mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-10 00:34:29 +00:00
holy hell it was a TYPE COERCION in the way linkml handles annotations and a version mismatch between CI and local
https://github.com/linkml/linkml-model/pull/162
This commit is contained in:
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3 changed files with 406 additions and 375 deletions
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@ -2,13 +2,13 @@
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[[package]]
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name = "annotated-types"
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version = "0.6.0"
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description = "Reusable constraint types to use with typing.Annotated"
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@ -38,17 +38,22 @@ files = [
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types-python-dateutil = ">=2.8.10"
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@ -70,32 +75,40 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
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||||||
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{file = "charset_normalizer-3.3.0-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a0ac5e7015a5920cfce654c06618ec40c33e12801711da6b4258af59a8eff00a"},
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||||||
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{file = "charset_normalizer-3.3.0-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:93aa7eef6ee71c629b51ef873991d6911b906d7312c6e8e99790c0f33c576f89"},
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{file = "charset_normalizer-3.3.0-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:7966951325782121e67c81299a031f4c115615e68046f79b85856b86ebffc4cd"},
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{file = "charset_normalizer-3.3.0-cp39-cp39-musllinux_1_1_ppc64le.whl", hash = "sha256:02673e456dc5ab13659f85196c534dc596d4ef260e4d86e856c3b2773ce09843"},
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||||||
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{file = "charset_normalizer-3.3.0-cp39-cp39-musllinux_1_1_s390x.whl", hash = "sha256:c2af80fb58f0f24b3f3adcb9148e6203fa67dd3f61c4af146ecad033024dde43"},
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||||||
|
{file = "charset_normalizer-3.3.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:153e7b6e724761741e0974fc4dcd406d35ba70b92bfe3fedcb497226c93b9da7"},
|
||||||
|
{file = "charset_normalizer-3.3.0-cp39-cp39-win32.whl", hash = "sha256:d47ecf253780c90ee181d4d871cd655a789da937454045b17b5798da9393901a"},
|
||||||
|
{file = "charset_normalizer-3.3.0-cp39-cp39-win_amd64.whl", hash = "sha256:d97d85fa63f315a8bdaba2af9a6a686e0eceab77b3089af45133252618e70884"},
|
||||||
|
{file = "charset_normalizer-3.3.0-py3-none-any.whl", hash = "sha256:e46cd37076971c1040fc8c41273a8b3e2c624ce4f2be3f5dfcb7a430c1d3acc2"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
|
|
@ -366,13 +394,13 @@ tests = ["coverage", "pytest"]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "dash"
|
name = "dash"
|
||||||
version = "2.13.0"
|
version = "2.14.0"
|
||||||
description = "A Python framework for building reactive web-apps. Developed by Plotly."
|
description = "A Python framework for building reactive web-apps. Developed by Plotly."
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.6"
|
python-versions = ">=3.6"
|
||||||
files = [
|
files = [
|
||||||
{file = "dash-2.13.0-py3-none-any.whl", hash = "sha256:ca21f01f720652c7e2d16d04d4e27803c2b60c4c2a382e750c3d8d778c06e209"},
|
{file = "dash-2.14.0-py3-none-any.whl", hash = "sha256:b88ffb53cb1bf54c12780ecf89943bb901c8914b3c075002e46519c9b17d7a72"},
|
||||||
{file = "dash-2.13.0.tar.gz", hash = "sha256:07c192db694b9bb4c87d57b6da877413f2695bfcb1d5c51f08995de7dcdd1e92"},
|
{file = "dash-2.14.0.tar.gz", hash = "sha256:bd28be70be24ae1d1f764b8217a03da35e9ed895406686d24dfb6ed4e331e5a9"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -381,6 +409,7 @@ dash-core-components = "2.0.0"
|
||||||
dash-html-components = "2.0.0"
|
dash-html-components = "2.0.0"
|
||||||
dash-table = "5.0.0"
|
dash-table = "5.0.0"
|
||||||
Flask = ">=1.0.4,<2.3.0"
|
Flask = ">=1.0.4,<2.3.0"
|
||||||
|
importlib-metadata = {version = "*", markers = "python_version >= \"3.7\""}
|
||||||
nest-asyncio = "*"
|
nest-asyncio = "*"
|
||||||
plotly = ">=5.0.0"
|
plotly = ">=5.0.0"
|
||||||
requests = "*"
|
requests = "*"
|
||||||
|
|
@ -391,7 +420,7 @@ Werkzeug = "<2.3.0"
|
||||||
|
|
||||||
[package.extras]
|
[package.extras]
|
||||||
celery = ["celery[redis] (>=5.1.2)", "importlib-metadata (<5)", "redis (>=3.5.3)"]
|
celery = ["celery[redis] (>=5.1.2)", "importlib-metadata (<5)", "redis (>=3.5.3)"]
|
||||||
ci = ["black (==21.6b0)", "black (==22.3.0)", "dash-dangerously-set-inner-html", "dash-flow-example (==0.0.5)", "flake8 (==3.9.2)", "flaky (==3.7.0)", "flask-talisman (==1.0.0)", "isort (==4.3.21)", "jupyterlab (<4.0.0)", "mimesis", "mock (==4.0.3)", "numpy", "openpyxl", "orjson (==3.5.4)", "orjson (==3.6.7)", "pandas (==1.1.5)", "pandas (>=1.4.0)", "preconditions", "pyarrow", "pyarrow (<3)", "pylint (==2.13.5)", "pytest-mock", "pytest-rerunfailures", "pytest-sugar (==0.9.6)", "xlrd (<2)", "xlrd (>=2.0.1)"]
|
ci = ["black (==21.6b0)", "black (==22.3.0)", "dash-dangerously-set-inner-html", "dash-flow-example (==0.0.5)", "flake8 (==3.9.2)", "flaky (==3.7.0)", "flask-talisman (==1.0.0)", "isort (==4.3.21)", "jupyterlab (<4.0.0)", "mimesis", "mock (==4.0.3)", "numpy (<=1.25.2)", "openpyxl", "orjson (==3.5.4)", "orjson (==3.6.7)", "pandas (==1.1.5)", "pandas (>=1.4.0)", "preconditions", "pyarrow", "pyarrow (<3)", "pylint (==2.13.5)", "pytest-mock", "pytest-rerunfailures", "pytest-sugar (==0.9.6)", "xlrd (<2)", "xlrd (>=2.0.1)"]
|
||||||
compress = ["flask-compress"]
|
compress = ["flask-compress"]
|
||||||
dev = ["PyYAML (>=5.4.1)", "coloredlogs (>=15.0.1)", "fire (>=0.4.0)"]
|
dev = ["PyYAML (>=5.4.1)", "coloredlogs (>=15.0.1)", "fire (>=0.4.0)"]
|
||||||
diskcache = ["diskcache (>=5.2.1)", "multiprocess (>=0.70.12)", "psutil (>=5.8.0)"]
|
diskcache = ["diskcache (>=5.2.1)", "multiprocess (>=0.70.12)", "psutil (>=5.8.0)"]
|
||||||
|
|
@ -446,13 +475,13 @@ files = [
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "dask"
|
name = "dask"
|
||||||
version = "2023.9.2"
|
version = "2023.9.3"
|
||||||
description = "Parallel PyData with Task Scheduling"
|
description = "Parallel PyData with Task Scheduling"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.9"
|
python-versions = ">=3.9"
|
||||||
files = [
|
files = [
|
||||||
{file = "dask-2023.9.2-py3-none-any.whl", hash = "sha256:5742bc3752a8caad1c8bbb24aa2986424c73c4c819d5ac5a9544c6f373d0094b"},
|
{file = "dask-2023.9.3-py3-none-any.whl", hash = "sha256:2e6c5de0dfce114ca9c0bb2b79d72d3a9e1499bf25cfef477659179614df5692"},
|
||||||
{file = "dask-2023.9.2.tar.gz", hash = "sha256:34e04ed79870cd01119217562f417c6ce575b10fb8fdcd866e9c5cd10c088944"},
|
{file = "dask-2023.9.3.tar.gz", hash = "sha256:712090788a7822d538cf8f43f5afc887eebe7471bc46cc331424e1cfa248764c"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -470,7 +499,7 @@ array = ["numpy (>=1.21)"]
|
||||||
complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)"]
|
complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)"]
|
||||||
dataframe = ["dask[array]", "pandas (>=1.3)"]
|
dataframe = ["dask[array]", "pandas (>=1.3)"]
|
||||||
diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
|
diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
|
||||||
distributed = ["distributed (==2023.9.2)"]
|
distributed = ["distributed (==2023.9.3)"]
|
||||||
test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
|
test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
|
|
@ -694,32 +723,36 @@ test = ["faulthandler", "objgraph", "psutil"]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "h5py"
|
name = "h5py"
|
||||||
version = "3.9.0"
|
version = "3.10.0"
|
||||||
description = "Read and write HDF5 files from Python"
|
description = "Read and write HDF5 files from Python"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.8"
|
python-versions = ">=3.8"
|
||||||
files = [
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files = [
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||||||
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||||||
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|
||||||
{file = "h5py-3.9.0.tar.gz", hash = "sha256:e604db6521c1e367c6bd7fad239c847f53cc46646f2d2651372d05ae5e95f817"},
|
{file = "h5py-3.10.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:d4682b94fd36ab217352be438abd44c8f357c5449b8995e63886b431d260f3d3"},
|
||||||
|
{file = "h5py-3.10.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:aece0e2e1ed2aab076c41802e50a0c3e5ef8816d60ece39107d68717d4559824"},
|
||||||
|
{file = "h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:43a61b2c2ad65b1fabc28802d133eed34debcc2c8b420cb213d3d4ef4d3e2229"},
|
||||||
|
{file = "h5py-3.10.0-cp39-cp39-win_amd64.whl", hash = "sha256:ae2f0201c950059676455daf92700eeb57dcf5caaf71b9e1328e6e6593601770"},
|
||||||
|
{file = "h5py-3.10.0.tar.gz", hash = "sha256:d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -957,13 +990,13 @@ referencing = ">=0.28.0"
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "linkml"
|
name = "linkml"
|
||||||
version = "1.5.7"
|
version = "1.6.1"
|
||||||
description = "Linked Open Data Modeling Language"
|
description = "Linked Open Data Modeling Language"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.7.6,<4.0.0"
|
python-versions = ">=3.8,<4.0"
|
||||||
files = [
|
files = [
|
||||||
{file = "linkml-1.5.7-py3-none-any.whl", hash = "sha256:677f4c5809dc51b151b86accc69e77482ad86b9c1326a212cef9b4a2a9a96c10"},
|
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|
||||||
{file = "linkml-1.5.7.tar.gz", hash = "sha256:bca3dd56837ced79749656843e1e20b8d1db1a89287e7b29d1ee145e4a75ad4d"},
|
{file = "linkml-1.6.1.tar.gz", hash = "sha256:65f73cf29a77518972238e71e91e012c081cf2e43d71d8965ca414c78c11e08e"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -976,7 +1009,7 @@ jinja2 = ">=3.1.0"
|
||||||
jsonasobj2 = ">=1.0.3,<2.0.0"
|
jsonasobj2 = ">=1.0.3,<2.0.0"
|
||||||
jsonschema = {version = ">=4.0.0", extras = ["format"]}
|
jsonschema = {version = ">=4.0.0", extras = ["format"]}
|
||||||
linkml-dataops = "*"
|
linkml-dataops = "*"
|
||||||
linkml-runtime = ">=1.5.4"
|
linkml-runtime = ">=1.6.0"
|
||||||
openpyxl = "*"
|
openpyxl = "*"
|
||||||
parse = "*"
|
parse = "*"
|
||||||
prefixcommons = ">=0.1.7"
|
prefixcommons = ">=0.1.7"
|
||||||
|
|
@ -1012,13 +1045,13 @@ linkml-runtime = ">=1.1.6"
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "linkml-runtime"
|
name = "linkml-runtime"
|
||||||
version = "1.5.7"
|
version = "1.6.0"
|
||||||
description = "Runtime environment for LinkML, the Linked open data modeling language"
|
description = "Runtime environment for LinkML, the Linked open data modeling language"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.7.6,<4.0.0"
|
python-versions = ">=3.7.6,<4.0.0"
|
||||||
files = [
|
files = [
|
||||||
{file = "linkml_runtime-1.5.7-py3-none-any.whl", hash = "sha256:8ea32b5f0de3637c2339edfbb88008bb08a9e2ff36d1aada20e002058263418f"},
|
{file = "linkml_runtime-1.6.0-py3-none-any.whl", hash = "sha256:1b6b698f8cf23d63ff833ae0be8055b2e945e1c0ef06a1ed6db359247194a2eb"},
|
||||||
{file = "linkml_runtime-1.5.7.tar.gz", hash = "sha256:c202799f01571b0c202bb521957f281b1052fabad106419c8e1368802088d6a4"},
|
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|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -1143,67 +1176,67 @@ files = [
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "msgpack"
|
name = "msgpack"
|
||||||
version = "1.0.6"
|
version = "1.0.7"
|
||||||
description = "MessagePack serializer"
|
description = "MessagePack serializer"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.8"
|
python-versions = ">=3.8"
|
||||||
files = [
|
files = [
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||||||
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||||||
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{file = "msgpack-1.0.7-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:5ed82f5a7af3697b1c4786053736f24a0efd0a1b8a130d4c7bfee4b9ded0f08f"},
|
||||||
{file = "msgpack-1.0.6-cp39-cp39-win32.whl", hash = "sha256:7baf16fd8908a025c4a8d7b699103e72d41f967e2aee5a2065432bcdbd9fd06e"},
|
{file = "msgpack-1.0.7-cp39-cp39-win32.whl", hash = "sha256:f26a07a6e877c76a88e3cecac8531908d980d3d5067ff69213653649ec0f60ad"},
|
||||||
{file = "msgpack-1.0.6-cp39-cp39-win_amd64.whl", hash = "sha256:fc97aa4b4fb928ff4d3b74da7c30b360d0cb3ede49a5a6e1fd9705f49aea1deb"},
|
{file = "msgpack-1.0.7-cp39-cp39-win_amd64.whl", hash = "sha256:1dc93e8e4653bdb5910aed79f11e165c85732067614f180f70534f056da97db3"},
|
||||||
{file = "msgpack-1.0.6.tar.gz", hash = "sha256:25d3746da40f3c8c59c3b1d001e49fd2aa17904438f980d9a391370366df001e"},
|
{file = "msgpack-1.0.7.tar.gz", hash = "sha256:572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
|
|
@ -1313,13 +1346,13 @@ files = [
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "nwb-schema-language"
|
name = "nwb-schema-language"
|
||||||
version = "0.1.1"
|
version = "0.1.3"
|
||||||
description = "Translation of the nwb-schema-language to LinkML"
|
description = "Translation of the nwb-schema-language to LinkML"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.9,<4.0"
|
python-versions = ">=3.9,<4.0"
|
||||||
files = [
|
files = [
|
||||||
{file = "nwb_schema_language-0.1.1-py3-none-any.whl", hash = "sha256:97af4c987af699574515440d44997c0eb6b5a5b84d60877f2641861165f747c3"},
|
{file = "nwb_schema_language-0.1.3-py3-none-any.whl", hash = "sha256:2eb86aac6614d490f7ec3fa68634bb9dceb3834d9820f5afc5645a9f3b0c3401"},
|
||||||
{file = "nwb_schema_language-0.1.1.tar.gz", hash = "sha256:d2ddcdefb46c39a173ed94634b6db5abd6a202653a2140d3f8a679ac07599c7c"},
|
{file = "nwb_schema_language-0.1.3.tar.gz", hash = "sha256:ad290e2896a9cde7e2f353bc3b8ddf42be865238d991167d397ff2e0d03c88ba"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -1342,13 +1375,13 @@ et-xmlfile = "*"
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "packaging"
|
name = "packaging"
|
||||||
version = "23.1"
|
version = "23.2"
|
||||||
description = "Core utilities for Python packages"
|
description = "Core utilities for Python packages"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.7"
|
python-versions = ">=3.7"
|
||||||
files = [
|
files = [
|
||||||
{file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"},
|
{file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
|
||||||
{file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
|
{file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
|
|
@ -1473,13 +1506,13 @@ files = [
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "pydantic"
|
name = "pydantic"
|
||||||
version = "2.4.1"
|
version = "2.4.2"
|
||||||
description = "Data validation using Python type hints"
|
description = "Data validation using Python type hints"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.7"
|
python-versions = ">=3.7"
|
||||||
files = [
|
files = [
|
||||||
{file = "pydantic-2.4.1-py3-none-any.whl", hash = "sha256:2b2240c8d54bb8f84b88e061fac1bdfa1761c2859c367f9d3afe0ec2966deddc"},
|
{file = "pydantic-2.4.2-py3-none-any.whl", hash = "sha256:bc3ddf669d234f4220e6e1c4d96b061abe0998185a8d7855c0126782b7abc8c1"},
|
||||||
{file = "pydantic-2.4.1.tar.gz", hash = "sha256:b172505886028e4356868d617d2d1a776d7af1625d1313450fd51bdd19d9d61f"},
|
{file = "pydantic-2.4.2.tar.gz", hash = "sha256:94f336138093a5d7f426aac732dcfe7ab4eb4da243c88f891d65deb4a2556ee7"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -1762,20 +1795,6 @@ future-fstrings = "*"
|
||||||
networkx = "*"
|
networkx = "*"
|
||||||
pytest = ">=3"
|
pytest = ">=3"
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "pytest-emoji"
|
|
||||||
version = "0.2.0"
|
|
||||||
description = "A pytest plugin that adds emojis to your test result report"
|
|
||||||
optional = false
|
|
||||||
python-versions = ">=3.4"
|
|
||||||
files = [
|
|
||||||
{file = "pytest-emoji-0.2.0.tar.gz", hash = "sha256:e1bd4790d87649c2d09c272c88bdfc4d37c1cc7c7a46583087d7c510944571e8"},
|
|
||||||
{file = "pytest_emoji-0.2.0-py3-none-any.whl", hash = "sha256:6e34ed21970fa4b80a56ad11417456bd873eb066c02315fe9df0fafe6d4d4436"},
|
|
||||||
]
|
|
||||||
|
|
||||||
[package.dependencies]
|
|
||||||
pytest = ">=4.2.1"
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "pytest-logging"
|
name = "pytest-logging"
|
||||||
version = "2015.11.4"
|
version = "2015.11.4"
|
||||||
|
|
@ -2039,13 +2058,13 @@ files = [
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "rich"
|
name = "rich"
|
||||||
version = "13.5.3"
|
version = "13.6.0"
|
||||||
description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
|
description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.7.0"
|
python-versions = ">=3.7.0"
|
||||||
files = [
|
files = [
|
||||||
{file = "rich-13.5.3-py3-none-any.whl", hash = "sha256:9257b468badc3d347e146a4faa268ff229039d4c2d176ab0cffb4c4fbc73d5d9"},
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{file = "rich-13.6.0-py3-none-any.whl", hash = "sha256:2b38e2fe9ca72c9a00170a1a2d20c63c790d0e10ef1fe35eba76e1e7b1d7d245"},
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||||||
{file = "rich-13.5.3.tar.gz", hash = "sha256:87b43e0543149efa1253f485cd845bb7ee54df16c9617b8a893650ab84b4acb6"},
|
{file = "rich-13.6.0.tar.gz", hash = "sha256:5c14d22737e6d5084ef4771b62d5d4363165b403455a30a1c8ca39dc7b644bef"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
|
|
@ -2057,123 +2076,125 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "rpds-py"
|
name = "rpds-py"
|
||||||
version = "0.10.3"
|
version = "0.10.6"
|
||||||
description = "Python bindings to Rust's persistent data structures (rpds)"
|
description = "Python bindings to Rust's persistent data structures (rpds)"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.8"
|
python-versions = ">=3.8"
|
||||||
files = [
|
files = [
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||||||
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||||||
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||||||
[[package]]
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||||||
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||||||
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||||||
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description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
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||||||
[package.dependencies]
|
[package.dependencies]
|
||||||
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"ruamel.yaml.clib" = {version = ">=0.2.7", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.13\""}
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||||||
|
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||||||
[package.extras]
|
[package.extras]
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docs = ["ryd"]
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|
@ -2181,48 +2202,47 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
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|
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[[package]]
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|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp310-cp310-win32.whl", hash = "sha256:763d65baa3b952479c4e972669f679fe490eee058d5aa85da483ebae2009d231"},
|
{file = "ruamel.yaml.clib-0.2.8-cp310-cp310-win32.whl", hash = "sha256:c69212f63169ec1cfc9bb44723bf2917cbbd8f6191a00ef3410f5a7fe300722d"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp310-cp310-win_amd64.whl", hash = "sha256:d000f258cf42fec2b1bbf2863c61d7b8918d31ffee905da62dede869254d3b8a"},
|
{file = "ruamel.yaml.clib-0.2.8-cp310-cp310-win_amd64.whl", hash = "sha256:cabddb8d8ead485e255fe80429f833172b4cadf99274db39abc080e068cbcc31"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:045e0626baf1c52e5527bd5db361bc83180faaba2ff586e763d3d5982a876a9e"},
|
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:bef08cd86169d9eafb3ccb0a39edb11d8e25f3dae2b28f5c52fd997521133069"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_13_0_arm64.whl", hash = "sha256:1a6391a7cabb7641c32517539ca42cf84b87b667bad38b78d4d42dd23e957c81"},
|
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-macosx_13_0_arm64.whl", hash = "sha256:b16420e621d26fdfa949a8b4b47ade8810c56002f5389970db4ddda51dbff248"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp311-cp311-manylinux2014_aarch64.whl", hash = "sha256:9c7617df90c1365638916b98cdd9be833d31d337dbcd722485597b43c4a215bf"},
|
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-manylinux2014_aarch64.whl", hash = "sha256:b5edda50e5e9e15e54a6a8a0070302b00c518a9d32accc2346ad6c984aacd279"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:41d0f1fa4c6830176eef5b276af04c89320ea616655d01327d5ce65e50575c94"},
|
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:25c515e350e5b739842fc3228d662413ef28f295791af5e5110b543cf0b57d9b"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp311-cp311-win32.whl", hash = "sha256:f6d3d39611ac2e4f62c3128a9eed45f19a6608670c5a2f4f07f24e8de3441d38"},
|
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-win32.whl", hash = "sha256:53a300ed9cea38cf5a2a9b069058137c2ca1ce658a874b79baceb8f892f915a7"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp311-cp311-win_amd64.whl", hash = "sha256:da538167284de58a52109a9b89b8f6a53ff8437dd6dc26d33b57bf6699153122"},
|
{file = "ruamel.yaml.clib-0.2.8-cp311-cp311-win_amd64.whl", hash = "sha256:c2a72e9109ea74e511e29032f3b670835f8a59bbdc9ce692c5b4ed91ccf1eedb"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:4b3a93bb9bc662fc1f99c5c3ea8e623d8b23ad22f861eb6fce9377ac07ad6072"},
|
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:ebc06178e8821efc9692ea7544aa5644217358490145629914d8020042c24aa1"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-macosx_12_0_arm64.whl", hash = "sha256:a234a20ae07e8469da311e182e70ef6b199d0fbeb6c6cc2901204dd87fb867e8"},
|
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-macosx_13_0_arm64.whl", hash = "sha256:edaef1c1200c4b4cb914583150dcaa3bc30e592e907c01117c08b13a07255ec2"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:15910ef4f3e537eea7fe45f8a5d19997479940d9196f357152a09031c5be59f3"},
|
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-manylinux2014_aarch64.whl", hash = "sha256:7048c338b6c86627afb27faecf418768acb6331fc24cfa56c93e8c9780f815fa"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:370445fd795706fd291ab00c9df38a0caed0f17a6fb46b0f607668ecb16ce763"},
|
{file = "ruamel.yaml.clib-0.2.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:d176b57452ab5b7028ac47e7b3cf644bcfdc8cacfecf7e71759f7f51a59e5c92"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-win32.whl", hash = "sha256:ecdf1a604009bd35c674b9225a8fa609e0282d9b896c03dd441a91e5f53b534e"},
|
{file = "ruamel.yaml.clib-0.2.8-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:a5aa27bad2bb83670b71683aae140a1f52b0857a2deff56ad3f6c13a017a26ed"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-win_amd64.whl", hash = "sha256:f34019dced51047d6f70cb9383b2ae2853b7fc4dce65129a5acd49f4f9256646"},
|
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:c58ecd827313af6864893e7af0a3bb85fd529f862b6adbefe14643947cfe2942"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:2aa261c29a5545adfef9296b7e33941f46aa5bbd21164228e833412af4c9c75f"},
|
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-macosx_12_0_arm64.whl", hash = "sha256:f481f16baec5290e45aebdc2a5168ebc6d35189ae6fea7a58787613a25f6e875"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp37-cp37m-macosx_12_0_arm64.whl", hash = "sha256:f01da5790e95815eb5a8a138508c01c758e5f5bc0ce4286c4f7028b8dd7ac3d0"},
|
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:3fcc54cb0c8b811ff66082de1680b4b14cf8a81dce0d4fbf665c2265a81e07a1"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:40d030e2329ce5286d6b231b8726959ebbe0404c92f0a578c0e2482182e38282"},
|
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:7f67a1ee819dc4562d444bbafb135832b0b909f81cc90f7aa00260968c9ca1b3"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:c3ca1fbba4ae962521e5eb66d72998b51f0f4d0f608d3c0347a48e1af262efa7"},
|
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-win32.whl", hash = "sha256:75e1ed13e1f9de23c5607fe6bd1aeaae21e523b32d83bb33918245361e9cc51b"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp37-cp37m-win32.whl", hash = "sha256:7bdb4c06b063f6fd55e472e201317a3bb6cdeeee5d5a38512ea5c01e1acbdd93"},
|
{file = "ruamel.yaml.clib-0.2.8-cp37-cp37m-win_amd64.whl", hash = "sha256:3f215c5daf6a9d7bbed4a0a4f760f3113b10e82ff4c5c44bec20a68c8014f675"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp37-cp37m-win_amd64.whl", hash = "sha256:be2a7ad8fd8f7442b24323d24ba0b56c51219513cfa45b9ada3b87b76c374d4b"},
|
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:1b617618914cb00bf5c34d4357c37aa15183fa229b24767259657746c9077615"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:91a789b4aa0097b78c93e3dc4b40040ba55bef518f84a40d4442f713b4094acb"},
|
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:a6a9ffd280b71ad062eae53ac1659ad86a17f59a0fdc7699fd9be40525153337"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:99e77daab5d13a48a4054803d052ff40780278240a902b880dd37a51ba01a307"},
|
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:665f58bfd29b167039f714c6998178d27ccd83984084c286110ef26b230f259f"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:3243f48ecd450eddadc2d11b5feb08aca941b5cd98c9b1db14b2fd128be8c697"},
|
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:700e4ebb569e59e16a976857c8798aee258dceac7c7d6b50cab63e080058df91"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:8831a2cedcd0f0927f788c5bdf6567d9dc9cc235646a434986a852af1cb54b4b"},
|
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-win32.whl", hash = "sha256:955eae71ac26c1ab35924203fda6220f84dce57d6d7884f189743e2abe3a9fbe"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp38-cp38-win32.whl", hash = "sha256:3110a99e0f94a4a3470ff67fc20d3f96c25b13d24c6980ff841e82bafe827cac"},
|
{file = "ruamel.yaml.clib-0.2.8-cp38-cp38-win_amd64.whl", hash = "sha256:56f4252222c067b4ce51ae12cbac231bce32aee1d33fbfc9d17e5b8d6966c312"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp38-cp38-win_amd64.whl", hash = "sha256:92460ce908546ab69770b2e576e4f99fbb4ce6ab4b245345a3869a0a0410488f"},
|
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:03d1162b6d1df1caa3a4bd27aa51ce17c9afc2046c31b0ad60a0a96ec22f8001"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:5bc0667c1eb8f83a3752b71b9c4ba55ef7c7058ae57022dd9b29065186a113d9"},
|
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:bba64af9fa9cebe325a62fa398760f5c7206b215201b0ec825005f1b18b9bccf"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:4a4d8d417868d68b979076a9be6a38c676eca060785abaa6709c7b31593c35d1"},
|
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:9eb5dee2772b0f704ca2e45b1713e4e5198c18f515b52743576d196348f374d3"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:bf9a6bc4a0221538b1a7de3ed7bca4c93c02346853f44e1cd764be0023cd3640"},
|
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:da09ad1c359a728e112d60116f626cc9f29730ff3e0e7db72b9a2dbc2e4beed5"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:a7b301ff08055d73223058b5c46c55638917f04d21577c95e00e0c4d79201a6b"},
|
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-win32.whl", hash = "sha256:84b554931e932c46f94ab306913ad7e11bba988104c5cff26d90d03f68258cd5"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp39-cp39-win32.whl", hash = "sha256:d5e51e2901ec2366b79f16c2299a03e74ba4531ddcfacc1416639c557aef0ad8"},
|
{file = "ruamel.yaml.clib-0.2.8-cp39-cp39-win_amd64.whl", hash = "sha256:25ac8c08322002b06fa1d49d1646181f0b2c72f5cbc15a85e80b4c30a544bb15"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7-cp39-cp39-win_amd64.whl", hash = "sha256:184faeaec61dbaa3cace407cffc5819f7b977e75360e8d5ca19461cd851a5fc5"},
|
{file = "ruamel.yaml.clib-0.2.8.tar.gz", hash = "sha256:beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512"},
|
||||||
{file = "ruamel.yaml.clib-0.2.7.tar.gz", hash = "sha256:1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497"},
|
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
|
|
@ -2436,6 +2456,17 @@ notebook = ["ipywidgets (>=6)"]
|
||||||
slack = ["slack-sdk"]
|
slack = ["slack-sdk"]
|
||||||
telegram = ["requests"]
|
telegram = ["requests"]
|
||||||
|
|
||||||
|
[[package]]
|
||||||
|
name = "types-python-dateutil"
|
||||||
|
version = "2.8.19.14"
|
||||||
|
description = "Typing stubs for python-dateutil"
|
||||||
|
optional = false
|
||||||
|
python-versions = "*"
|
||||||
|
files = [
|
||||||
|
{file = "types-python-dateutil-2.8.19.14.tar.gz", hash = "sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b"},
|
||||||
|
{file = "types_python_dateutil-2.8.19.14-py3-none-any.whl", hash = "sha256:f977b8de27787639986b4e28963263fd0e5158942b3ecef91b9335c130cb1ce9"},
|
||||||
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "typing-extensions"
|
name = "typing-extensions"
|
||||||
version = "4.8.0"
|
version = "4.8.0"
|
||||||
|
|
@ -2463,13 +2494,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "urllib3"
|
name = "urllib3"
|
||||||
version = "2.0.5"
|
version = "2.0.6"
|
||||||
description = "HTTP library with thread-safe connection pooling, file post, and more."
|
description = "HTTP library with thread-safe connection pooling, file post, and more."
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.7"
|
python-versions = ">=3.7"
|
||||||
files = [
|
files = [
|
||||||
{file = "urllib3-2.0.5-py3-none-any.whl", hash = "sha256:ef16afa8ba34a1f989db38e1dbbe0c302e4289a47856990d0682e374563ce35e"},
|
{file = "urllib3-2.0.6-py3-none-any.whl", hash = "sha256:7a7c7003b000adf9e7ca2a377c9688bbc54ed41b985789ed576570342a375cd2"},
|
||||||
{file = "urllib3-2.0.5.tar.gz", hash = "sha256:13abf37382ea2ce6fb744d4dad67838eec857c9f4f57009891805e0b5e123594"},
|
{file = "urllib3-2.0.6.tar.gz", hash = "sha256:b19e1a85d206b56d7df1d5e683df4a7725252a964e3993648dd0fb5a1c157564"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[package.extras]
|
[package.extras]
|
||||||
|
|
@ -2655,4 +2686,4 @@ tests = ["coverage", "coveralls", "pytest", "pytest-cov", "pytest-depends", "pyt
|
||||||
[metadata]
|
[metadata]
|
||||||
lock-version = "2.0"
|
lock-version = "2.0"
|
||||||
python-versions = ">=3.11,<3.13"
|
python-versions = ">=3.11,<3.13"
|
||||||
content-hash = "b4afc2881969650e4a9f75c4148aeaa1d1af308f27170ebd76a1c79fcdf71555"
|
content-hash = "a3ce11b1eb6ecff528a0a7bce0695368a24218766d6eb0385002fb4e8d3ea8b4"
|
||||||
|
|
|
||||||
|
|
@ -20,10 +20,10 @@ include = [
|
||||||
[tool.poetry.dependencies]
|
[tool.poetry.dependencies]
|
||||||
python = ">=3.11,<3.13"
|
python = ">=3.11,<3.13"
|
||||||
pyyaml = "^6.0"
|
pyyaml = "^6.0"
|
||||||
linkml-runtime = "^1.5.6"
|
linkml-runtime = "^1.6.0"
|
||||||
nwb_schema_language = "^0.1.3"
|
nwb_schema_language = "^0.1.3"
|
||||||
rich = "^13.5.2"
|
rich = "^13.5.2"
|
||||||
linkml = "^1.5.7"
|
linkml = "^1.6.1"
|
||||||
nptyping = "^2.5.0"
|
nptyping = "^2.5.0"
|
||||||
pydantic = "^2.3.0"
|
pydantic = "^2.3.0"
|
||||||
h5py = "^3.9.0"
|
h5py = "^3.9.0"
|
||||||
|
|
|
||||||
|
|
@ -10,7 +10,7 @@ from ..fixtures import tmp_output_dir, data_dir
|
||||||
from nwb_linkml.io.hdf5 import HDF5IO
|
from nwb_linkml.io.hdf5 import HDF5IO
|
||||||
from nwb_linkml.io.hdf5 import truncate_file
|
from nwb_linkml.io.hdf5 import truncate_file
|
||||||
|
|
||||||
@pytest.mark.skip()
|
|
||||||
@pytest.mark.parametrize('dset', ['aibs.nwb'])
|
@pytest.mark.parametrize('dset', ['aibs.nwb'])
|
||||||
def test_hdf_read(data_dir, dset):
|
def test_hdf_read(data_dir, dset):
|
||||||
NWBFILE = data_dir / dset
|
NWBFILE = data_dir / dset
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue