files = [
|
|||
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|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "partd"
|
||||
version = "1.4.2"
|
||||
requires_python = ">=3.9"
|
||||
summary = "Appendable key-value storage"
|
||||
groups = ["default"]
|
||||
dependencies = [
|
||||
"locket",
|
||||
"toolz",
|
||||
]
|
||||
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||||
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|
||||
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|
||||
|
||||
[[package]]
|
||||
name = "pathspec"
|
||||
version = "0.12.1"
|
||||
|
|
@ -1616,35 +1537,39 @@ files = [
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|||
|
||||
[[package]]
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
|
||||
[[package]]
|
||||
|
|
@ -1796,63 +1721,63 @@ files = [
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|||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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[[package]]
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|
||||
{file = "toolz-0.12.1.tar.gz", hash = "sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"},
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "tqdm"
|
||||
version = "4.66.5"
|
||||
|
|
@ -2276,7 +2190,7 @@ name = "zipp"
|
|||
version = "3.19.2"
|
||||
requires_python = ">=3.8"
|
||||
summary = "Backport of pathlib-compatible object wrapper for zip files"
|
||||
groups = ["default", "dev", "plot", "tests"]
|
||||
groups = ["dev", "plot", "tests"]
|
||||
files = [
|
||||
{file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
|
||||
{file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
|
||||
|
|
|
|||
|
|
@ -15,11 +15,9 @@ dependencies = [
|
|||
"rich>=13.5.2",
|
||||
#"linkml>=1.7.10",
|
||||
"linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml",
|
||||
"nptyping>=2.5.0",
|
||||
"pydantic>=2.3.0",
|
||||
"h5py>=3.9.0",
|
||||
"pydantic-settings>=2.0.3",
|
||||
"dask>=2023.9.2",
|
||||
"tqdm>=4.66.1",
|
||||
'typing-extensions>=4.12.2;python_version<"3.11"',
|
||||
"numpydantic>=1.3.0",
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
Mapping from one domain to another
|
||||
"""
|
||||
|
||||
from nwb_linkml.maps.dtype import flat_to_linkml, flat_to_np, flat_to_nptyping
|
||||
from nwb_linkml.maps.dtype import flat_to_linkml, flat_to_np
|
||||
from nwb_linkml.maps.map import Map
|
||||
from nwb_linkml.maps.postload import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
|
||||
from nwb_linkml.maps.quantity import QUANTITY_MAP
|
||||
|
|
@ -14,5 +14,4 @@ __all__ = [
|
|||
"Map",
|
||||
"flat_to_linkml",
|
||||
"flat_to_np",
|
||||
"flat_to_nptyping",
|
||||
]
|
||||
|
|
|
|||
|
|
@ -3,9 +3,8 @@ Dtype mappings
|
|||
"""
|
||||
|
||||
from datetime import datetime
|
||||
from typing import Any, Type
|
||||
from typing import Any
|
||||
|
||||
import nptyping
|
||||
import numpy as np
|
||||
|
||||
from nwb_schema_language import CompoundDtype, DTypeType, FlatDtype, ReferenceDtype
|
||||
|
|
@ -40,37 +39,6 @@ flat_to_linkml = {
|
|||
Map between the flat data types and the simpler linkml base types
|
||||
"""
|
||||
|
||||
flat_to_nptyping = {
|
||||
"float": "Float",
|
||||
"float32": "Float32",
|
||||
"double": "Double",
|
||||
"float64": "Float64",
|
||||
"long": "LongLong",
|
||||
"int64": "Int64",
|
||||
"int": "Int",
|
||||
"int32": "Int32",
|
||||
"int16": "Int16",
|
||||
"short": "Short",
|
||||
"int8": "Int8",
|
||||
"uint": "UInt",
|
||||
"uint32": "UInt32",
|
||||
"uint16": "UInt16",
|
||||
"uint8": "UInt8",
|
||||
"uint64": "UInt64",
|
||||
"numeric": "Number",
|
||||
"text": "String",
|
||||
"utf": "Unicode",
|
||||
"utf8": "Unicode",
|
||||
"utf_8": "Unicode",
|
||||
"string": "Unicode",
|
||||
"str": "Unicode",
|
||||
"ascii": "String",
|
||||
"bool": "Bool",
|
||||
"isodatetime": "Datetime64",
|
||||
"AnyType": "Any",
|
||||
"object": "Object",
|
||||
}
|
||||
|
||||
flat_to_np = {
|
||||
"float": float,
|
||||
"float32": np.float32,
|
||||
|
|
@ -175,20 +143,6 @@ https://github.com/hdmf-dev/hdmf/blob/ddc842b5c81d96e0b957b96e88533b16c137e206/s
|
|||
"""
|
||||
|
||||
|
||||
def struct_from_dtype(dtype: np.dtype) -> Type[nptyping.Structure]:
|
||||
"""
|
||||
Create a nptyping Structure from a compound numpy dtype
|
||||
|
||||
nptyping structures have the form::
|
||||
|
||||
Structure["name: Str, age: Int"]
|
||||
|
||||
"""
|
||||
struct_pieces = [f"{k}: {flat_to_nptyping[v[0].name]}" for k, v in dtype.fields.items()]
|
||||
struct_dtype = ", ".join(struct_pieces)
|
||||
return nptyping.Structure[struct_dtype]
|
||||
|
||||
|
||||
def handle_dtype(dtype: DTypeType | None) -> str:
|
||||
"""
|
||||
Get the string form of a dtype
|
||||
|
|
|
|||
|
|
@ -2,69 +2,9 @@
|
|||
Mapping functions for handling HDMF classes like DynamicTables
|
||||
"""
|
||||
|
||||
from typing import Any, List, Optional, Type
|
||||
from typing import Any, List, Optional
|
||||
|
||||
import dask.array as da
|
||||
import h5py
|
||||
import numpy as np
|
||||
from numpydantic import NDArray
|
||||
from numpydantic.interface.hdf5 import H5ArrayPath
|
||||
from pydantic import BaseModel, create_model
|
||||
|
||||
from nwb_linkml.maps.dtype import struct_from_dtype
|
||||
from nwb_linkml.types.hdf5 import HDF5_Path
|
||||
|
||||
|
||||
def model_from_dynamictable(group: h5py.Group, base: Optional[BaseModel] = None) -> Type[BaseModel]:
|
||||
"""
|
||||
Create a pydantic model from a dynamic table
|
||||
"""
|
||||
colnames = group.attrs["colnames"]
|
||||
types = {}
|
||||
for col in colnames:
|
||||
|
||||
nptype = group[col].dtype
|
||||
nptype = struct_from_dtype(nptype) if nptype.type == np.void else nptype.type
|
||||
|
||||
type_ = Optional[NDArray[Any, nptype]]
|
||||
|
||||
# FIXME: handling nested column types that appear only in some versions?
|
||||
# types[col] = (List[type_ | None], ...)
|
||||
types[col] = (type_, None)
|
||||
|
||||
model = create_model(group.name.split("/")[-1], **types, __base__=base)
|
||||
return model
|
||||
|
||||
|
||||
def dynamictable_to_model(
|
||||
group: h5py.Group,
|
||||
model: Optional[Type[BaseModel]] = None,
|
||||
base: Optional[Type[BaseModel]] = None,
|
||||
) -> BaseModel:
|
||||
"""
|
||||
Instantiate a dynamictable model
|
||||
|
||||
Calls :func:`.model_from_dynamictable` if ``model`` is not provided.
|
||||
"""
|
||||
if model is None:
|
||||
model = model_from_dynamictable(group, base)
|
||||
|
||||
items = {}
|
||||
for col, col_type in model.model_fields.items():
|
||||
if col not in group:
|
||||
if col in group.attrs:
|
||||
items[col] = group.attrs[col]
|
||||
continue
|
||||
|
||||
if col_type.annotation is HDF5_Path:
|
||||
items[col] = [HDF5_Path(group[d].name) for d in group[col][:]]
|
||||
else:
|
||||
try:
|
||||
items[col] = da.from_array(group[col])
|
||||
except NotImplementedError:
|
||||
items[col] = H5ArrayPath(file=group.file.filename, path=group[col].name)
|
||||
|
||||
return model.model_construct(hdf5_path=group.name, name=group.name.split("/")[-1], **items)
|
||||
|
||||
|
||||
def dereference_reference_vector(dset: h5py.Dataset, data: Optional[List[Any]]) -> List:
|
||||
|
|
|
|||
|
|
@ -5,56 +5,6 @@ Monkeypatches to external modules
|
|||
# ruff: noqa: ANN001 - not well defined types for this module
|
||||
|
||||
|
||||
def patch_npytyping_perf() -> None:
|
||||
"""
|
||||
npytyping makes an expensive call to inspect.stack()
|
||||
that makes imports of pydantic models take ~200x longer than
|
||||
they should:
|
||||
|
||||
References:
|
||||
- https://github.com/ramonhagenaars/nptyping/issues/110
|
||||
"""
|
||||
import inspect
|
||||
from types import FrameType
|
||||
|
||||
from nptyping import base_meta_classes, ndarray, recarray
|
||||
from nptyping.pandas_ import dataframe
|
||||
|
||||
# make a new __module__ methods for the affected classes
|
||||
def new_module_ndarray(cls) -> str:
|
||||
return cls._get_module(inspect.currentframe(), "nptyping.ndarray")
|
||||
|
||||
def new_module_recarray(cls) -> str:
|
||||
return cls._get_module(inspect.currentframe(), "nptyping.recarray")
|
||||
|
||||
def new_module_dataframe(cls) -> str:
|
||||
return cls._get_module(inspect.currentframe(), "nptyping.pandas_.dataframe")
|
||||
|
||||
# and a new _get_module method for the parent class
|
||||
def new_get_module(cls, stack: FrameType, module: str) -> str:
|
||||
return (
|
||||
"typing"
|
||||
if inspect.getframeinfo(stack.f_back).function == "formatannotation"
|
||||
else module
|
||||
)
|
||||
|
||||
# now apply the patches
|
||||
ndarray.NDArrayMeta.__module__ = property(new_module_ndarray)
|
||||
recarray.RecArrayMeta.__module__ = property(new_module_recarray)
|
||||
dataframe.DataFrameMeta.__module__ = property(new_module_dataframe)
|
||||
base_meta_classes.SubscriptableMeta._get_module = new_get_module
|
||||
|
||||
|
||||
def patch_nptyping_warnings() -> None:
|
||||
"""
|
||||
nptyping shits out a bunch of numpy deprecation warnings from using
|
||||
olde aliases
|
||||
"""
|
||||
import warnings
|
||||
|
||||
warnings.filterwarnings("ignore", category=DeprecationWarning, module="nptyping.*")
|
||||
|
||||
|
||||
def patch_schemaview() -> None:
|
||||
"""
|
||||
Patch schemaview to correctly resolve multiple layers of relative imports.
|
||||
|
|
@ -211,8 +161,6 @@ def patch_pretty_print() -> None:
|
|||
|
||||
def apply_patches() -> None:
|
||||
"""Apply all monkeypatches"""
|
||||
patch_npytyping_perf()
|
||||
patch_nptyping_warnings()
|
||||
patch_schemaview()
|
||||
patch_array_expression()
|
||||
patch_pretty_print()
|
||||
|
|
|
|||
|
|
@ -1,11 +0,0 @@
|
|||
import nptyping
|
||||
import numpy as np
|
||||
|
||||
from nwb_linkml.maps.dtype import struct_from_dtype
|
||||
|
||||
|
||||
def test_struct_from_dtype():
|
||||
# Super weak test with fixed values, will expand with parameterize if needed
|
||||
np_dtype = np.dtype([("name1", "int32"), ("name2", "object"), ("name3", "str")])
|
||||
struct = struct_from_dtype(np_dtype)
|
||||
assert struct == nptyping.Structure["name1: Int32, name2: Object, name3: Unicode"]
|
||||
Loading…
Reference in a new issue