p2p-ld/nwb-linkml
1
0
Fork 0
mirror of https://github.com/p2p-ld/nwb-linkml.git synced 2024-09-19 15:34:28 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions

Merge pull request #9 from p2p-ld/perf-generator
Some checks failed
Lint / Ruff Linting (push) Has been cancelled
Details
Lint / Black Formatting (push) Has been cancelled
Details
Lint / Check for spelling errors (push) Has been cancelled
Details
Model Rebuild / build_models (push) Has been cancelled
Details
Tests / test (3.10) (push) Has been cancelled
Details
Tests / test (3.11) (push) Has been cancelled
Details
Tests / test (3.12) (push) Has been cancelled
Details
Tests / finish-coverage (push) Has been cancelled
Details

Browse source 
[perf] Parallel builds
This commit is contained in:
Jonny Saunders 2024-08-27 21:08:13 -07:00 committed by GitHub
commit 0e4058520a
No known key found for this signature in database
GPG key ID: B5690EEEBB952194
258 changed files with 5743 additions and 5353 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

9
.gitattributes vendored Normal file
View file

@ -0,0 +1,9 @@
nwb_models/src/nwb_models/models/** linguist-generated
nwb_models/src/nwb_models/schema/** linguist-generated
nwb_models/src/nwb_models/models/pydantic/core/v2_7_0/** -linguist-generated
nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_8_0/** -linguist-generated
nwb_models/src/nwb_models/models/pydantic/hdmf_experimental/v0_5_0/** -linguist-generated
nwb_models/src/nwb_models/schema/linkml/core/v2_7_0/** -linguist-generated
nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/** -linguist-generated
nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/** -linguist-generated

4
.github/workflows/tests.yml vendored
View file

@ -30,6 +30,10 @@ jobs:
with: with:
python-version: ${{ matrix.python-version }} python-version: ${{ matrix.python-version }}
cache: 'pip' cache: 'pip'
cache-dependency-path: |
nwb_linkml/pyproject.toml
nwb_schema_language/pyproject.toml
nwb_models/pyproject.toml
- name: Install dependencies - name: Install dependencies
run: pip install -e .[tests] run: pip install -e .[tests]

3
.gitignore vendored
View file

@ -167,4 +167,5 @@ jupyter_execute
.pdm-python .pdm-python
.venv* .venv*
requests-cache.sqlite requests-cache.sqlite
*.pstats

217
nwb_linkml/pdm.lock
View file

@ -5,7 +5,7 @@
groups = ["default", "dev", "plot", "tests"] groups = ["default", "dev", "plot", "tests"]
strategy = ["inherit_metadata"] strategy = ["inherit_metadata"]
lock_version = "4.5.0" lock_version = "4.5.0"
content_hash = "sha256:3223b7fb1c0ac9877a6d8af33e55f10e54fe8eb3a8b4fa053d3e7082863260ac" content_hash = "sha256:f219083028bd024c53bc55626c8b6088d6eb5c2ade56bd694a7a112098aa9bfc"
[[metadata.targets]] [[metadata.targets]]
requires_python = ">=3.10,<3.13" requires_python = ">=3.10,<3.13"
@ -582,18 +582,18 @@ files = [
[[package]] [[package]]
name = "idna" name = "idna"
version = "3.7" version = "3.8"
requires_python = ">=3.5" requires_python = ">=3.6"
summary = "Internationalized Domain Names in Applications (IDNA)" summary = "Internationalized Domain Names in Applications (IDNA)"
groups = ["default", "dev", "plot", "tests"] groups = ["default", "dev", "plot", "tests"]
files = [ files = [
{file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"}, {file = "idna-3.8-py3-none-any.whl", hash = "sha256:050b4e5baadcd44d760cedbd2b8e639f2ff89bbc7a5730fcc662954303377aac"},
{file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, {file = "idna-3.8.tar.gz", hash = "sha256:d838c2c0ed6fced7693d5e8ab8e734d5f8fda53a039c0164afb0b82e771e3603"},
] ]
[[package]] [[package]]
name = "importlib-metadata" name = "importlib-metadata"
version = "8.2.0" version = "8.4.0"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Read metadata from Python packages" summary = "Read metadata from Python packages"
groups = ["plot"] groups = ["plot"]
@ -602,8 +602,8 @@ dependencies = [
"zipp>=0.5", "zipp>=0.5",
] ]
files = [ files = [
{file = "importlib_metadata-8.2.0-py3-none-any.whl", hash = "sha256:11901fa0c2f97919b288679932bb64febaeacf289d18ac84dd68cb2e74213369"}, {file = "importlib_metadata-8.4.0-py3-none-any.whl", hash = "sha256:66f342cc6ac9818fc6ff340576acd24d65ba0b3efabb2b4ac08b598965a4a2f1"},
{file = "importlib_metadata-8.2.0.tar.gz", hash = "sha256:72e8d4399996132204f9a16dcc751af254a48f8d1b20b9ff0f98d4a8f901e73d"}, {file = "importlib_metadata-8.4.0.tar.gz", hash = "sha256:9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5"},
] ]
[[package]] [[package]]
@ -809,7 +809,7 @@ version = "0.0.0"
requires_python = "<4.0.0,>=3.8.1" requires_python = "<4.0.0,>=3.8.1"
git = "https://github.com/sneakers-the-rat/linkml" git = "https://github.com/sneakers-the-rat/linkml"
ref = "nwb-linkml" ref = "nwb-linkml"
revision = "0a6578bff4713688260f64b3076b197bd6decce9" revision = "0247c0b1e1a87366e0e047449e604881870c4e98"
summary = "Linked Open Data Modeling Language" summary = "Linked Open Data Modeling Language"
groups = ["default"] groups = ["default"]
dependencies = [ dependencies = [
@ -822,7 +822,7 @@ dependencies = [
"jsonasobj2==1.*,>=1.0.0,>=1.0.3", "jsonasobj2==1.*,>=1.0.0,>=1.0.3",
"jsonschema[format]>=4.0.0", "jsonschema[format]>=4.0.0",
"linkml-dataops", "linkml-dataops",
"linkml-runtime==1.8.0", "linkml-runtime<2.0.0,>=1.8.1",
"openpyxl", "openpyxl",
"parse", "parse",
"prefixcommons>=0.1.7", "prefixcommons>=0.1.7",
@ -860,7 +860,7 @@ files = [
[[package]] [[package]]
name = "linkml-runtime" name = "linkml-runtime"
version = "1.8.0" version = "1.8.2"
requires_python = "<4.0,>=3.8" requires_python = "<4.0,>=3.8"
summary = "Runtime environment for LinkML, the Linked open data modeling language" summary = "Runtime environment for LinkML, the Linked open data modeling language"
groups = ["default"] groups = ["default"]
@ -880,8 +880,8 @@ dependencies = [
"requests", "requests",
] ]
files = [ files = [
{file = "linkml_runtime-1.8.0-py3-none-any.whl", hash = "sha256:e99a809eda52640633f07a9e8b391d1a9da863eb68a475dfd74a79335b909931"}, {file = "linkml_runtime-1.8.2-py3-none-any.whl", hash = "sha256:a66d7b5b82cb57b2d6c603c75ca22db4bae0409e0fb2b9e7835f921a23716096"},
{file = "linkml_runtime-1.8.0.tar.gz", hash = "sha256:436381a7bf791e9af4ef0a5adcac86762d451b77670fbdb3ba083d2c177fb5f2"}, {file = "linkml_runtime-1.8.2.tar.gz", hash = "sha256:f5067aeeb96c8d3ca1761b55b82d927af88d810459d533fb1f7876a90224b130"},
] ]
[[package]] [[package]]
@ -984,42 +984,45 @@ files = [
[[package]] [[package]]
name = "numpy" name = "numpy"
version = "2.0.1" version = "2.1.0"
requires_python = ">=3.9" requires_python = ">=3.10"
summary = "Fundamental package for array computing in Python" summary = "Fundamental package for array computing in Python"
groups = ["default"] groups = ["default"]
files = [ files = [
{file = "numpy-2.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0fbb536eac80e27a2793ffd787895242b7f18ef792563d742c2d673bfcb75134"}, {file = "numpy-2.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6326ab99b52fafdcdeccf602d6286191a79fe2fda0ae90573c5814cd2b0bc1b8"},
{file = "numpy-2.0.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:69ff563d43c69b1baba77af455dd0a839df8d25e8590e79c90fcbe1499ebde42"}, {file = "numpy-2.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0937e54c09f7a9a68da6889362ddd2ff584c02d015ec92672c099b61555f8911"},
{file = "numpy-2.0.1-cp310-cp310-macosx_14_0_arm64.whl", hash = "sha256:1b902ce0e0a5bb7704556a217c4f63a7974f8f43e090aff03fcf262e0b135e02"}, {file = "numpy-2.1.0-cp310-cp310-macosx_14_0_arm64.whl", hash = "sha256:30014b234f07b5fec20f4146f69e13cfb1e33ee9a18a1879a0142fbb00d47673"},
{file = "numpy-2.0.1-cp310-cp310-macosx_14_0_x86_64.whl", hash = "sha256:f1659887361a7151f89e79b276ed8dff3d75877df906328f14d8bb40bb4f5101"}, {file = "numpy-2.1.0-cp310-cp310-macosx_14_0_x86_64.whl", hash = "sha256:899da829b362ade41e1e7eccad2cf274035e1cb36ba73034946fccd4afd8606b"},
{file = "numpy-2.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4658c398d65d1b25e1760de3157011a80375da861709abd7cef3bad65d6543f9"}, {file = "numpy-2.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:08801848a40aea24ce16c2ecde3b756f9ad756586fb2d13210939eb69b023f5b"},
{file = "numpy-2.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4127d4303b9ac9f94ca0441138acead39928938660ca58329fe156f84b9f3015"}, {file = "numpy-2.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:398049e237d1aae53d82a416dade04defed1a47f87d18d5bd615b6e7d7e41d1f"},
{file = "numpy-2.0.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:e5eeca8067ad04bc8a2a8731183d51d7cbaac66d86085d5f4766ee6bf19c7f87"}, {file = "numpy-2.1.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:0abb3916a35d9090088a748636b2c06dc9a6542f99cd476979fb156a18192b84"},
{file = "numpy-2.0.1-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:9adbd9bb520c866e1bfd7e10e1880a1f7749f1f6e5017686a5fbb9b72cf69f82"}, {file = "numpy-2.1.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:10e2350aea18d04832319aac0f887d5fcec1b36abd485d14f173e3e900b83e33"},
{file = "numpy-2.0.1-cp310-cp310-win32.whl", hash = "sha256:7b9853803278db3bdcc6cd5beca37815b133e9e77ff3d4733c247414e78eb8d1"}, {file = "numpy-2.1.0-cp310-cp310-win32.whl", hash = "sha256:f6b26e6c3b98adb648243670fddc8cab6ae17473f9dc58c51574af3e64d61211"},
{file = "numpy-2.0.1-cp310-cp310-win_amd64.whl", hash = "sha256:81b0893a39bc5b865b8bf89e9ad7807e16717f19868e9d234bdaf9b1f1393868"}, {file = "numpy-2.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:f505264735ee074250a9c78247ee8618292091d9d1fcc023290e9ac67e8f1afa"},
{file = "numpy-2.0.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:75b4e316c5902d8163ef9d423b1c3f2f6252226d1aa5cd8a0a03a7d01ffc6268"}, {file = "numpy-2.1.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:76368c788ccb4f4782cf9c842b316140142b4cbf22ff8db82724e82fe1205dce"},
{file = "numpy-2.0.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:6e4eeb6eb2fced786e32e6d8df9e755ce5be920d17f7ce00bc38fcde8ccdbf9e"}, {file = "numpy-2.1.0-cp311-cp311-macosx_14_0_arm64.whl", hash = "sha256:f8e93a01a35be08d31ae33021e5268f157a2d60ebd643cfc15de6ab8e4722eb1"},
{file = "numpy-2.0.1-cp311-cp311-macosx_14_0_arm64.whl", hash = "sha256:a1e01dcaab205fbece13c1410253a9eea1b1c9b61d237b6fa59bcc46e8e89343"}, {file = "numpy-2.1.0-cp311-cp311-macosx_14_0_x86_64.whl", hash = "sha256:9523f8b46485db6939bd069b28b642fec86c30909cea90ef550373787f79530e"},
{file = "numpy-2.0.1-cp311-cp311-macosx_14_0_x86_64.whl", hash = "sha256:a8fc2de81ad835d999113ddf87d1ea2b0f4704cbd947c948d2f5513deafe5a7b"}, {file = "numpy-2.1.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:54139e0eb219f52f60656d163cbe67c31ede51d13236c950145473504fa208cb"},
{file = "numpy-2.0.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5a3d94942c331dd4e0e1147f7a8699a4aa47dffc11bf8a1523c12af8b2e91bbe"}, {file = "numpy-2.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f5ebbf9fbdabed208d4ecd2e1dfd2c0741af2f876e7ae522c2537d404ca895c3"},
{file = "numpy-2.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:15eb4eca47d36ec3f78cde0a3a2ee24cf05ca7396ef808dda2c0ddad7c2bde67"}, {file = "numpy-2.1.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:378cb4f24c7d93066ee4103204f73ed046eb88f9ad5bb2275bb9fa0f6a02bd36"},
{file = "numpy-2.0.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:b83e16a5511d1b1f8a88cbabb1a6f6a499f82c062a4251892d9ad5d609863fb7"}, {file = "numpy-2.1.0-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:d8f699a709120b220dfe173f79c73cb2a2cab2c0b88dd59d7b49407d032b8ebd"},
{file = "numpy-2.0.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:1f87fec1f9bc1efd23f4227becff04bd0e979e23ca50cc92ec88b38489db3b55"}, {file = "numpy-2.1.0-cp311-cp311-win32.whl", hash = "sha256:ffbd6faeb190aaf2b5e9024bac9622d2ee549b7ec89ef3a9373fa35313d44e0e"},
{file = "numpy-2.0.1-cp311-cp311-win32.whl", hash = "sha256:36d3a9405fd7c511804dc56fc32974fa5533bdeb3cd1604d6b8ff1d292b819c4"}, {file = "numpy-2.1.0-cp311-cp311-win_amd64.whl", hash = "sha256:0af3a5987f59d9c529c022c8c2a64805b339b7ef506509fba7d0556649b9714b"},
{file = "numpy-2.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:08458fbf403bff5e2b45f08eda195d4b0c9b35682311da5a5a0a0925b11b9bd8"}, {file = "numpy-2.1.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:fe76d75b345dc045acdbc006adcb197cc680754afd6c259de60d358d60c93736"},
{file = "numpy-2.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:6bf4e6f4a2a2e26655717a1983ef6324f2664d7011f6ef7482e8c0b3d51e82ac"}, {file = "numpy-2.1.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:f358ea9e47eb3c2d6eba121ab512dfff38a88db719c38d1e67349af210bc7529"},
{file = "numpy-2.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:7d6fddc5fe258d3328cd8e3d7d3e02234c5d70e01ebe377a6ab92adb14039cb4"}, {file = "numpy-2.1.0-cp312-cp312-macosx_14_0_arm64.whl", hash = "sha256:dd94ce596bda40a9618324547cfaaf6650b1a24f5390350142499aa4e34e53d1"},
{file = "numpy-2.0.1-cp312-cp312-macosx_14_0_arm64.whl", hash = "sha256:5daab361be6ddeb299a918a7c0864fa8618af66019138263247af405018b04e1"}, {file = "numpy-2.1.0-cp312-cp312-macosx_14_0_x86_64.whl", hash = "sha256:b47c551c6724960479cefd7353656498b86e7232429e3a41ab83be4da1b109e8"},
{file = "numpy-2.0.1-cp312-cp312-macosx_14_0_x86_64.whl", hash = "sha256:ea2326a4dca88e4a274ba3a4405eb6c6467d3ffbd8c7d38632502eaae3820587"}, {file = "numpy-2.1.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0756a179afa766ad7cb6f036de622e8a8f16ffdd55aa31f296c870b5679d745"},
{file = "numpy-2.0.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:529af13c5f4b7a932fb0e1911d3a75da204eff023ee5e0e79c1751564221a5c8"}, {file = "numpy-2.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:24003ba8ff22ea29a8c306e61d316ac74111cebf942afbf692df65509a05f111"},
{file = "numpy-2.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6790654cb13eab303d8402354fabd47472b24635700f631f041bd0b65e37298a"}, {file = "numpy-2.1.0-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:b34fa5e3b5d6dc7e0a4243fa0f81367027cb6f4a7215a17852979634b5544ee0"},
{file = "numpy-2.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:cbab9fc9c391700e3e1287666dfd82d8666d10e69a6c4a09ab97574c0b7ee0a7"}, {file = "numpy-2.1.0-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:c4f982715e65036c34897eb598d64aef15150c447be2cfc6643ec7a11af06574"},
{file = "numpy-2.0.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:99d0d92a5e3613c33a5f01db206a33f8fdf3d71f2912b0de1739894668b7a93b"}, {file = "numpy-2.1.0-cp312-cp312-win32.whl", hash = "sha256:c4cd94dfefbefec3f8b544f61286584292d740e6e9d4677769bc76b8f41deb02"},
{file = "numpy-2.0.1-cp312-cp312-win32.whl", hash = "sha256:173a00b9995f73b79eb0191129f2455f1e34c203f559dd118636858cc452a1bf"}, {file = "numpy-2.1.0-cp312-cp312-win_amd64.whl", hash = "sha256:a0cdef204199278f5c461a0bed6ed2e052998276e6d8ab2963d5b5c39a0500bc"},
{file = "numpy-2.0.1-cp312-cp312-win_amd64.whl", hash = "sha256:bb2124fdc6e62baae159ebcfa368708867eb56806804d005860b6007388df171"}, {file = "numpy-2.1.0-pp310-pypy310_pp73-macosx_10_15_x86_64.whl", hash = "sha256:15ef8b2177eeb7e37dd5ef4016f30b7659c57c2c0b57a779f1d537ff33a72c7b"},
{file = "numpy-2.0.1.tar.gz", hash = "sha256:485b87235796410c3519a699cfe1faab097e509e90ebb05dcd098db2ae87e7b3"}, {file = "numpy-2.1.0-pp310-pypy310_pp73-macosx_14_0_x86_64.whl", hash = "sha256:e5f0642cdf4636198a4990de7a71b693d824c56a757862230454629cf62e323d"},
{file = "numpy-2.1.0-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f15976718c004466406342789f31b6673776360f3b1e3c575f25302d7e789575"},
{file = "numpy-2.1.0-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:6c1de77ded79fef664d5098a66810d4d27ca0224e9051906e634b3f7ead134c2"},
{file = "numpy-2.1.0.tar.gz", hash = "sha256:7dc90da0081f7e1da49ec4e398ede6a8e9cc4f5ebe5f9e06b443ed889ee9aaa2"},
] ]
[[package]] [[package]]
@ -1349,13 +1352,13 @@ files = [
[[package]] [[package]]
name = "pyparsing" name = "pyparsing"
version = "3.1.2" version = "3.1.4"
requires_python = ">=3.6.8" requires_python = ">=3.6.8"
summary = "pyparsing module - Classes and methods to define and execute parsing grammars" summary = "pyparsing module - Classes and methods to define and execute parsing grammars"
groups = ["default"] groups = ["default"]
files = [ files = [
{file = "pyparsing-3.1.2-py3-none-any.whl", hash = "sha256:f9db75911801ed778fe61bb643079ff86601aca99fcae6345aa67292038fb742"}, {file = "pyparsing-3.1.4-py3-none-any.whl", hash = "sha256:a6a7ee4235a3f944aa1fa2249307708f893fe5717dc603503c6c7969c070fb7c"},
{file = "pyparsing-3.1.2.tar.gz", hash = "sha256:a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad"}, {file = "pyparsing-3.1.4.tar.gz", hash = "sha256:f86ec8d1a83f11977c9a6ea7598e8c27fc5cddfa5b07ea2241edbbde1d7bc032"},
] ]
[[package]] [[package]]
@ -1679,7 +1682,7 @@ files = [
[[package]] [[package]]
name = "rich" name = "rich"
version = "13.7.1" version = "13.8.0"
requires_python = ">=3.7.0" requires_python = ">=3.7.0"
summary = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" summary = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
groups = ["default"] groups = ["default"]
@ -1689,8 +1692,8 @@ dependencies = [
"typing-extensions<5.0,>=4.0.0; python_version < \"3.9\"", "typing-extensions<5.0,>=4.0.0; python_version < \"3.9\"",
] ]
files = [ files = [
{file = "rich-13.7.1-py3-none-any.whl", hash = "sha256:4edbae314f59eb482f54e9e30bf00d33350aaa94f4bfcd4e9e3110e64d0d7222"}, {file = "rich-13.8.0-py3-none-any.whl", hash = "sha256:2e85306a063b9492dffc86278197a60cbece75bcb766022f3436f567cae11bdc"},
{file = "rich-13.7.1.tar.gz", hash = "sha256:9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432"}, {file = "rich-13.8.0.tar.gz", hash = "sha256:a5ac1f1cd448ade0d59cc3356f7db7a7ccda2c8cbae9c7a90c28ff463d3e91f4"},
] ]
[[package]] [[package]]
@ -1805,40 +1808,40 @@ files = [
[[package]] [[package]]
name = "ruff" name = "ruff"
version = "0.6.0" version = "0.6.2"
requires_python = ">=3.7" requires_python = ">=3.7"
summary = "An extremely fast Python linter and code formatter, written in Rust." summary = "An extremely fast Python linter and code formatter, written in Rust."
groups = ["dev"] groups = ["dev"]
files = [ files = [
{file = "ruff-0.6.0-py3-none-linux_armv6l.whl", hash = "sha256:92dcce923e5df265781e5fc76f9a1edad52201a7aafe56e586b90988d5239013"}, {file = "ruff-0.6.2-py3-none-linux_armv6l.whl", hash = "sha256:5c8cbc6252deb3ea840ad6a20b0f8583caab0c5ef4f9cca21adc5a92b8f79f3c"},
{file = "ruff-0.6.0-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:31b90ff9dc79ed476c04e957ba7e2b95c3fceb76148f2079d0d68a908d2cfae7"}, {file = "ruff-0.6.2-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:17002fe241e76544448a8e1e6118abecbe8cd10cf68fde635dad480dba594570"},
{file = "ruff-0.6.0-py3-none-macosx_11_0_arm64.whl", hash = "sha256:6d834a9ec9f8287dd6c3297058b3a265ed6b59233db22593379ee38ebc4b9768"}, {file = "ruff-0.6.2-py3-none-macosx_11_0_arm64.whl", hash = "sha256:3dbeac76ed13456f8158b8f4fe087bf87882e645c8e8b606dd17b0b66c2c1158"},
{file = "ruff-0.6.0-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f2089267692696aba342179471831a085043f218706e642564812145df8b8d0d"}, {file = "ruff-0.6.2-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:094600ee88cda325988d3f54e3588c46de5c18dae09d683ace278b11f9d4d534"},
{file = "ruff-0.6.0-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:aa62b423ee4bbd8765f2c1dbe8f6aac203e0583993a91453dc0a449d465c84da"}, {file = "ruff-0.6.2-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:316d418fe258c036ba05fbf7dfc1f7d3d4096db63431546163b472285668132b"},
{file = "ruff-0.6.0-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7344e1a964b16b1137ea361d6516ce4ee61a0403fa94252a1913ecc1311adcae"}, {file = "ruff-0.6.2-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:d72b8b3abf8a2d51b7b9944a41307d2f442558ccb3859bbd87e6ae9be1694a5d"},
{file = "ruff-0.6.0-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:487f3a35c3f33bf82be212ce15dc6278ea854e35573a3f809442f73bec8b2760"}, {file = "ruff-0.6.2-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:2aed7e243be68487aa8982e91c6e260982d00da3f38955873aecd5a9204b1d66"},
{file = "ruff-0.6.0-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:75db409984077a793cf344d499165298a6f65449e905747ac65983b12e3e64b1"}, {file = "ruff-0.6.2-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:d371f7fc9cec83497fe7cf5eaf5b76e22a8efce463de5f775a1826197feb9df8"},
{file = "ruff-0.6.0-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:84908bd603533ecf1db456d8fc2665d1f4335d722e84bc871d3bbd2d1116c272"}, {file = "ruff-0.6.2-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:a8f310d63af08f583363dfb844ba8f9417b558199c58a5999215082036d795a1"},
{file = "ruff-0.6.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0f1749a0aef3ec41ed91a0e2127a6ae97d2e2853af16dbd4f3c00d7a3af726c5"}, {file = "ruff-0.6.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7db6880c53c56addb8638fe444818183385ec85eeada1d48fc5abe045301b2f1"},
{file = "ruff-0.6.0-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:016fea751e2bcfbbd2f8cb19b97b37b3fd33148e4df45b526e87096f4e17354f"}, {file = "ruff-0.6.2-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:1175d39faadd9a50718f478d23bfc1d4da5743f1ab56af81a2b6caf0a2394f23"},
{file = "ruff-0.6.0-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:6ae80f141b53b2e36e230017e64f5ea2def18fac14334ffceaae1b780d70c4f7"}, {file = "ruff-0.6.2-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:5b939f9c86d51635fe486585389f54582f0d65b8238e08c327c1534844b3bb9a"},
{file = "ruff-0.6.0-py3-none-musllinux_1_2_i686.whl", hash = "sha256:eaaaf33ea4b3f63fd264d6a6f4a73fa224bbfda4b438ffea59a5340f4afa2bb5"}, {file = "ruff-0.6.2-py3-none-musllinux_1_2_i686.whl", hash = "sha256:d0d62ca91219f906caf9b187dea50d17353f15ec9bb15aae4a606cd697b49b4c"},
{file = "ruff-0.6.0-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:7667ddd1fc688150a7ca4137140867584c63309695a30016880caf20831503a0"}, {file = "ruff-0.6.2-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:7438a7288f9d67ed3c8ce4d059e67f7ed65e9fe3aa2ab6f5b4b3610e57e3cb56"},
{file = "ruff-0.6.0-py3-none-win32.whl", hash = "sha256:ae48365aae60d40865a412356f8c6f2c0be1c928591168111eaf07eaefa6bea3"}, {file = "ruff-0.6.2-py3-none-win32.whl", hash = "sha256:279d5f7d86696df5f9549b56b9b6a7f6c72961b619022b5b7999b15db392a4da"},
{file = "ruff-0.6.0-py3-none-win_amd64.whl", hash = "sha256:774032b507c96f0c803c8237ce7d2ef3934df208a09c40fa809c2931f957fe5e"}, {file = "ruff-0.6.2-py3-none-win_amd64.whl", hash = "sha256:d9f3469c7dd43cd22eb1c3fc16926fb8258d50cb1b216658a07be95dd117b0f2"},
{file = "ruff-0.6.0-py3-none-win_arm64.whl", hash = "sha256:a5366e8c3ae6b2dc32821749b532606c42e609a99b0ae1472cf601da931a048c"}, {file = "ruff-0.6.2-py3-none-win_arm64.whl", hash = "sha256:f28fcd2cd0e02bdf739297516d5643a945cc7caf09bd9bcb4d932540a5ea4fa9"},
{file = "ruff-0.6.0.tar.gz", hash = "sha256:272a81830f68f9bd19d49eaf7fa01a5545c5a2e86f32a9935bb0e4bb9a1db5b8"}, {file = "ruff-0.6.2.tar.gz", hash = "sha256:239ee6beb9e91feb8e0ec384204a763f36cb53fb895a1a364618c6abb076b3be"},
] ]
[[package]] [[package]]
name = "setuptools" name = "setuptools"
version = "72.2.0" version = "74.0.0"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Easily download, build, install, upgrade, and uninstall Python packages" summary = "Easily download, build, install, upgrade, and uninstall Python packages"
groups = ["plot"] groups = ["plot"]
files = [ files = [
{file = "setuptools-72.2.0-py3-none-any.whl", hash = "sha256:f11dd94b7bae3a156a95ec151f24e4637fb4fa19c878e4d191bfb8b2d82728c4"}, {file = "setuptools-74.0.0-py3-none-any.whl", hash = "sha256:0274581a0037b638b9fc1c6883cc71c0210865aaa76073f7882376b641b84e8f"},
{file = "setuptools-72.2.0.tar.gz", hash = "sha256:80aacbf633704e9c8bfa1d99fa5dd4dc59573efcf9e4042c13d3bcef91ac2ef9"}, {file = "setuptools-74.0.0.tar.gz", hash = "sha256:a85e96b8be2b906f3e3e789adec6a9323abf79758ecfa3065bd740d81158b11e"},
] ]
[[package]] [[package]]
@ -1995,13 +1998,13 @@ files = [
[[package]] [[package]]
name = "types-python-dateutil" name = "types-python-dateutil"
version = "2.9.0.20240316" version = "2.9.0.20240821"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Typing stubs for python-dateutil" summary = "Typing stubs for python-dateutil"
groups = ["default"] groups = ["default"]
files = [ files = [
{file = "types-python-dateutil-2.9.0.20240316.tar.gz", hash = "sha256:5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202"}, {file = "types-python-dateutil-2.9.0.20240821.tar.gz", hash = "sha256:9649d1dcb6fef1046fb18bebe9ea2aa0028b160918518c34589a46045f6ebd98"},
{file = "types_python_dateutil-2.9.0.20240316-py3-none-any.whl", hash = "sha256:6b8cb66d960771ce5ff974e9dd45e38facb81718cc1e208b10b1baccbfdbee3b"}, {file = "types_python_dateutil-2.9.0.20240821-py3-none-any.whl", hash = "sha256:f5889fcb4e63ed4aaa379b44f93c32593d50b9a94c9a60a0c854d8cc3511cd57"},
] ]
[[package]] [[package]]
@ -2064,33 +2067,33 @@ files = [
[[package]] [[package]]
name = "watchdog" name = "watchdog"
version = "4.0.2" version = "5.0.0"
requires_python = ">=3.8" requires_python = ">=3.9"
summary = "Filesystem events monitoring" summary = "Filesystem events monitoring"
groups = ["default"] groups = ["default"]
files = [ files = [
{file = "watchdog-4.0.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ede7f010f2239b97cc79e6cb3c249e72962404ae3865860855d5cbe708b0fd22"}, {file = "watchdog-5.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:bf3216ec994eabb2212df9861f19056ca0d4cd3516d56cb95801933876519bfe"},
{file = "watchdog-4.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a2cffa171445b0efa0726c561eca9a27d00a1f2b83846dbd5a4f639c4f8ca8e1"}, {file = "watchdog-5.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:cb59ad83a1700304fc1ac7bc53ae9e5cbe9d60a52ed9bba8e2e2d782a201bb2b"},
{file = "watchdog-4.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c50f148b31b03fbadd6d0b5980e38b558046b127dc483e5e4505fcef250f9503"}, {file = "watchdog-5.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1228cb097e855d1798b550be8f0e9f0cfbac4384f9a3e91f66d250d03e11294e"},
{file = "watchdog-4.0.2-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:7c7d4bf585ad501c5f6c980e7be9c4f15604c7cc150e942d82083b31a7548930"}, {file = "watchdog-5.0.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:3c177085c3d210d1c73cb4569442bdaef706ebebc423bd7aed9e90fc12b2e553"},
{file = "watchdog-4.0.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:914285126ad0b6eb2258bbbcb7b288d9dfd655ae88fa28945be05a7b475a800b"}, {file = "watchdog-5.0.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:01ab36cddc836a0f202c66267daaef92ba5c17c7d6436deff0587bb61234c5c9"},
{file = "watchdog-4.0.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:984306dc4720da5498b16fc037b36ac443816125a3705dfde4fd90652d8028ef"}, {file = "watchdog-5.0.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:0834c21efa3e767849b09e667274604c7cdfe30b49eb95d794565c53f4db3c1e"},
{file = "watchdog-4.0.2-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:1cdcfd8142f604630deef34722d695fb455d04ab7cfe9963055df1fc69e6727a"}, {file = "watchdog-5.0.0-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:1e26f570dd7f5178656affb24d6f0e22ce66c8daf88d4061a27bfb9ac866b40d"},
{file = "watchdog-4.0.2-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:d7ab624ff2f663f98cd03c8b7eedc09375a911794dfea6bf2a359fcc266bff29"}, {file = "watchdog-5.0.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:d146331e6b206baa9f6dd40f72b5783ad2302c240df68e7fce196d30588ccf7b"},
{file = "watchdog-4.0.2-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:132937547a716027bd5714383dfc40dc66c26769f1ce8a72a859d6a48f371f3a"}, {file = "watchdog-5.0.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:6c96b1706430839872a3e33b9370ee3f7a0079f6b828129d88498ad1f96a0f45"},
{file = "watchdog-4.0.2-pp310-pypy310_pp73-macosx_10_15_x86_64.whl", hash = "sha256:10b6683df70d340ac3279eff0b2766813f00f35a1d37515d2c99959ada8f05fa"}, {file = "watchdog-5.0.0-pp310-pypy310_pp73-macosx_10_15_x86_64.whl", hash = "sha256:bc16d448a74a929b896ed9578c25756b2125400b19b3258be8d9a681c7ae8e71"},
{file = "watchdog-4.0.2-pp310-pypy310_pp73-macosx_11_0_arm64.whl", hash = "sha256:f7c739888c20f99824f7aa9d31ac8a97353e22d0c0e54703a547a218f6637eb3"}, {file = "watchdog-5.0.0-pp310-pypy310_pp73-macosx_11_0_arm64.whl", hash = "sha256:7e6b0e9b8a9dc3865d65888b5f5222da4ba9c4e09eab13cff5e305e7b7e7248f"},
{file = "watchdog-4.0.2-py3-none-manylinux2014_aarch64.whl", hash = "sha256:936acba76d636f70db8f3c66e76aa6cb5136a936fc2a5088b9ce1c7a3508fc83"}, {file = "watchdog-5.0.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:d76efab5248aafbf8a2c2a63cd7b9545e6b346ad1397af8b862a3bb3140787d8"},
{file = "watchdog-4.0.2-py3-none-manylinux2014_armv7l.whl", hash = "sha256:e252f8ca942a870f38cf785aef420285431311652d871409a64e2a0a52a2174c"}, {file = "watchdog-5.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:ff4e957c45c446de34c513eadce01d0b65da7eee47c01dce472dd136124552c9"},
{file = "watchdog-4.0.2-py3-none-manylinux2014_i686.whl", hash = "sha256:0e83619a2d5d436a7e58a1aea957a3c1ccbf9782c43c0b4fed80580e5e4acd1a"}, {file = "watchdog-5.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:16c1aa3377bb1f82c5e24277fcbf4e2cac3c4ce46aaaf7212d53caa9076eb7b7"},
{file = "watchdog-4.0.2-py3-none-manylinux2014_ppc64.whl", hash = "sha256:88456d65f207b39f1981bf772e473799fcdc10801062c36fd5ad9f9d1d463a73"}, {file = "watchdog-5.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:22fcad6168fc43cf0e709bd854be5b8edbb0b260f0a6f28f1ea9baa53c6907f7"},
{file = "watchdog-4.0.2-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:32be97f3b75693a93c683787a87a0dc8db98bb84701539954eef991fb35f5fbc"}, {file = "watchdog-5.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:0120b2fa65732797ffa65fa8ee5540c288aa861d91447df298626d6385a24658"},
{file = "watchdog-4.0.2-py3-none-manylinux2014_s390x.whl", hash = "sha256:c82253cfc9be68e3e49282831afad2c1f6593af80c0daf1287f6a92657986757"}, {file = "watchdog-5.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:2aa59fab7ff75281778c649557275ca3085eccbdf825a0e2a5ca3810e977afe5"},
{file = "watchdog-4.0.2-py3-none-manylinux2014_x86_64.whl", hash = "sha256:c0b14488bd336c5b1845cee83d3e631a1f8b4e9c5091ec539406e4a324f882d8"}, {file = "watchdog-5.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:78db0fe0336958fc0e1269545c980b6f33d04d184ba191b2800a8b71d3e971a9"},
{file = "watchdog-4.0.2-py3-none-win32.whl", hash = "sha256:0d8a7e523ef03757a5aa29f591437d64d0d894635f8a50f370fe37f913ce4e19"}, {file = "watchdog-5.0.0-py3-none-win32.whl", hash = "sha256:d1acef802916083f2ad7988efc7decf07e46e266916c0a09d8fb9d387288ea12"},
{file = "watchdog-4.0.2-py3-none-win_amd64.whl", hash = "sha256:c344453ef3bf875a535b0488e3ad28e341adbd5a9ffb0f7d62cefacc8824ef2b"}, {file = "watchdog-5.0.0-py3-none-win_amd64.whl", hash = "sha256:3c2d50fdb86aa6df3973313272f5a17eb26eab29ff5a0bf54b6d34597b4dc4e4"},
{file = "watchdog-4.0.2-py3-none-win_ia64.whl", hash = "sha256:baececaa8edff42cd16558a639a9b0ddf425f93d892e8392a56bf904f5eff22c"}, {file = "watchdog-5.0.0-py3-none-win_ia64.whl", hash = "sha256:1d17ec7e022c34fa7ddc72aa41bf28c9d1207ffb193df18ba4f6fde453725b3c"},
{file = "watchdog-4.0.2.tar.gz", hash = "sha256:b4dfbb6c49221be4535623ea4474a4d6ee0a9cef4a80b20c28db4d858b64e270"}, {file = "watchdog-5.0.0.tar.gz", hash = "sha256:990aedb9e2f336b45a70aed9c014450e7c4a70fd99c5f5b1834d57e1453a177e"},
] ]
[[package]] [[package]]
@ -2106,7 +2109,7 @@ files = [
[[package]] [[package]]
name = "werkzeug" name = "werkzeug"
version = "3.0.3" version = "3.0.4"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "The comprehensive WSGI web application library." summary = "The comprehensive WSGI web application library."
groups = ["plot"] groups = ["plot"]
@ -2114,8 +2117,8 @@ dependencies = [
"MarkupSafe>=2.1.1", "MarkupSafe>=2.1.1",
] ]
files = [ files = [
{file = "werkzeug-3.0.3-py3-none-any.whl", hash = "sha256:fc9645dc43e03e4d630d23143a04a7f947a9a3b5727cd535fdfe155a17cc48c8"}, {file = "werkzeug-3.0.4-py3-none-any.whl", hash = "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c"},
{file = "werkzeug-3.0.3.tar.gz", hash = "sha256:097e5bfda9f0aba8da6b8545146def481d06aa7d3266e7448e2cccf67dd8bd18"}, {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"},
] ]
[[package]] [[package]]
@ -2161,11 +2164,11 @@ files = [
[[package]] [[package]]
name = "zipp" name = "zipp"
version = "3.20.0" version = "3.20.1"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Backport of pathlib-compatible object wrapper for zip files" summary = "Backport of pathlib-compatible object wrapper for zip files"
groups = ["plot"] groups = ["plot"]
files = [ files = [
{file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"}, {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"},
{file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"}, {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"},
] ]

1
nwb_linkml/pyproject.toml
View file

@ -16,6 +16,7 @@ dependencies = [
"rich>=13.5.2", "rich>=13.5.2",
#"linkml>=1.7.10", #"linkml>=1.7.10",
"linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml", "linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml",
"linkml-runtime>=1.8.2",
"pydantic>=2.3.0", "pydantic>=2.3.0",
"h5py>=3.9.0", "h5py>=3.9.0",
"pydantic-settings>=2.0.3", "pydantic-settings>=2.0.3",

16
nwb_linkml/src/nwb_linkml/generators/pydantic.py
View file

@ -15,6 +15,7 @@ from typing import ClassVar, Dict, List, Optional, Tuple
from linkml.generators import PydanticGenerator from linkml.generators import PydanticGenerator
from linkml.generators.pydanticgen.array import ArrayRepresentation, NumpydanticArray from linkml.generators.pydanticgen.array import ArrayRepresentation, NumpydanticArray
from linkml.generators.pydanticgen.build import ClassResult, SlotResult from linkml.generators.pydanticgen.build import ClassResult, SlotResult
from linkml.generators.pydanticgen.pydanticgen import SplitMode
from linkml.generators.pydanticgen.template import Import, Imports, PydanticModule from linkml.generators.pydanticgen.template import Import, Imports, PydanticModule
from linkml_runtime.linkml_model.meta import ( from linkml_runtime.linkml_model.meta import (
ArrayExpression, ArrayExpression,
@ -60,7 +61,7 @@ class NWBPydanticGenerator(PydanticGenerator):
array_representations: List[ArrayRepresentation] = field( array_representations: List[ArrayRepresentation] = field(
default_factory=lambda: [ArrayRepresentation.NUMPYDANTIC] default_factory=lambda: [ArrayRepresentation.NUMPYDANTIC]
) )
black: bool = True black: bool = False
inlined: bool = True inlined: bool = True
emit_metadata: bool = True emit_metadata: bool = True
gen_classvars: bool = True gen_classvars: bool = True
@ -94,6 +95,19 @@ class NWBPydanticGenerator(PydanticGenerator):
if not base_range_subsumes_any_of: if not base_range_subsumes_any_of:
raise ValueError("Slot cannot have both range and any_of defined") raise ValueError("Slot cannot have both range and any_of defined")
def render(self) -> PydanticModule:
"""
Override of super's render method to switch the split_mode before generation depending
on whether it's a namespace schema or not
"""
is_namespace = False
ns_annotation = self.schemaview.schema.annotations.get("is_namespace", None)
if ns_annotation:
is_namespace = ns_annotation.value
self.split_mode = SplitMode.FULL if is_namespace else SplitMode.AUTO
return super().render()
def before_generate_slot(self, slot: SlotDefinition, sv: SchemaView) -> SlotDefinition: def before_generate_slot(self, slot: SlotDefinition, sv: SchemaView) -> SlotDefinition:
""" """
Force some properties to be optional Force some properties to be optional

140
nwb_linkml/src/nwb_linkml/monkeypatch.py
View file

@ -5,67 +5,6 @@ Monkeypatches to external modules
# ruff: noqa: ANN001 - not well defined types for this module # ruff: noqa: ANN001 - not well defined types for this module
def patch_schemaview() -> None:
"""
Patch schemaview to correctly resolve multiple layers of relative imports.
References:
Returns:
"""
from functools import lru_cache
from typing import List
from linkml_runtime.linkml_model import SchemaDefinitionName
from linkml_runtime.utils.schemaview import SchemaView
@lru_cache
def imports_closure(
self, imports: bool = True, traverse=True, inject_metadata=True
) -> List[SchemaDefinitionName]:
"""
Return all imports
:param traverse: if true, traverse recursively
:return: all schema names in the transitive reflexive imports closure
"""
if not imports:
return [self.schema.name]
if self.schema_map is None:
self.schema_map = {self.schema.name: self.schema}
closure = []
visited = set()
todo = [self.schema.name]
if not traverse:
return todo
while len(todo) > 0:
sn = todo.pop()
visited.add(sn)
if sn not in self.schema_map:
imported_schema = self.load_import(sn)
self.schema_map[sn] = imported_schema
s = self.schema_map[sn]
if sn not in closure:
closure.append(sn)
for i in s.imports:
if sn.startswith(".") and ":" not in i:
# prepend the relative part
i = "/".join(sn.split("/")[:-1]) + "/" + i
if i not in visited:
todo.append(i)
if inject_metadata:
for s in self.schema_map.values():
for x in {**s.classes, **s.enums, **s.slots, **s.subsets, **s.types}.values():
x.from_schema = s.id
for c in s.classes.values():
for a in c.attributes.values():
a.from_schema = s.id
return closure
SchemaView.imports_closure = imports_closure
def patch_array_expression() -> None: def patch_array_expression() -> None:
""" """
Allow SlotDefinitions to use `any_of` with `array` Allow SlotDefinitions to use `any_of` with `array`
@ -75,7 +14,7 @@ def patch_array_expression() -> None:
from dataclasses import field, make_dataclass from dataclasses import field, make_dataclass
from typing import Optional from typing import Optional
from linkml_runtime.linkml_model import meta from linkml_runtime.linkml_model import meta, types
new_dataclass = make_dataclass( new_dataclass = make_dataclass(
"AnonymousSlotExpression", "AnonymousSlotExpression",
@ -83,84 +22,9 @@ def patch_array_expression() -> None:
bases=(meta.AnonymousSlotExpression,), bases=(meta.AnonymousSlotExpression,),
) )
meta.AnonymousSlotExpression = new_dataclass meta.AnonymousSlotExpression = new_dataclass
types.AnonymousSlotExpression = new_dataclass
def patch_pretty_print() -> None:
"""
Fix the godforsaken linkml dataclass reprs
See: https://github.com/linkml/linkml-runtime/pull/314
"""
import re
import textwrap
from dataclasses import field, is_dataclass, make_dataclass
from pprint import pformat
from typing import Any
from linkml_runtime.linkml_model import meta
from linkml_runtime.utils.formatutils import items
def _pformat(fields: dict, cls_name: str, indent: str = " ") -> str:
"""
pretty format the fields of the items of a ``YAMLRoot`` object without the wonky
indentation of pformat.
see ``YAMLRoot.__repr__``.
formatting is similar to black - items at similar levels of nesting have similar levels
of indentation,
rather than getting placed at essentially random levels of indentation depending on what
came before them.
"""
res = []
total_len = 0
for key, val in fields:
if val == [] or val == {} or val is None:
continue
# pformat handles everything else that isn't a YAMLRoot object,
# but it sure does look ugly
# use it to split lines and as the thing of last resort, but otherwise indent = 0,
# we'll do that
val_str = pformat(val, indent=0, compact=True, sort_dicts=False)
# now we indent everything except the first line by indenting
# and then using regex to remove just the first indent
val_str = re.sub(rf"\A{re.escape(indent)}", "", textwrap.indent(val_str, indent))
# now recombine with the key in a format that can be re-eval'd
# into an object if indent is just whitespace
val_str = f"'{key}': " + val_str
# count the total length of this string so we know if we need to linebreak or not later
total_len += len(val_str)
res.append(val_str)
if total_len > 80:
inside = ",\n".join(res)
# we indent twice - once for the inner contents of every inner object, and one to
# offset from the root element.
# that keeps us from needing to be recursive except for the
# single pformat call
inside = textwrap.indent(inside, indent)
return cls_name + "({\n" + inside + "\n})"
else:
return cls_name + "({" + ", ".join(res) + "})"
def __repr__(self) -> str:
return _pformat(items(self), self.__class__.__name__)
for cls_name in dir(meta):
cls = getattr(meta, cls_name)
if is_dataclass(cls):
new_dataclass = make_dataclass(
cls.__name__,
fields=[("__dummy__", Any, field(default=None))],
bases=(cls,),
repr=False,
)
new_dataclass.__repr__ = __repr__
new_dataclass.__str__ = __repr__
setattr(meta, cls.__name__, new_dataclass)
def apply_patches() -> None: def apply_patches() -> None:
"""Apply all monkeypatches""" """Apply all monkeypatches"""
patch_schemaview()
patch_array_expression() patch_array_expression()
patch_pretty_print()

111
nwb_linkml/src/nwb_linkml/providers/pydantic.py
View file

@ -3,22 +3,25 @@ Provider for pydantic models.
""" """
import importlib import importlib
import multiprocessing as mp
import re import re
import sys import sys
from importlib.abc import MetaPathFinder from importlib.abc import MetaPathFinder
from importlib.machinery import ModuleSpec from importlib.machinery import ModuleSpec
from pathlib import Path from pathlib import Path
from types import ModuleType from types import ModuleType
from typing import List, Optional, Type from typing import TYPE_CHECKING, List, Optional, Type
from linkml.generators.pydanticgen.pydanticgen import SplitMode, _ensure_inits, _import_to_path from linkml.generators.pydanticgen.pydanticgen import SplitMode, _ensure_inits, _import_to_path
from linkml_runtime.linkml_model.meta import SchemaDefinition
from pydantic import BaseModel from pydantic import BaseModel
from nwb_linkml.generators.pydantic import NWBPydanticGenerator from nwb_linkml.generators.pydantic import NWBPydanticGenerator
from nwb_linkml.maps.naming import module_case, version_module_case from nwb_linkml.maps.naming import module_case, version_module_case
from nwb_linkml.providers import LinkMLProvider, Provider from nwb_linkml.providers import LinkMLProvider, Provider
if TYPE_CHECKING:
from linkml_runtime.linkml_model.meta import SchemaDefinition
class PydanticProvider(Provider): class PydanticProvider(Provider):
""" """
@ -65,6 +68,7 @@ class PydanticProvider(Provider):
split: bool = True, split: bool = True,
dump: bool = True, dump: bool = True,
force: bool = False, force: bool = False,
parallel: bool = False,
**kwargs: dict, **kwargs: dict,
) -> str | List[str]: ) -> str | List[str]:
""" """
@ -88,6 +92,8 @@ class PydanticProvider(Provider):
otherwise just return the serialized string of built pydantic model otherwise just return the serialized string of built pydantic model
force (bool): If ``False`` (default), don't build the model if it already exists, force (bool): If ``False`` (default), don't build the model if it already exists,
if ``True`` , delete and rebuild any model if ``True`` , delete and rebuild any model
parallel (bool): If ``True``, build imported models using multiprocessing,
if ``False`` (default), don't.
**kwargs: Passed to :class:`.NWBPydanticGenerator` **kwargs: Passed to :class:`.NWBPydanticGenerator`
Returns: Returns:
@ -136,7 +142,9 @@ class PydanticProvider(Provider):
return serialized return serialized
def _build_split(self, path: Path, dump: bool, force: bool, **kwargs) -> List[str]: def _build_split(
self, path: Path, dump: bool, force: bool, parallel: bool = False, **kwargs
) -> List[str]:
# FIXME: This is messy as all fuck, we're just getting it to work again # FIXME: This is messy as all fuck, we're just getting it to work again
# so we can start iterating on the models themselves # so we can start iterating on the models themselves
res = [] res = []
@ -174,48 +182,81 @@ class PydanticProvider(Provider):
imported_schema: dict[str, SchemaDefinition] = { imported_schema: dict[str, SchemaDefinition] = {
gen.generate_module_import(sch): sch for sch in gen.schemaview.schema_map.values() gen.generate_module_import(sch): sch for sch in gen.schemaview.schema_map.values()
} }
for generated_import in [i for i in rendered.python_imports if i.schema]: generated_imports = [i for i in rendered.python_imports if i.is_schema]
import_file = (ns_file.parent / _import_to_path(generated_import.module)).resolve() # each task has an expected output file a corresponding SchemaDefinition
import_paths = [
(ns_file.parent / _import_to_path(an_import.module)).resolve()
for an_import in generated_imports
]
import_schemas = [
Path(path).parent / imported_schema[an_import.module].source_file
for an_import in generated_imports
]
if not import_file.exists() or force: tasks = [
import_file.parent.mkdir(exist_ok=True, parents=True) (
schema = imported_schema[generated_import.module] import_path,
is_namespace = False import_schema,
ns_annotation = schema.annotations.get("is_namespace", None) force,
if ns_annotation: self.SPLIT_PATTERN,
is_namespace = ns_annotation.value dump,
)
for import_path, import_schema in zip(import_paths, import_schemas)
]
# fix schema source to absolute path so schemaview can find imports if parallel:
schema.source_file = ( with mp.Pool(min(mp.cpu_count(), len(tasks))) as pool:
Path(gen.schemaview.schema.source_file).parent / schema.source_file mp_results = [pool.apply_async(self._generate_single, t) for t in tasks]
).resolve() for result in mp_results:
res.append(result.get()) # noqa: PERF401 - false positive
import_gen = NWBPydanticGenerator( else:
schema, for task in tasks:
split=True, res.append(self._generate_single(*task)) # noqa: PERF401 - false positive
split_pattern=self.SPLIT_PATTERN,
split_mode=SplitMode.FULL if is_namespace else SplitMode.AUTO,
)
serialized = import_gen.serialize()
if dump:
with open(import_file, "w") as ofile:
ofile.write(serialized)
module_paths.append(import_file)
else:
with open(import_file) as ofile:
serialized = ofile.read()
res.append(serialized)
# make __init__.py files if we generated any files # make __init__.py files if we generated any files
if len(module_paths) > 0: if len(module_paths) > 0:
_ensure_inits(module_paths) _ensure_inits(import_paths)
# then extra_inits that usually aren't generated bc we're one layer deeper # then extra_inits that usually aren't generated bc we're one layer deeper
self._make_inits(ns_file) self._make_inits(ns_file)
return res return res
@staticmethod
def _generate_single(
import_file: Path,
# schema: "SchemaDefinition",
schema: Path,
force: bool,
split_pattern: str,
dump: bool,
) -> str:
"""
Interior generator method for _build_split to be called in parallel
.. TODO::
split up and consolidate this build behavior, very spaghetti.
"""
if not import_file.exists() or force:
import_file.parent.mkdir(exist_ok=True, parents=True)
import_gen = NWBPydanticGenerator(
schema,
split=True,
split_pattern=split_pattern,
)
serialized = import_gen.serialize()
if dump:
with open(import_file, "w") as ofile:
ofile.write(serialized)
else:
with open(import_file) as ofile:
serialized = ofile.read()
return serialized
def _make_inits(self, out_file: Path) -> None: def _make_inits(self, out_file: Path) -> None:
""" """
Make __init__.py files for the directory a model is output to and its immediate parent. Make __init__.py files for the directory a model is output to and its immediate parent.

1
nwb_models/src/nwb_models/models/pydantic/__init__.py generated
View file

@ -0,0 +1 @@
from .pydantic.core.v2_7_0.namespace import *

1
nwb_models/src/nwb_models/models/pydantic/core/__init__.py generated
View file

@ -0,0 +1 @@

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_base.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_0.hdmf_common_table import Data, Container, DynamicTable from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...hdmf_common.v1_1_0.hdmf_common_table import Container, Data, DynamicTable
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

18
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_behavior.py generated
View file

@ -1,20 +1,24 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...core.v2_2_0.core_nwb_misc import IntervalSeries from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_0.core_nwb_base import ( from ...core.v2_2_0.core_nwb_base import (
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
) )
from ...core.v2_2_0.core_nwb_misc import IntervalSeries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_device.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_0.core_nwb_base import NWBContainer from ...core.v2_2_0.core_nwb_base import NWBContainer
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_ecephys.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTableRegion from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_0.core_nwb_device import Device
from ...core.v2_2_0.core_nwb_base import ( from ...core.v2_2_0.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
NWBContainer,
) )
from numpydantic import NDArray, Shape from ...core.v2_2_0.core_nwb_device import Device
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

20
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_epoch.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, VectorIndex, VectorData
from ...core.v2_2_0.core_nwb_base import TimeSeries from ...core.v2_2_0.core_nwb_base import TimeSeries
from numpydantic import NDArray, Shape from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

28
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_file.py generated
View file

@ -1,27 +1,31 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_0.core_nwb_misc import Units from numpydantic import NDArray, Shape
from ...core.v2_2_0.core_nwb_device import Device from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_0.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_0.core_nwb_ophys import ImagingPlane
from ...core.v2_2_0.core_nwb_base import ( from ...core.v2_2_0.core_nwb_base import (
NWBContainer, NWBContainer,
NWBDataInterface, NWBDataInterface,
ProcessingModule, ProcessingModule,
TimeSeries, TimeSeries,
) )
from ...core.v2_2_0.core_nwb_device import Device
from ...core.v2_2_0.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_0.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, VectorData, VectorIndex
from ...core.v2_2_0.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_0.core_nwb_epoch import TimeIntervals from ...core.v2_2_0.core_nwb_epoch import TimeIntervals
from ...core.v2_2_0.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_0.core_nwb_misc import Units
from ...core.v2_2_0.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_0.core_nwb_ophys import ImagingPlane
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

34
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_icephys.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_0.core_nwb_base import ( from numpydantic import NDArray, Shape
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
NWBContainer,
)
from ...core.v2_2_0.core_nwb_device import Device
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, VectorIndex, VectorData from ...core.v2_2_0.core_nwb_base import (
NWBContainer,
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
)
from ...core.v2_2_0.core_nwb_device import Device
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_image.py generated
View file

@ -1,15 +1,19 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_0.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from ...core.v2_2_0.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

24
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_misc.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_0.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_0.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_2_0.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_0.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_0.hdmf_common_table import ( from ...hdmf_common.v1_1_0.hdmf_common_table import (
DynamicTable, DynamicTable,
DynamicTableRegion,
VectorData, VectorData,
VectorIndex, VectorIndex,
DynamicTableRegion,
) )
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"
@ -178,7 +182,7 @@ class AbstractFeatureSeriesData(ConfiguredBaseModel):
json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}}, json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}},
) )
unit: Optional[str] = Field( unit: Optional[str] = Field(
"see 'feature_units'", "see ",
description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""", description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""",
json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}}, json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}},
) )

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_ogen.py generated
View file

@ -1,21 +1,25 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_0.core_nwb_base import ( from ...core.v2_2_0.core_nwb_base import (
NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBContainer,
) )
from ...core.v2_2_0.core_nwb_device import Device from ...core.v2_2_0.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

30
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_ophys.py generated
View file

@ -1,31 +1,35 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_0.core_nwb_image import ImageSeries, ImageSeriesExternalFile from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTableRegion, DynamicTable
from ...core.v2_2_0.core_nwb_device import Device
from numpydantic import NDArray, Shape
from ...core.v2_2_0.core_nwb_base import ( from ...core.v2_2_0.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries,
NWBDataInterface,
NWBContainer,
) )
from ...core.v2_2_0.core_nwb_device import Device
from ...core.v2_2_0.core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_1_0.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

22
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_retinotopy.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_0.core_nwb_image import GrayscaleImage from numpydantic import NDArray, Shape
from ...core.v2_2_0.core_nwb_base import NWBData, NWBDataInterface
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...core.v2_2_0.core_nwb_base import NWBData, NWBDataInterface
from ...core.v2_2_0.core_nwb_image import GrayscaleImage
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

196
nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/namespace.py generated
View file

@ -1,84 +1,78 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_0.hdmf_common_sparse import ( from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
CSRMatrix,
CSRMatrixIndices,
CSRMatrixIndptr,
CSRMatrixData,
)
from ...hdmf_common.v1_1_0.hdmf_common_table import (
Data,
Index,
VectorData,
VectorIndex,
ElementIdentifiers,
DynamicTableRegion,
Container,
DynamicTable,
)
from ...core.v2_2_0.core_nwb_retinotopy import (
RetinotopyMap,
AxisMap,
RetinotopyImage,
ImagingRetinotopy,
ImagingRetinotopyFocalDepthImage,
)
from ...core.v2_2_0.core_nwb_image import (
GrayscaleImage,
RGBImage,
RGBAImage,
ImageSeries,
ImageSeriesExternalFile,
ImageMaskSeries,
OpticalSeries,
IndexSeries,
)
from ...core.v2_2_0.core_nwb_base import ( from ...core.v2_2_0.core_nwb_base import (
NWBData,
Image, Image,
Images,
NWBContainer, NWBContainer,
NWBData,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
TimeSeries, TimeSeries,
TimeSeriesData, TimeSeriesData,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
ProcessingModule,
Images,
) )
from ...core.v2_2_0.core_nwb_ophys import ( from ...core.v2_2_0.core_nwb_behavior import (
TwoPhotonSeries, BehavioralEpochs,
RoiResponseSeries, BehavioralEvents,
DfOverF, BehavioralTimeSeries,
Fluorescence, CompassDirection,
ImageSegmentation, EyeTracking,
ImagingPlane, Position,
ImagingPlaneManifold, PupilTracking,
ImagingPlaneOriginCoords, SpatialSeries,
ImagingPlaneGridSpacing, SpatialSeriesData,
OpticalChannel,
MotionCorrection,
) )
from ...core.v2_2_0.core_nwb_device import Device from ...core.v2_2_0.core_nwb_device import Device
from ...core.v2_2_0.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite from ...core.v2_2_0.core_nwb_ecephys import (
ClusterWaveforms,
Clustering,
ElectricalSeries,
ElectrodeGroup,
ElectrodeGroupPosition,
EventDetection,
EventWaveform,
FeatureExtraction,
FilteredEphys,
LFP,
SpikeEventSeries,
)
from ...core.v2_2_0.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
from ...core.v2_2_0.core_nwb_file import (
ExtracellularEphysElectrodes,
GeneralExtracellularEphys,
GeneralIntracellularEphys,
GeneralSourceScript,
NWBFile,
NWBFileGeneral,
NWBFileIntervals,
NWBFileStimulus,
Subject,
)
from ...core.v2_2_0.core_nwb_icephys import ( from ...core.v2_2_0.core_nwb_icephys import (
PatchClampSeries,
PatchClampSeriesData,
CurrentClampSeries, CurrentClampSeries,
CurrentClampSeriesData, CurrentClampSeriesData,
IZeroClampSeries,
CurrentClampStimulusSeries, CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData, CurrentClampStimulusSeriesData,
IZeroClampSeries,
IntracellularElectrode,
PatchClampSeries,
PatchClampSeriesData,
SweepTable,
VoltageClampSeries, VoltageClampSeries,
VoltageClampSeriesData,
VoltageClampSeriesCapacitanceFast, VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow, VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesData,
VoltageClampSeriesResistanceCompBandwidth, VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection, VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction, VoltageClampSeriesResistanceCompPrediction,
@ -86,56 +80,66 @@ from ...core.v2_2_0.core_nwb_icephys import (
VoltageClampSeriesWholeCellSeriesResistanceComp, VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries, VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData, VoltageClampStimulusSeriesData,
IntracellularElectrode,
SweepTable,
) )
from ...core.v2_2_0.core_nwb_ecephys import ( from ...core.v2_2_0.core_nwb_image import (
ElectricalSeries, GrayscaleImage,
SpikeEventSeries, ImageMaskSeries,
FeatureExtraction, ImageSeries,
EventDetection, ImageSeriesExternalFile,
EventWaveform, IndexSeries,
FilteredEphys, OpticalSeries,
LFP, RGBAImage,
ElectrodeGroup, RGBImage,
ElectrodeGroupPosition,
ClusterWaveforms,
Clustering,
)
from ...core.v2_2_0.core_nwb_behavior import (
SpatialSeries,
SpatialSeriesData,
BehavioralEpochs,
BehavioralEvents,
BehavioralTimeSeries,
PupilTracking,
EyeTracking,
CompassDirection,
Position,
) )
from ...core.v2_2_0.core_nwb_misc import ( from ...core.v2_2_0.core_nwb_misc import (
AbstractFeatureSeries, AbstractFeatureSeries,
AbstractFeatureSeriesData, AbstractFeatureSeriesData,
AnnotationSeries, AnnotationSeries,
IntervalSeries,
DecompositionSeries, DecompositionSeries,
DecompositionSeriesData,
DecompositionSeriesBands, DecompositionSeriesBands,
DecompositionSeriesData,
IntervalSeries,
Units, Units,
UnitsSpikeTimes, UnitsSpikeTimes,
) )
from ...core.v2_2_0.core_nwb_file import ( from ...core.v2_2_0.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
NWBFile, from ...core.v2_2_0.core_nwb_ophys import (
NWBFileStimulus, DfOverF,
NWBFileGeneral, Fluorescence,
GeneralSourceScript, ImageSegmentation,
Subject, ImagingPlane,
GeneralExtracellularEphys, ImagingPlaneGridSpacing,
ExtracellularEphysElectrodes, ImagingPlaneManifold,
GeneralIntracellularEphys, ImagingPlaneOriginCoords,
NWBFileIntervals, MotionCorrection,
OpticalChannel,
RoiResponseSeries,
TwoPhotonSeries,
) )
from ...core.v2_2_0.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries from ...core.v2_2_0.core_nwb_retinotopy import (
AxisMap,
ImagingRetinotopy,
ImagingRetinotopyFocalDepthImage,
RetinotopyImage,
RetinotopyMap,
)
from ...hdmf_common.v1_1_0.hdmf_common_sparse import (
CSRMatrix,
CSRMatrixData,
CSRMatrixIndices,
CSRMatrixIndptr,
)
from ...hdmf_common.v1_1_0.hdmf_common_table import (
Container,
Data,
DynamicTable,
DynamicTableRegion,
ElementIdentifiers,
Index,
VectorData,
VectorIndex,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.2.0" version = "2.2.0"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_base.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_2.hdmf_common_table import Data, Container, DynamicTable from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...hdmf_common.v1_1_2.hdmf_common_table import Container, Data, DynamicTable
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

18
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_behavior.py generated
View file

@ -1,20 +1,24 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...core.v2_2_1.core_nwb_misc import IntervalSeries from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_1.core_nwb_base import ( from ...core.v2_2_1.core_nwb_base import (
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
) )
from ...core.v2_2_1.core_nwb_misc import IntervalSeries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_device.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_1.core_nwb_base import NWBContainer from ...core.v2_2_1.core_nwb_base import NWBContainer
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_ecephys.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTableRegion from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_1.core_nwb_device import Device
from ...core.v2_2_1.core_nwb_base import ( from ...core.v2_2_1.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
NWBContainer,
) )
from numpydantic import NDArray, Shape from ...core.v2_2_1.core_nwb_device import Device
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

20
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_epoch.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, VectorIndex, VectorData
from ...core.v2_2_1.core_nwb_base import TimeSeries from ...core.v2_2_1.core_nwb_base import TimeSeries
from numpydantic import NDArray, Shape from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

28
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_file.py generated
View file

@ -1,27 +1,31 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_1.core_nwb_misc import Units from numpydantic import NDArray, Shape
from ...core.v2_2_1.core_nwb_device import Device from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_1.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_1.core_nwb_ophys import ImagingPlane
from ...core.v2_2_1.core_nwb_base import ( from ...core.v2_2_1.core_nwb_base import (
NWBContainer, NWBContainer,
NWBDataInterface, NWBDataInterface,
ProcessingModule, ProcessingModule,
TimeSeries, TimeSeries,
) )
from ...core.v2_2_1.core_nwb_device import Device
from ...core.v2_2_1.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_1.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, VectorData, VectorIndex
from ...core.v2_2_1.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_1.core_nwb_epoch import TimeIntervals from ...core.v2_2_1.core_nwb_epoch import TimeIntervals
from ...core.v2_2_1.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_1.core_nwb_misc import Units
from ...core.v2_2_1.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_1.core_nwb_ophys import ImagingPlane
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

34
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_icephys.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_1.core_nwb_base import ( from numpydantic import NDArray, Shape
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
NWBContainer,
)
from ...core.v2_2_1.core_nwb_device import Device
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, VectorIndex, VectorData from ...core.v2_2_1.core_nwb_base import (
NWBContainer,
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
)
from ...core.v2_2_1.core_nwb_device import Device
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_image.py generated
View file

@ -1,15 +1,19 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_1.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from ...core.v2_2_1.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

24
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_misc.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_1.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_1.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_2_1.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_1.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_2.hdmf_common_table import ( from ...hdmf_common.v1_1_2.hdmf_common_table import (
DynamicTable, DynamicTable,
DynamicTableRegion,
VectorData, VectorData,
VectorIndex, VectorIndex,
DynamicTableRegion,
) )
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"
@ -178,7 +182,7 @@ class AbstractFeatureSeriesData(ConfiguredBaseModel):
json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}}, json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}},
) )
unit: Optional[str] = Field( unit: Optional[str] = Field(
"see 'feature_units'", "see ",
description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""", description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""",
json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}}, json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}},
) )

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_ogen.py generated
View file

@ -1,21 +1,25 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_1.core_nwb_base import ( from ...core.v2_2_1.core_nwb_base import (
NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBContainer,
) )
from ...core.v2_2_1.core_nwb_device import Device from ...core.v2_2_1.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

30
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_ophys.py generated
View file

@ -1,31 +1,35 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_1.core_nwb_image import ImageSeries, ImageSeriesExternalFile from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTableRegion, DynamicTable
from ...core.v2_2_1.core_nwb_device import Device
from numpydantic import NDArray, Shape
from ...core.v2_2_1.core_nwb_base import ( from ...core.v2_2_1.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries,
NWBDataInterface,
NWBContainer,
) )
from ...core.v2_2_1.core_nwb_device import Device
from ...core.v2_2_1.core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_1_2.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

22
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/core_nwb_retinotopy.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_1.core_nwb_image import GrayscaleImage from numpydantic import NDArray, Shape
from ...core.v2_2_1.core_nwb_base import NWBData, NWBDataInterface
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...core.v2_2_1.core_nwb_base import NWBData, NWBDataInterface
from ...core.v2_2_1.core_nwb_image import GrayscaleImage
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

196
nwb_models/src/nwb_models/models/pydantic/core/v2_2_1/namespace.py generated
View file

@ -1,84 +1,78 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_2.hdmf_common_sparse import ( from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
CSRMatrix,
CSRMatrixIndices,
CSRMatrixIndptr,
CSRMatrixData,
)
from ...hdmf_common.v1_1_2.hdmf_common_table import (
Data,
Index,
VectorData,
VectorIndex,
ElementIdentifiers,
DynamicTableRegion,
Container,
DynamicTable,
)
from ...core.v2_2_1.core_nwb_retinotopy import (
RetinotopyMap,
AxisMap,
RetinotopyImage,
ImagingRetinotopy,
ImagingRetinotopyFocalDepthImage,
)
from ...core.v2_2_1.core_nwb_image import (
GrayscaleImage,
RGBImage,
RGBAImage,
ImageSeries,
ImageSeriesExternalFile,
ImageMaskSeries,
OpticalSeries,
IndexSeries,
)
from ...core.v2_2_1.core_nwb_base import ( from ...core.v2_2_1.core_nwb_base import (
NWBData,
Image, Image,
Images,
NWBContainer, NWBContainer,
NWBData,
NWBDataInterface, NWBDataInterface,
ProcessingModule,
TimeSeries, TimeSeries,
TimeSeriesData, TimeSeriesData,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
ProcessingModule,
Images,
) )
from ...core.v2_2_1.core_nwb_ophys import ( from ...core.v2_2_1.core_nwb_behavior import (
TwoPhotonSeries, BehavioralEpochs,
RoiResponseSeries, BehavioralEvents,
DfOverF, BehavioralTimeSeries,
Fluorescence, CompassDirection,
ImageSegmentation, EyeTracking,
ImagingPlane, Position,
ImagingPlaneManifold, PupilTracking,
ImagingPlaneOriginCoords, SpatialSeries,
ImagingPlaneGridSpacing, SpatialSeriesData,
OpticalChannel,
MotionCorrection,
) )
from ...core.v2_2_1.core_nwb_device import Device from ...core.v2_2_1.core_nwb_device import Device
from ...core.v2_2_1.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite from ...core.v2_2_1.core_nwb_ecephys import (
ClusterWaveforms,
Clustering,
ElectricalSeries,
ElectrodeGroup,
ElectrodeGroupPosition,
EventDetection,
EventWaveform,
FeatureExtraction,
FilteredEphys,
LFP,
SpikeEventSeries,
)
from ...core.v2_2_1.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
from ...core.v2_2_1.core_nwb_file import (
ExtracellularEphysElectrodes,
GeneralExtracellularEphys,
GeneralIntracellularEphys,
GeneralSourceScript,
NWBFile,
NWBFileGeneral,
NWBFileIntervals,
NWBFileStimulus,
Subject,
)
from ...core.v2_2_1.core_nwb_icephys import ( from ...core.v2_2_1.core_nwb_icephys import (
PatchClampSeries,
PatchClampSeriesData,
CurrentClampSeries, CurrentClampSeries,
CurrentClampSeriesData, CurrentClampSeriesData,
IZeroClampSeries,
CurrentClampStimulusSeries, CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData, CurrentClampStimulusSeriesData,
IZeroClampSeries,
IntracellularElectrode,
PatchClampSeries,
PatchClampSeriesData,
SweepTable,
VoltageClampSeries, VoltageClampSeries,
VoltageClampSeriesData,
VoltageClampSeriesCapacitanceFast, VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow, VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesData,
VoltageClampSeriesResistanceCompBandwidth, VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection, VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction, VoltageClampSeriesResistanceCompPrediction,
@ -86,56 +80,66 @@ from ...core.v2_2_1.core_nwb_icephys import (
VoltageClampSeriesWholeCellSeriesResistanceComp, VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries, VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData, VoltageClampStimulusSeriesData,
IntracellularElectrode,
SweepTable,
) )
from ...core.v2_2_1.core_nwb_ecephys import ( from ...core.v2_2_1.core_nwb_image import (
ElectricalSeries, GrayscaleImage,
SpikeEventSeries, ImageMaskSeries,
FeatureExtraction, ImageSeries,
EventDetection, ImageSeriesExternalFile,
EventWaveform, IndexSeries,
FilteredEphys, OpticalSeries,
LFP, RGBAImage,
ElectrodeGroup, RGBImage,
ElectrodeGroupPosition,
ClusterWaveforms,
Clustering,
)
from ...core.v2_2_1.core_nwb_behavior import (
SpatialSeries,
SpatialSeriesData,
BehavioralEpochs,
BehavioralEvents,
BehavioralTimeSeries,
PupilTracking,
EyeTracking,
CompassDirection,
Position,
) )
from ...core.v2_2_1.core_nwb_misc import ( from ...core.v2_2_1.core_nwb_misc import (
AbstractFeatureSeries, AbstractFeatureSeries,
AbstractFeatureSeriesData, AbstractFeatureSeriesData,
AnnotationSeries, AnnotationSeries,
IntervalSeries,
DecompositionSeries, DecompositionSeries,
DecompositionSeriesData,
DecompositionSeriesBands, DecompositionSeriesBands,
DecompositionSeriesData,
IntervalSeries,
Units, Units,
UnitsSpikeTimes, UnitsSpikeTimes,
) )
from ...core.v2_2_1.core_nwb_file import ( from ...core.v2_2_1.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
NWBFile, from ...core.v2_2_1.core_nwb_ophys import (
NWBFileStimulus, DfOverF,
NWBFileGeneral, Fluorescence,
GeneralSourceScript, ImageSegmentation,
Subject, ImagingPlane,
GeneralExtracellularEphys, ImagingPlaneGridSpacing,
ExtracellularEphysElectrodes, ImagingPlaneManifold,
GeneralIntracellularEphys, ImagingPlaneOriginCoords,
NWBFileIntervals, MotionCorrection,
OpticalChannel,
RoiResponseSeries,
TwoPhotonSeries,
) )
from ...core.v2_2_1.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries from ...core.v2_2_1.core_nwb_retinotopy import (
AxisMap,
ImagingRetinotopy,
ImagingRetinotopyFocalDepthImage,
RetinotopyImage,
RetinotopyMap,
)
from ...hdmf_common.v1_1_2.hdmf_common_sparse import (
CSRMatrix,
CSRMatrixData,
CSRMatrixIndices,
CSRMatrixIndptr,
)
from ...hdmf_common.v1_1_2.hdmf_common_table import (
Container,
Data,
DynamicTable,
DynamicTableRegion,
ElementIdentifiers,
Index,
VectorData,
VectorIndex,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.2.1" version = "2.2.1"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_base.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import Data, Container, DynamicTable from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...hdmf_common.v1_1_3.hdmf_common_table import Container, Data, DynamicTable
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

18
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_behavior.py generated
View file

@ -1,20 +1,24 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...core.v2_2_2.core_nwb_misc import IntervalSeries from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_2.core_nwb_base import ( from ...core.v2_2_2.core_nwb_base import (
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
) )
from ...core.v2_2_2.core_nwb_misc import IntervalSeries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_device.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_2.core_nwb_base import NWBContainer from ...core.v2_2_2.core_nwb_base import NWBContainer
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_ecephys.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTableRegion from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_2.core_nwb_device import Device
from ...core.v2_2_2.core_nwb_base import ( from ...core.v2_2_2.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
NWBContainer,
) )
from numpydantic import NDArray, Shape from ...core.v2_2_2.core_nwb_device import Device
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

20
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_epoch.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorIndex, VectorData
from ...core.v2_2_2.core_nwb_base import TimeSeries from ...core.v2_2_2.core_nwb_base import TimeSeries
from numpydantic import NDArray, Shape from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

28
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_file.py generated
View file

@ -1,27 +1,31 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_2.core_nwb_misc import Units from numpydantic import NDArray, Shape
from ...core.v2_2_2.core_nwb_device import Device from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_2.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_2.core_nwb_ophys import ImagingPlane
from ...core.v2_2_2.core_nwb_base import ( from ...core.v2_2_2.core_nwb_base import (
NWBContainer, NWBContainer,
NWBDataInterface, NWBDataInterface,
ProcessingModule, ProcessingModule,
TimeSeries, TimeSeries,
) )
from ...core.v2_2_2.core_nwb_device import Device
from ...core.v2_2_2.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_2.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
from ...core.v2_2_2.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_2.core_nwb_epoch import TimeIntervals from ...core.v2_2_2.core_nwb_epoch import TimeIntervals
from ...core.v2_2_2.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_2.core_nwb_misc import Units
from ...core.v2_2_2.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_2.core_nwb_ophys import ImagingPlane
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

34
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_icephys.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_2.core_nwb_base import ( from numpydantic import NDArray, Shape
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
NWBContainer,
)
from ...core.v2_2_2.core_nwb_device import Device
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorIndex, VectorData from ...core.v2_2_2.core_nwb_base import (
NWBContainer,
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
)
from ...core.v2_2_2.core_nwb_device import Device
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_image.py generated
View file

@ -1,15 +1,19 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_2.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from ...core.v2_2_2.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

24
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_misc.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_2.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_2.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_2_2.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_2.core_nwb_ecephys import ElectrodeGroup
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable, DynamicTable,
DynamicTableRegion,
VectorData, VectorData,
VectorIndex, VectorIndex,
DynamicTableRegion,
) )
from numpydantic import NDArray, Shape
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"
@ -178,7 +182,7 @@ class AbstractFeatureSeriesData(ConfiguredBaseModel):
json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}}, json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}},
) )
unit: Optional[str] = Field( unit: Optional[str] = Field(
"see 'feature_units'", "see ",
description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""", description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""",
json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}}, json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}},
) )

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_ogen.py generated
View file

@ -1,21 +1,25 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_2.core_nwb_base import ( from ...core.v2_2_2.core_nwb_base import (
NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBContainer,
) )
from ...core.v2_2_2.core_nwb_device import Device from ...core.v2_2_2.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

30
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_ophys.py generated
View file

@ -1,31 +1,35 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_2.core_nwb_image import ImageSeries, ImageSeriesExternalFile from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTableRegion, DynamicTable
from ...core.v2_2_2.core_nwb_device import Device
from numpydantic import NDArray, Shape
from ...core.v2_2_2.core_nwb_base import ( from ...core.v2_2_2.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries,
NWBDataInterface,
NWBContainer,
) )
from ...core.v2_2_2.core_nwb_device import Device
from ...core.v2_2_2.core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/core_nwb_retinotopy.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_2.core_nwb_base import NWBDataInterface
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_2.core_nwb_base import NWBDataInterface
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

250
nwb_models/src/nwb_models/models/pydantic/core/v2_2_2/namespace.py generated
View file

@ -1,27 +1,120 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_sparse import ( from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
CSRMatrix,
CSRMatrixIndices, from ...core.v2_2_2.core_nwb_base import (
CSRMatrixIndptr, Image,
CSRMatrixData, Images,
NWBContainer,
NWBData,
NWBDataInterface,
ProcessingModule,
TimeSeries,
TimeSeriesData,
TimeSeriesStartingTime,
TimeSeriesSync,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...core.v2_2_2.core_nwb_behavior import (
Data, BehavioralEpochs,
Index, BehavioralEvents,
VectorData, BehavioralTimeSeries,
VectorIndex, CompassDirection,
ElementIdentifiers, EyeTracking,
DynamicTableRegion, Position,
Container, PupilTracking,
DynamicTable, SpatialSeries,
SpatialSeriesData,
)
from ...core.v2_2_2.core_nwb_device import Device
from ...core.v2_2_2.core_nwb_ecephys import (
ClusterWaveforms,
Clustering,
ElectricalSeries,
ElectrodeGroup,
ElectrodeGroupPosition,
EventDetection,
EventWaveform,
FeatureExtraction,
FilteredEphys,
LFP,
SpikeEventSeries,
)
from ...core.v2_2_2.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
from ...core.v2_2_2.core_nwb_file import (
ExtracellularEphysElectrodes,
GeneralExtracellularEphys,
GeneralIntracellularEphys,
GeneralSourceScript,
NWBFile,
NWBFileGeneral,
NWBFileIntervals,
NWBFileStimulus,
Subject,
)
from ...core.v2_2_2.core_nwb_icephys import (
CurrentClampSeries,
CurrentClampSeriesData,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
IZeroClampSeries,
IntracellularElectrode,
PatchClampSeries,
PatchClampSeriesData,
SweepTable,
VoltageClampSeries,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesData,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
)
from ...core.v2_2_2.core_nwb_image import (
GrayscaleImage,
ImageMaskSeries,
ImageSeries,
ImageSeriesExternalFile,
IndexSeries,
OpticalSeries,
RGBAImage,
RGBImage,
)
from ...core.v2_2_2.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
DecompositionSeries,
DecompositionSeriesBands,
DecompositionSeriesData,
IntervalSeries,
Units,
UnitsSpikeTimes,
)
from ...core.v2_2_2.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_2_2.core_nwb_ophys import (
DfOverF,
Fluorescence,
ImageSegmentation,
ImagingPlane,
ImagingPlaneGridSpacing,
ImagingPlaneManifold,
ImagingPlaneOriginCoords,
MotionCorrection,
OpticalChannel,
RoiResponseSeries,
TwoPhotonSeries,
) )
from ...core.v2_2_2.core_nwb_retinotopy import ( from ...core.v2_2_2.core_nwb_retinotopy import (
ImagingRetinotopy, ImagingRetinotopy,
@ -33,112 +126,23 @@ from ...core.v2_2_2.core_nwb_retinotopy import (
ImagingRetinotopySignMap, ImagingRetinotopySignMap,
ImagingRetinotopyVasculatureImage, ImagingRetinotopyVasculatureImage,
) )
from ...core.v2_2_2.core_nwb_base import ( from ...hdmf_common.v1_1_3.hdmf_common_sparse import (
NWBData, CSRMatrix,
Image, CSRMatrixData,
NWBContainer, CSRMatrixIndices,
NWBDataInterface, CSRMatrixIndptr,
TimeSeries,
TimeSeriesData,
TimeSeriesStartingTime,
TimeSeriesSync,
ProcessingModule,
Images,
) )
from ...core.v2_2_2.core_nwb_ophys import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
TwoPhotonSeries, Container,
RoiResponseSeries, Data,
DfOverF, DynamicTable,
Fluorescence, DynamicTableRegion,
ImageSegmentation, ElementIdentifiers,
ImagingPlane, Index,
ImagingPlaneManifold, VectorData,
ImagingPlaneOriginCoords, VectorIndex,
ImagingPlaneGridSpacing,
OpticalChannel,
MotionCorrection,
) )
from ...core.v2_2_2.core_nwb_device import Device
from ...core.v2_2_2.core_nwb_image import (
GrayscaleImage,
RGBImage,
RGBAImage,
ImageSeries,
ImageSeriesExternalFile,
ImageMaskSeries,
OpticalSeries,
IndexSeries,
)
from ...core.v2_2_2.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_2_2.core_nwb_icephys import (
PatchClampSeries,
PatchClampSeriesData,
CurrentClampSeries,
CurrentClampSeriesData,
IZeroClampSeries,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
VoltageClampSeries,
VoltageClampSeriesData,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
IntracellularElectrode,
SweepTable,
)
from ...core.v2_2_2.core_nwb_ecephys import (
ElectricalSeries,
SpikeEventSeries,
FeatureExtraction,
EventDetection,
EventWaveform,
FilteredEphys,
LFP,
ElectrodeGroup,
ElectrodeGroupPosition,
ClusterWaveforms,
Clustering,
)
from ...core.v2_2_2.core_nwb_behavior import (
SpatialSeries,
SpatialSeriesData,
BehavioralEpochs,
BehavioralEvents,
BehavioralTimeSeries,
PupilTracking,
EyeTracking,
CompassDirection,
Position,
)
from ...core.v2_2_2.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
IntervalSeries,
DecompositionSeries,
DecompositionSeriesData,
DecompositionSeriesBands,
Units,
UnitsSpikeTimes,
)
from ...core.v2_2_2.core_nwb_file import (
NWBFile,
NWBFileStimulus,
NWBFileGeneral,
GeneralSourceScript,
Subject,
GeneralExtracellularEphys,
ExtracellularEphysElectrodes,
GeneralIntracellularEphys,
NWBFileIntervals,
)
from ...core.v2_2_2.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.2" version = "2.2.2"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_base.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import Data, Container, DynamicTable from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...hdmf_common.v1_1_3.hdmf_common_table import Container, Data, DynamicTable
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

18
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_behavior.py generated
View file

@ -1,20 +1,24 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...core.v2_2_4.core_nwb_misc import IntervalSeries from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_4.core_nwb_base import ( from ...core.v2_2_4.core_nwb_base import (
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
) )
from ...core.v2_2_4.core_nwb_misc import IntervalSeries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_device.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_4.core_nwb_base import NWBContainer from ...core.v2_2_4.core_nwb_base import NWBContainer
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_ecephys.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTableRegion from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_4.core_nwb_device import Device
from ...core.v2_2_4.core_nwb_base import ( from ...core.v2_2_4.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
NWBContainer,
) )
from numpydantic import NDArray, Shape from ...core.v2_2_4.core_nwb_device import Device
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

20
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_epoch.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorIndex, VectorData
from ...core.v2_2_4.core_nwb_base import TimeSeries from ...core.v2_2_4.core_nwb_base import TimeSeries
from numpydantic import NDArray, Shape from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

32
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_file.py generated
View file

@ -1,28 +1,32 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_4.core_nwb_misc import Units
from ...core.v2_2_4.core_nwb_device import Device
from ...core.v2_2_4.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_4.core_nwb_ophys import ImagingPlane
from ...core.v2_2_4.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_4.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_4.core_nwb_epoch import TimeIntervals
from ...core.v2_2_4.core_nwb_base import ( from ...core.v2_2_4.core_nwb_base import (
NWBData,
NWBContainer, NWBContainer,
NWBData,
NWBDataInterface, NWBDataInterface,
ProcessingModule, ProcessingModule,
TimeSeries, TimeSeries,
) )
from ...core.v2_2_4.core_nwb_device import Device
from ...core.v2_2_4.core_nwb_ecephys import ElectrodeGroup
from ...core.v2_2_4.core_nwb_epoch import TimeIntervals
from ...core.v2_2_4.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_4.core_nwb_misc import Units
from ...core.v2_2_4.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_4.core_nwb_ophys import ImagingPlane
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

34
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_icephys.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_4.core_nwb_base import ( from numpydantic import NDArray, Shape
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
NWBContainer,
)
from ...core.v2_2_4.core_nwb_device import Device
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorIndex, VectorData from ...core.v2_2_4.core_nwb_base import (
NWBContainer,
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
)
from ...core.v2_2_4.core_nwb_device import Device
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_image.py generated
View file

@ -1,15 +1,19 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_4.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from ...core.v2_2_4.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

24
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_misc.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_4.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_4.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_2_4.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_4.core_nwb_ecephys import ElectrodeGroup
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable, DynamicTable,
DynamicTableRegion,
VectorData, VectorData,
VectorIndex, VectorIndex,
DynamicTableRegion,
) )
from numpydantic import NDArray, Shape
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"
@ -178,7 +182,7 @@ class AbstractFeatureSeriesData(ConfiguredBaseModel):
json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}}, json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}},
) )
unit: Optional[str] = Field( unit: Optional[str] = Field(
"see 'feature_units'", "see ",
description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""", description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""",
json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}}, json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}},
) )

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_ogen.py generated
View file

@ -1,21 +1,25 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_4.core_nwb_base import ( from ...core.v2_2_4.core_nwb_base import (
NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBContainer,
) )
from ...core.v2_2_4.core_nwb_device import Device from ...core.v2_2_4.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

38
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_ophys.py generated
View file

@ -1,36 +1,40 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTableRegion,
DynamicTable,
VectorIndex,
VectorData,
)
from ...core.v2_2_4.core_nwb_device import Device
from numpydantic import NDArray, Shape
from ...core.v2_2_4.core_nwb_base import ( from ...core.v2_2_4.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries,
NWBDataInterface,
NWBContainer,
) )
from ...core.v2_2_4.core_nwb_device import Device
from ...core.v2_2_4.core_nwb_image import ImageSeries, ImageSeriesExternalFile from ...core.v2_2_4.core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorData,
VectorIndex,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/core_nwb_retinotopy.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_4.core_nwb_base import NWBDataInterface
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_4.core_nwb_base import NWBDataInterface
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

264
nwb_models/src/nwb_models/models/pydantic/core/v2_2_4/namespace.py generated
View file

@ -1,27 +1,127 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_sparse import ( from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
CSRMatrix,
CSRMatrixIndices, from ...core.v2_2_4.core_nwb_base import (
CSRMatrixIndptr, Image,
CSRMatrixData, Images,
NWBContainer,
NWBData,
NWBDataInterface,
ProcessingModule,
TimeSeries,
TimeSeriesData,
TimeSeriesStartingTime,
TimeSeriesSync,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...core.v2_2_4.core_nwb_behavior import (
Data, BehavioralEpochs,
Index, BehavioralEvents,
VectorData, BehavioralTimeSeries,
VectorIndex, CompassDirection,
ElementIdentifiers, EyeTracking,
DynamicTableRegion, Position,
Container, PupilTracking,
DynamicTable, SpatialSeries,
SpatialSeriesData,
)
from ...core.v2_2_4.core_nwb_device import Device
from ...core.v2_2_4.core_nwb_ecephys import (
ClusterWaveforms,
Clustering,
ElectricalSeries,
ElectrodeGroup,
ElectrodeGroupPosition,
EventDetection,
EventWaveform,
FeatureExtraction,
FilteredEphys,
LFP,
SpikeEventSeries,
)
from ...core.v2_2_4.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
from ...core.v2_2_4.core_nwb_file import (
ExtracellularEphysElectrodes,
GeneralExtracellularEphys,
GeneralIntracellularEphys,
GeneralSourceScript,
LabMetaData,
NWBFile,
NWBFileGeneral,
NWBFileIntervals,
NWBFileStimulus,
ScratchData,
Subject,
)
from ...core.v2_2_4.core_nwb_icephys import (
CurrentClampSeries,
CurrentClampSeriesData,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
IZeroClampSeries,
IntracellularElectrode,
PatchClampSeries,
PatchClampSeriesData,
SweepTable,
VoltageClampSeries,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesData,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
)
from ...core.v2_2_4.core_nwb_image import (
GrayscaleImage,
ImageMaskSeries,
ImageSeries,
ImageSeriesExternalFile,
IndexSeries,
OpticalSeries,
RGBAImage,
RGBImage,
)
from ...core.v2_2_4.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
DecompositionSeries,
DecompositionSeriesBands,
DecompositionSeriesData,
IntervalSeries,
Units,
UnitsSpikeTimes,
)
from ...core.v2_2_4.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_2_4.core_nwb_ophys import (
CorrectedImageStack,
DfOverF,
Fluorescence,
ImageSegmentation,
ImagingPlane,
ImagingPlaneGridSpacing,
ImagingPlaneManifold,
ImagingPlaneOriginCoords,
MotionCorrection,
OpticalChannel,
PlaneSegmentation,
PlaneSegmentationImageMask,
PlaneSegmentationPixelMask,
PlaneSegmentationVoxelMask,
RoiResponseSeries,
TwoPhotonSeries,
) )
from ...core.v2_2_4.core_nwb_retinotopy import ( from ...core.v2_2_4.core_nwb_retinotopy import (
ImagingRetinotopy, ImagingRetinotopy,
@ -33,119 +133,23 @@ from ...core.v2_2_4.core_nwb_retinotopy import (
ImagingRetinotopySignMap, ImagingRetinotopySignMap,
ImagingRetinotopyVasculatureImage, ImagingRetinotopyVasculatureImage,
) )
from ...core.v2_2_4.core_nwb_base import ( from ...hdmf_common.v1_1_3.hdmf_common_sparse import (
NWBData, CSRMatrix,
Image, CSRMatrixData,
NWBContainer, CSRMatrixIndices,
NWBDataInterface, CSRMatrixIndptr,
TimeSeries,
TimeSeriesData,
TimeSeriesStartingTime,
TimeSeriesSync,
ProcessingModule,
Images,
) )
from ...core.v2_2_4.core_nwb_ophys import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
TwoPhotonSeries, Container,
RoiResponseSeries, Data,
DfOverF, DynamicTable,
Fluorescence, DynamicTableRegion,
ImageSegmentation, ElementIdentifiers,
PlaneSegmentation, Index,
PlaneSegmentationImageMask, VectorData,
PlaneSegmentationPixelMask, VectorIndex,
PlaneSegmentationVoxelMask,
ImagingPlane,
ImagingPlaneManifold,
ImagingPlaneOriginCoords,
ImagingPlaneGridSpacing,
OpticalChannel,
MotionCorrection,
CorrectedImageStack,
) )
from ...core.v2_2_4.core_nwb_device import Device
from ...core.v2_2_4.core_nwb_image import (
GrayscaleImage,
RGBImage,
RGBAImage,
ImageSeries,
ImageSeriesExternalFile,
ImageMaskSeries,
OpticalSeries,
IndexSeries,
)
from ...core.v2_2_4.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_2_4.core_nwb_icephys import (
PatchClampSeries,
PatchClampSeriesData,
CurrentClampSeries,
CurrentClampSeriesData,
IZeroClampSeries,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
VoltageClampSeries,
VoltageClampSeriesData,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
IntracellularElectrode,
SweepTable,
)
from ...core.v2_2_4.core_nwb_ecephys import (
ElectricalSeries,
SpikeEventSeries,
FeatureExtraction,
EventDetection,
EventWaveform,
FilteredEphys,
LFP,
ElectrodeGroup,
ElectrodeGroupPosition,
ClusterWaveforms,
Clustering,
)
from ...core.v2_2_4.core_nwb_behavior import (
SpatialSeries,
SpatialSeriesData,
BehavioralEpochs,
BehavioralEvents,
BehavioralTimeSeries,
PupilTracking,
EyeTracking,
CompassDirection,
Position,
)
from ...core.v2_2_4.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
IntervalSeries,
DecompositionSeries,
DecompositionSeriesData,
DecompositionSeriesBands,
Units,
UnitsSpikeTimes,
)
from ...core.v2_2_4.core_nwb_file import (
ScratchData,
NWBFile,
NWBFileStimulus,
NWBFileGeneral,
GeneralSourceScript,
GeneralExtracellularEphys,
ExtracellularEphysElectrodes,
GeneralIntracellularEphys,
NWBFileIntervals,
LabMetaData,
Subject,
)
from ...core.v2_2_4.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.4" version = "2.2.4"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_base.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import Data, Container, DynamicTable from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...hdmf_common.v1_1_3.hdmf_common_table import Container, Data, DynamicTable
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

18
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_behavior.py generated
View file

@ -1,20 +1,24 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...core.v2_2_5.core_nwb_misc import IntervalSeries from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_5.core_nwb_base import ( from ...core.v2_2_5.core_nwb_base import (
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
) )
from ...core.v2_2_5.core_nwb_misc import IntervalSeries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_device.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_5.core_nwb_base import NWBContainer from ...core.v2_2_5.core_nwb_base import NWBContainer
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_ecephys.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTableRegion from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_5.core_nwb_device import Device
from ...core.v2_2_5.core_nwb_base import ( from ...core.v2_2_5.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
NWBContainer,
) )
from numpydantic import NDArray, Shape from ...core.v2_2_5.core_nwb_device import Device
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

20
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_epoch.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorIndex, VectorData
from ...core.v2_2_5.core_nwb_base import TimeSeries from ...core.v2_2_5.core_nwb_base import TimeSeries
from numpydantic import NDArray, Shape from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

32
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_file.py generated
View file

@ -1,28 +1,32 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_5.core_nwb_misc import Units
from ...core.v2_2_5.core_nwb_device import Device
from ...core.v2_2_5.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_5.core_nwb_ophys import ImagingPlane
from ...core.v2_2_5.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_5.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_5.core_nwb_epoch import TimeIntervals
from ...core.v2_2_5.core_nwb_base import ( from ...core.v2_2_5.core_nwb_base import (
NWBData,
NWBContainer, NWBContainer,
NWBData,
NWBDataInterface, NWBDataInterface,
ProcessingModule, ProcessingModule,
TimeSeries, TimeSeries,
) )
from ...core.v2_2_5.core_nwb_device import Device
from ...core.v2_2_5.core_nwb_ecephys import ElectrodeGroup
from ...core.v2_2_5.core_nwb_epoch import TimeIntervals
from ...core.v2_2_5.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_2_5.core_nwb_misc import Units
from ...core.v2_2_5.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_2_5.core_nwb_ophys import ImagingPlane
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

34
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_icephys.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_5.core_nwb_base import ( from numpydantic import NDArray, Shape
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
NWBContainer,
)
from ...core.v2_2_5.core_nwb_device import Device
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorIndex, VectorData from ...core.v2_2_5.core_nwb_base import (
NWBContainer,
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
)
from ...core.v2_2_5.core_nwb_device import Device
from ...hdmf_common.v1_1_3.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_image.py generated
View file

@ -1,15 +1,19 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_5.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from ...core.v2_2_5.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

24
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_misc.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_2_5.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_2_5.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_2_5.core_nwb_ecephys import ElectrodeGroup from ...core.v2_2_5.core_nwb_ecephys import ElectrodeGroup
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable, DynamicTable,
DynamicTableRegion,
VectorData, VectorData,
VectorIndex, VectorIndex,
DynamicTableRegion,
) )
from numpydantic import NDArray, Shape
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"
@ -178,7 +182,7 @@ class AbstractFeatureSeriesData(ConfiguredBaseModel):
json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}}, json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}},
) )
unit: Optional[str] = Field( unit: Optional[str] = Field(
"see 'feature_units'", "see ",
description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""", description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""",
json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}}, json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}},
) )

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_ogen.py generated
View file

@ -1,21 +1,25 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_5.core_nwb_base import ( from ...core.v2_2_5.core_nwb_base import (
NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBContainer,
) )
from ...core.v2_2_5.core_nwb_device import Device from ...core.v2_2_5.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

38
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_ophys.py generated
View file

@ -1,36 +1,40 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTableRegion,
DynamicTable,
VectorIndex,
VectorData,
)
from ...core.v2_2_5.core_nwb_device import Device
from numpydantic import NDArray, Shape
from ...core.v2_2_5.core_nwb_base import ( from ...core.v2_2_5.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries,
NWBDataInterface,
NWBContainer,
) )
from ...core.v2_2_5.core_nwb_device import Device
from ...core.v2_2_5.core_nwb_image import ImageSeries, ImageSeriesExternalFile from ...core.v2_2_5.core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_1_3.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorData,
VectorIndex,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/core_nwb_retinotopy.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_2_5.core_nwb_base import NWBDataInterface
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_2_5.core_nwb_base import NWBDataInterface
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

264
nwb_models/src/nwb_models/models/pydantic/core/v2_2_5/namespace.py generated
View file

@ -1,27 +1,127 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_1_3.hdmf_common_sparse import ( from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
CSRMatrix,
CSRMatrixIndices, from ...core.v2_2_5.core_nwb_base import (
CSRMatrixIndptr, Image,
CSRMatrixData, Images,
NWBContainer,
NWBData,
NWBDataInterface,
ProcessingModule,
TimeSeries,
TimeSeriesData,
TimeSeriesStartingTime,
TimeSeriesSync,
) )
from ...hdmf_common.v1_1_3.hdmf_common_table import ( from ...core.v2_2_5.core_nwb_behavior import (
Data, BehavioralEpochs,
Index, BehavioralEvents,
VectorData, BehavioralTimeSeries,
VectorIndex, CompassDirection,
ElementIdentifiers, EyeTracking,
DynamicTableRegion, Position,
Container, PupilTracking,
DynamicTable, SpatialSeries,
SpatialSeriesData,
)
from ...core.v2_2_5.core_nwb_device import Device
from ...core.v2_2_5.core_nwb_ecephys import (
ClusterWaveforms,
Clustering,
ElectricalSeries,
ElectrodeGroup,
ElectrodeGroupPosition,
EventDetection,
EventWaveform,
FeatureExtraction,
FilteredEphys,
LFP,
SpikeEventSeries,
)
from ...core.v2_2_5.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
from ...core.v2_2_5.core_nwb_file import (
ExtracellularEphysElectrodes,
GeneralExtracellularEphys,
GeneralIntracellularEphys,
GeneralSourceScript,
LabMetaData,
NWBFile,
NWBFileGeneral,
NWBFileIntervals,
NWBFileStimulus,
ScratchData,
Subject,
)
from ...core.v2_2_5.core_nwb_icephys import (
CurrentClampSeries,
CurrentClampSeriesData,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
IZeroClampSeries,
IntracellularElectrode,
PatchClampSeries,
PatchClampSeriesData,
SweepTable,
VoltageClampSeries,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesData,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
)
from ...core.v2_2_5.core_nwb_image import (
GrayscaleImage,
ImageMaskSeries,
ImageSeries,
ImageSeriesExternalFile,
IndexSeries,
OpticalSeries,
RGBAImage,
RGBImage,
)
from ...core.v2_2_5.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
DecompositionSeries,
DecompositionSeriesBands,
DecompositionSeriesData,
IntervalSeries,
Units,
UnitsSpikeTimes,
)
from ...core.v2_2_5.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_2_5.core_nwb_ophys import (
CorrectedImageStack,
DfOverF,
Fluorescence,
ImageSegmentation,
ImagingPlane,
ImagingPlaneGridSpacing,
ImagingPlaneManifold,
ImagingPlaneOriginCoords,
MotionCorrection,
OpticalChannel,
PlaneSegmentation,
PlaneSegmentationImageMask,
PlaneSegmentationPixelMask,
PlaneSegmentationVoxelMask,
RoiResponseSeries,
TwoPhotonSeries,
) )
from ...core.v2_2_5.core_nwb_retinotopy import ( from ...core.v2_2_5.core_nwb_retinotopy import (
ImagingRetinotopy, ImagingRetinotopy,
@ -33,119 +133,23 @@ from ...core.v2_2_5.core_nwb_retinotopy import (
ImagingRetinotopySignMap, ImagingRetinotopySignMap,
ImagingRetinotopyVasculatureImage, ImagingRetinotopyVasculatureImage,
) )
from ...core.v2_2_5.core_nwb_base import ( from ...hdmf_common.v1_1_3.hdmf_common_sparse import (
NWBData, CSRMatrix,
Image, CSRMatrixData,
NWBContainer, CSRMatrixIndices,
NWBDataInterface, CSRMatrixIndptr,
TimeSeries,
TimeSeriesData,
TimeSeriesStartingTime,
TimeSeriesSync,
ProcessingModule,
Images,
) )
from ...core.v2_2_5.core_nwb_ophys import ( from ...hdmf_common.v1_1_3.hdmf_common_table import (
TwoPhotonSeries, Container,
RoiResponseSeries, Data,
DfOverF, DynamicTable,
Fluorescence, DynamicTableRegion,
ImageSegmentation, ElementIdentifiers,
PlaneSegmentation, Index,
PlaneSegmentationImageMask, VectorData,
PlaneSegmentationPixelMask, VectorIndex,
PlaneSegmentationVoxelMask,
ImagingPlane,
ImagingPlaneManifold,
ImagingPlaneOriginCoords,
ImagingPlaneGridSpacing,
OpticalChannel,
MotionCorrection,
CorrectedImageStack,
) )
from ...core.v2_2_5.core_nwb_device import Device
from ...core.v2_2_5.core_nwb_image import (
GrayscaleImage,
RGBImage,
RGBAImage,
ImageSeries,
ImageSeriesExternalFile,
ImageMaskSeries,
OpticalSeries,
IndexSeries,
)
from ...core.v2_2_5.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_2_5.core_nwb_icephys import (
PatchClampSeries,
PatchClampSeriesData,
CurrentClampSeries,
CurrentClampSeriesData,
IZeroClampSeries,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
VoltageClampSeries,
VoltageClampSeriesData,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
IntracellularElectrode,
SweepTable,
)
from ...core.v2_2_5.core_nwb_ecephys import (
ElectricalSeries,
SpikeEventSeries,
FeatureExtraction,
EventDetection,
EventWaveform,
FilteredEphys,
LFP,
ElectrodeGroup,
ElectrodeGroupPosition,
ClusterWaveforms,
Clustering,
)
from ...core.v2_2_5.core_nwb_behavior import (
SpatialSeries,
SpatialSeriesData,
BehavioralEpochs,
BehavioralEvents,
BehavioralTimeSeries,
PupilTracking,
EyeTracking,
CompassDirection,
Position,
)
from ...core.v2_2_5.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
IntervalSeries,
DecompositionSeries,
DecompositionSeriesData,
DecompositionSeriesBands,
Units,
UnitsSpikeTimes,
)
from ...core.v2_2_5.core_nwb_file import (
ScratchData,
NWBFile,
NWBFileStimulus,
NWBFileGeneral,
GeneralSourceScript,
GeneralExtracellularEphys,
ExtracellularEphysElectrodes,
GeneralIntracellularEphys,
NWBFileIntervals,
LabMetaData,
Subject,
)
from ...core.v2_2_5.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
metamodel_version = "None" metamodel_version = "None"
version = "2.2.5" version = "2.2.5"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_base.py generated
View file

@ -1,16 +1,20 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_base import Data, Container
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...hdmf_common.v1_5_0.hdmf_common_base import Container, Data
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

18
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_behavior.py generated
View file

@ -1,20 +1,24 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...core.v2_3_0.core_nwb_misc import IntervalSeries from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_3_0.core_nwb_base import ( from ...core.v2_3_0.core_nwb_base import (
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
) )
from ...core.v2_3_0.core_nwb_misc import IntervalSeries
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_device.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_3_0.core_nwb_base import NWBContainer from ...core.v2_3_0.core_nwb_base import NWBContainer
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_ecephys.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTableRegion from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_3_0.core_nwb_device import Device
from ...core.v2_3_0.core_nwb_base import ( from ...core.v2_3_0.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
NWBContainer,
) )
from numpydantic import NDArray, Shape from ...core.v2_3_0.core_nwb_device import Device
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

20
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_epoch.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorIndex, VectorData
from ...core.v2_3_0.core_nwb_base import TimeSeries from ...core.v2_3_0.core_nwb_base import TimeSeries
from numpydantic import NDArray, Shape from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

32
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_file.py generated
View file

@ -1,28 +1,32 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_3_0.core_nwb_misc import Units
from ...core.v2_3_0.core_nwb_device import Device
from ...core.v2_3_0.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_3_0.core_nwb_ophys import ImagingPlane
from ...core.v2_3_0.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_3_0.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_3_0.core_nwb_epoch import TimeIntervals
from ...core.v2_3_0.core_nwb_base import ( from ...core.v2_3_0.core_nwb_base import (
NWBData,
NWBContainer, NWBContainer,
NWBData,
NWBDataInterface, NWBDataInterface,
ProcessingModule, ProcessingModule,
TimeSeries, TimeSeries,
) )
from ...core.v2_3_0.core_nwb_device import Device
from ...core.v2_3_0.core_nwb_ecephys import ElectrodeGroup
from ...core.v2_3_0.core_nwb_epoch import TimeIntervals
from ...core.v2_3_0.core_nwb_icephys import IntracellularElectrode, SweepTable
from ...core.v2_3_0.core_nwb_misc import Units
from ...core.v2_3_0.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_3_0.core_nwb_ophys import ImagingPlane
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

34
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_icephys.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_3_0.core_nwb_base import ( from numpydantic import NDArray, Shape
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
NWBContainer,
)
from ...core.v2_3_0.core_nwb_device import Device
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from numpydantic import NDArray, Shape
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorIndex, VectorData from ...core.v2_3_0.core_nwb_base import (
NWBContainer,
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
)
from ...core.v2_3_0.core_nwb_device import Device
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_image.py generated
View file

@ -1,15 +1,19 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_3_0.core_nwb_device import Device
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_3_0.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from ...core.v2_3_0.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_3_0.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_misc.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_3_0.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from numpydantic import NDArray, Shape
from ...core.v2_3_0.core_nwb_ecephys import ElectrodeGroup
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_3_0.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_3_0.core_nwb_ecephys import ElectrodeGroup
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
DynamicTable, DynamicTable,
DynamicTableRegion,
VectorData, VectorData,
VectorIndex, VectorIndex,
) )
from numpydantic import NDArray, Shape
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"
@ -178,7 +182,7 @@ class AbstractFeatureSeriesData(ConfiguredBaseModel):
json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}}, json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}},
) )
unit: Optional[str] = Field( unit: Optional[str] = Field(
"see 'feature_units'", "see ",
description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""", description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""",
json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}}, json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}},
) )

16
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_ogen.py generated
View file

@ -1,21 +1,25 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_3_0.core_nwb_base import ( from ...core.v2_3_0.core_nwb_base import (
NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBContainer,
) )
from ...core.v2_3_0.core_nwb_device import Device from ...core.v2_3_0.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

38
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_ophys.py generated
View file

@ -1,36 +1,40 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
DynamicTable,
VectorIndex,
VectorData,
)
from ...core.v2_3_0.core_nwb_device import Device
from numpydantic import NDArray, Shape
from ...core.v2_3_0.core_nwb_base import ( from ...core.v2_3_0.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries,
NWBDataInterface,
NWBContainer,
) )
from ...core.v2_3_0.core_nwb_device import Device
from ...core.v2_3_0.core_nwb_image import ImageSeries, ImageSeriesExternalFile from ...core.v2_3_0.core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorData,
VectorIndex,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/core_nwb_retinotopy.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_3_0.core_nwb_base import NWBDataInterface
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_3_0.core_nwb_base import NWBDataInterface
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

270
nwb_models/src/nwb_models/models/pydantic/core/v2_3_0/namespace.py generated
View file

@ -1,31 +1,128 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...hdmf_experimental.v0_1_0.hdmf_experimental_resources import ( from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
ExternalResources,
ExternalResourcesKeys, from ...core.v2_3_0.core_nwb_base import (
ExternalResourcesEntities, Image,
ExternalResourcesResources, Images,
ExternalResourcesObjects, NWBContainer,
ExternalResourcesObjectKeys, NWBData,
NWBDataInterface,
ProcessingModule,
TimeSeries,
TimeSeriesData,
TimeSeriesStartingTime,
TimeSeriesSync,
) )
from ...hdmf_common.v1_5_0.hdmf_common_sparse import CSRMatrix, CSRMatrixData from ...core.v2_3_0.core_nwb_behavior import (
from ...hdmf_common.v1_5_0.hdmf_common_base import Data, Container, SimpleMultiContainer BehavioralEpochs,
from ...hdmf_common.v1_5_0.hdmf_common_table import ( BehavioralEvents,
VectorData, BehavioralTimeSeries,
VectorIndex, CompassDirection,
ElementIdentifiers, EyeTracking,
DynamicTableRegion, Position,
DynamicTable, PupilTracking,
AlignedDynamicTable, SpatialSeries,
SpatialSeriesData,
)
from ...core.v2_3_0.core_nwb_device import Device
from ...core.v2_3_0.core_nwb_ecephys import (
ClusterWaveforms,
Clustering,
ElectricalSeries,
ElectrodeGroup,
ElectrodeGroupPosition,
EventDetection,
EventWaveform,
FeatureExtraction,
FilteredEphys,
LFP,
SpikeEventSeries,
)
from ...core.v2_3_0.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
from ...core.v2_3_0.core_nwb_file import (
ExtracellularEphysElectrodes,
GeneralExtracellularEphys,
GeneralIntracellularEphys,
GeneralSourceScript,
LabMetaData,
NWBFile,
NWBFileGeneral,
NWBFileIntervals,
NWBFileStimulus,
ScratchData,
Subject,
)
from ...core.v2_3_0.core_nwb_icephys import (
CurrentClampSeries,
CurrentClampSeriesData,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
IZeroClampSeries,
IntracellularElectrode,
PatchClampSeries,
PatchClampSeriesData,
SweepTable,
VoltageClampSeries,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesData,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
)
from ...core.v2_3_0.core_nwb_image import (
GrayscaleImage,
ImageMaskSeries,
ImageSeries,
ImageSeriesExternalFile,
IndexSeries,
OpticalSeries,
RGBAImage,
RGBImage,
)
from ...core.v2_3_0.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
DecompositionSeries,
DecompositionSeriesBands,
DecompositionSeriesData,
IntervalSeries,
Units,
UnitsSpikeTimes,
)
from ...core.v2_3_0.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_3_0.core_nwb_ophys import (
CorrectedImageStack,
DfOverF,
Fluorescence,
ImageSegmentation,
ImagingPlane,
ImagingPlaneGridSpacing,
ImagingPlaneManifold,
ImagingPlaneOriginCoords,
MotionCorrection,
OpticalChannel,
PlaneSegmentation,
PlaneSegmentationImageMask,
PlaneSegmentationPixelMask,
PlaneSegmentationVoxelMask,
RoiResponseSeries,
TwoPhotonSeries,
) )
from ...hdmf_experimental.v0_1_0.hdmf_experimental_experimental import EnumData
from ...core.v2_3_0.core_nwb_retinotopy import ( from ...core.v2_3_0.core_nwb_retinotopy import (
ImagingRetinotopy, ImagingRetinotopy,
ImagingRetinotopyAxis1PhaseMap, ImagingRetinotopyAxis1PhaseMap,
@ -36,119 +133,26 @@ from ...core.v2_3_0.core_nwb_retinotopy import (
ImagingRetinotopySignMap, ImagingRetinotopySignMap,
ImagingRetinotopyVasculatureImage, ImagingRetinotopyVasculatureImage,
) )
from ...core.v2_3_0.core_nwb_base import ( from ...hdmf_common.v1_5_0.hdmf_common_base import Container, Data, SimpleMultiContainer
NWBData, from ...hdmf_common.v1_5_0.hdmf_common_sparse import CSRMatrix, CSRMatrixData
Image, from ...hdmf_common.v1_5_0.hdmf_common_table import (
NWBContainer, AlignedDynamicTable,
NWBDataInterface, DynamicTable,
TimeSeries, DynamicTableRegion,
TimeSeriesData, ElementIdentifiers,
TimeSeriesStartingTime, VectorData,
TimeSeriesSync, VectorIndex,
ProcessingModule,
Images,
) )
from ...core.v2_3_0.core_nwb_ophys import ( from ...hdmf_experimental.v0_1_0.hdmf_experimental_experimental import EnumData
TwoPhotonSeries, from ...hdmf_experimental.v0_1_0.hdmf_experimental_resources import (
RoiResponseSeries, ExternalResources,
DfOverF, ExternalResourcesEntities,
Fluorescence, ExternalResourcesKeys,
ImageSegmentation, ExternalResourcesObjectKeys,
PlaneSegmentation, ExternalResourcesObjects,
PlaneSegmentationImageMask, ExternalResourcesResources,
PlaneSegmentationPixelMask,
PlaneSegmentationVoxelMask,
ImagingPlane,
ImagingPlaneManifold,
ImagingPlaneOriginCoords,
ImagingPlaneGridSpacing,
OpticalChannel,
MotionCorrection,
CorrectedImageStack,
) )
from ...core.v2_3_0.core_nwb_device import Device
from ...core.v2_3_0.core_nwb_image import (
GrayscaleImage,
RGBImage,
RGBAImage,
ImageSeries,
ImageSeriesExternalFile,
ImageMaskSeries,
OpticalSeries,
IndexSeries,
)
from ...core.v2_3_0.core_nwb_ogen import OptogeneticSeries, OptogeneticStimulusSite
from ...core.v2_3_0.core_nwb_icephys import (
PatchClampSeries,
PatchClampSeriesData,
CurrentClampSeries,
CurrentClampSeriesData,
IZeroClampSeries,
CurrentClampStimulusSeries,
CurrentClampStimulusSeriesData,
VoltageClampSeries,
VoltageClampSeriesData,
VoltageClampSeriesCapacitanceFast,
VoltageClampSeriesCapacitanceSlow,
VoltageClampSeriesResistanceCompBandwidth,
VoltageClampSeriesResistanceCompCorrection,
VoltageClampSeriesResistanceCompPrediction,
VoltageClampSeriesWholeCellCapacitanceComp,
VoltageClampSeriesWholeCellSeriesResistanceComp,
VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData,
IntracellularElectrode,
SweepTable,
)
from ...core.v2_3_0.core_nwb_ecephys import (
ElectricalSeries,
SpikeEventSeries,
FeatureExtraction,
EventDetection,
EventWaveform,
FilteredEphys,
LFP,
ElectrodeGroup,
ElectrodeGroupPosition,
ClusterWaveforms,
Clustering,
)
from ...core.v2_3_0.core_nwb_behavior import (
SpatialSeries,
SpatialSeriesData,
BehavioralEpochs,
BehavioralEvents,
BehavioralTimeSeries,
PupilTracking,
EyeTracking,
CompassDirection,
Position,
)
from ...core.v2_3_0.core_nwb_misc import (
AbstractFeatureSeries,
AbstractFeatureSeriesData,
AnnotationSeries,
IntervalSeries,
DecompositionSeries,
DecompositionSeriesData,
DecompositionSeriesBands,
Units,
UnitsSpikeTimes,
)
from ...core.v2_3_0.core_nwb_file import (
ScratchData,
NWBFile,
NWBFileStimulus,
NWBFileGeneral,
GeneralSourceScript,
GeneralExtracellularEphys,
ExtracellularEphysElectrodes,
GeneralIntracellularEphys,
NWBFileIntervals,
LabMetaData,
Subject,
)
from ...core.v2_3_0.core_nwb_epoch import TimeIntervals, TimeIntervalsTimeseries
metamodel_version = "None" metamodel_version = "None"
version = "2.3.0" version = "2.3.0"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_base.py generated
View file

@ -1,28 +1,32 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
import numpy as np from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import ( from typing import (
Any, Any,
ClassVar, ClassVar,
List,
Literal,
Dict, Dict,
Optional,
Union,
Generic, Generic,
Iterable, Iterable,
List,
Literal,
Optional,
Tuple, Tuple,
TypeVar, TypeVar,
Union,
overload, overload,
) )
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
from ...hdmf_common.v1_5_0.hdmf_common_base import Data, Container import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_5_0.hdmf_common_table import VectorData, DynamicTable from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator, model_validator
from ...hdmf_common.v1_5_0.hdmf_common_base import Container, Data
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

18
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_behavior.py generated
View file

@ -1,20 +1,24 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...core.v2_4_0.core_nwb_misc import IntervalSeries from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_4_0.core_nwb_base import ( from ...core.v2_4_0.core_nwb_base import (
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
) )
from ...core.v2_4_0.core_nwb_misc import IntervalSeries
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

14
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_device.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_4_0.core_nwb_base import NWBContainer from ...core.v2_4_0.core_nwb_base import NWBContainer
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_ecephys.py generated
View file

@ -1,30 +1,34 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTableRegion from numpydantic import NDArray, Shape
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_4_0.core_nwb_device import Device
from ...core.v2_4_0.core_nwb_base import ( from ...core.v2_4_0.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBDataInterface,
NWBContainer,
) )
from numpydantic import NDArray, Shape from ...core.v2_4_0.core_nwb_device import Device
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTableRegion
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

20
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_epoch.py generated
View file

@ -1,23 +1,27 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorIndex, VectorData
from ...core.v2_4_0.core_nwb_base import TimeSeries from ...core.v2_4_0.core_nwb_base import TimeSeries
from numpydantic import NDArray, Shape from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData, VectorIndex
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

48
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_file.py generated
View file

@ -1,36 +1,40 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_4_0.core_nwb_misc import Units
from ...core.v2_4_0.core_nwb_device import Device
from ...core.v2_4_0.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_4_0.core_nwb_ophys import ImagingPlane
from ...core.v2_4_0.core_nwb_ecephys import ElectrodeGroup
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_4_0.core_nwb_icephys import (
IntracellularElectrode,
SweepTable,
IntracellularRecordingsTable,
SimultaneousRecordingsTable,
SequentialRecordingsTable,
RepetitionsTable,
ExperimentalConditionsTable,
)
from ...core.v2_4_0.core_nwb_epoch import TimeIntervals
from ...core.v2_4_0.core_nwb_base import ( from ...core.v2_4_0.core_nwb_base import (
NWBData,
NWBContainer, NWBContainer,
NWBData,
NWBDataInterface, NWBDataInterface,
ProcessingModule, ProcessingModule,
TimeSeries, TimeSeries,
) )
from ...core.v2_4_0.core_nwb_device import Device
from ...core.v2_4_0.core_nwb_ecephys import ElectrodeGroup
from ...core.v2_4_0.core_nwb_epoch import TimeIntervals
from ...core.v2_4_0.core_nwb_icephys import (
ExperimentalConditionsTable,
IntracellularElectrode,
IntracellularRecordingsTable,
RepetitionsTable,
SequentialRecordingsTable,
SimultaneousRecordingsTable,
SweepTable,
)
from ...core.v2_4_0.core_nwb_misc import Units
from ...core.v2_4_0.core_nwb_ogen import OptogeneticStimulusSite
from ...core.v2_4_0.core_nwb_ophys import ImagingPlane
from ...hdmf_common.v1_5_0.hdmf_common_table import DynamicTable, VectorData
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

40
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_icephys.py generated
View file

@ -1,36 +1,40 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_4_0.core_nwb_device import Device from numpydantic import NDArray, Shape
from ...core.v2_4_0.core_nwb_base import (
TimeSeries,
TimeSeriesStartingTime,
TimeSeriesSync,
NWBContainer,
TimeSeriesReferenceVectorData,
)
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_4_0.core_nwb_base import (
NWBContainer,
TimeSeries,
TimeSeriesReferenceVectorData,
TimeSeriesStartingTime,
TimeSeriesSync,
)
from ...core.v2_4_0.core_nwb_device import Device
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
VectorIndex,
VectorData,
AlignedDynamicTable, AlignedDynamicTable,
DynamicTable,
DynamicTableRegion, DynamicTableRegion,
VectorData,
VectorIndex,
) )
from numpydantic import NDArray, Shape
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_image.py generated
View file

@ -1,15 +1,19 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_4_0.core_nwb_device import Device
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_4_0.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from ...core.v2_4_0.core_nwb_base import Image, TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_4_0.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

26
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_misc.py generated
View file

@ -1,29 +1,33 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from ...core.v2_4_0.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync from numpydantic import NDArray, Shape
from ...core.v2_4_0.core_nwb_ecephys import ElectrodeGroup
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...core.v2_4_0.core_nwb_base import TimeSeries, TimeSeriesStartingTime, TimeSeriesSync
from ...core.v2_4_0.core_nwb_ecephys import ElectrodeGroup
from ...hdmf_common.v1_5_0.hdmf_common_table import ( from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
DynamicTable, DynamicTable,
DynamicTableRegion,
VectorData, VectorData,
VectorIndex, VectorIndex,
) )
from numpydantic import NDArray, Shape
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"
@ -178,7 +182,7 @@ class AbstractFeatureSeriesData(ConfiguredBaseModel):
json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}}, json_schema_extra={"linkml_meta": {"equals_string": "data", "ifabsent": "string(data)"}},
) )
unit: Optional[str] = Field( unit: Optional[str] = Field(
"see 'feature_units'", "see ",
description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""", description="""Since there can be different units for different features, store the units in 'feature_units'. The default value for this attribute is \"see 'feature_units'\".""",
json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}}, json_schema_extra={"linkml_meta": {"ifabsent": "string(see 'feature_units')"}},
) )

16
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_ogen.py generated
View file

@ -1,21 +1,25 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_4_0.core_nwb_base import ( from ...core.v2_4_0.core_nwb_base import (
NWBContainer,
TimeSeries, TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
NWBContainer,
) )
from ...core.v2_4_0.core_nwb_device import Device from ...core.v2_4_0.core_nwb_device import Device
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

38
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_ophys.py generated
View file

@ -1,36 +1,40 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from datetime import date, datetime, time
from decimal import Decimal
from enum import Enum
from typing import Annotated, Any, ClassVar, Dict, List, Literal, Optional, Type, TypeVar, Union
import numpy as np import numpy as np
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union, Annotated, Type, TypeVar from numpydantic import NDArray, Shape
from pydantic import ( from pydantic import (
BaseModel, BaseModel,
BeforeValidator,
ConfigDict, ConfigDict,
Field, Field,
RootModel, RootModel,
field_validator,
ValidationInfo, ValidationInfo,
BeforeValidator, field_validator,
) )
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTableRegion,
DynamicTable,
VectorIndex,
VectorData,
)
from ...core.v2_4_0.core_nwb_device import Device
from numpydantic import NDArray, Shape
from ...core.v2_4_0.core_nwb_base import ( from ...core.v2_4_0.core_nwb_base import (
NWBContainer,
NWBDataInterface,
TimeSeries,
TimeSeriesStartingTime, TimeSeriesStartingTime,
TimeSeriesSync, TimeSeriesSync,
TimeSeries,
NWBDataInterface,
NWBContainer,
) )
from ...core.v2_4_0.core_nwb_device import Device
from ...core.v2_4_0.core_nwb_image import ImageSeries, ImageSeriesExternalFile from ...core.v2_4_0.core_nwb_image import ImageSeries, ImageSeriesExternalFile
from ...hdmf_common.v1_5_0.hdmf_common_table import (
DynamicTable,
DynamicTableRegion,
VectorData,
VectorIndex,
)
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

16
nwb_models/src/nwb_models/models/pydantic/core/v2_4_0/core_nwb_retinotopy.py generated
View file

@ -1,14 +1,18 @@
from __future__ import annotations from __future__ import annotations
from datetime import datetime, date
from decimal import Decimal
from enum import Enum
import re import re
import sys import sys
from typing import Any, ClassVar, List, Literal, Dict, Optional, Union from datetime import date, datetime, time
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator from decimal import Decimal
from enum import Enum
from typing import Any, ClassVar, Dict, List, Literal, Optional, Union
import numpy as np import numpy as np
from ...core.v2_4_0.core_nwb_base import NWBDataInterface
from numpydantic import NDArray, Shape from numpydantic import NDArray, Shape
from pydantic import BaseModel, ConfigDict, Field, RootModel, field_validator
from ...core.v2_4_0.core_nwb_base import NWBDataInterface
metamodel_version = "None" metamodel_version = "None"
version = "2.4.0" version = "2.4.0"

Some files were not shown because too many files have changed in this diff Show more