nwb-linkml/nwb_linkml/pyproject.toml

[tool.poetry]
name = "nwb-linkml"
version = "0.1.0"
description = "Translating NWB schema language to LinkML"
authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
license = "GPL-3.0"
readme = "README.md"
homepage = "https://nwb-linkml.readthedocs.io"
repository = "https://github.com/p2p-ld/nwb-linkml/"
documentation = "https://nwb-linkml.readthedocs.io"
packages = [
    {include = "nwb_linkml", from="src"},
    #{include = "nwb_schema_language", from="../nwb_schema_language/src"}
]
include = [
    'src/nwb_linkml/schema/**/*'
]


[tool.poetry.dependencies]
python = ">=3.11,<3.13"
pyyaml = "^6.0"
linkml-runtime = "^1.6.0"
nwb_schema_language = "^0.1.3"
rich = "^13.5.2"
linkml = "^1.6.1"
nptyping = "^2.5.0"
pydantic = "^2.3.0"
h5py = "^3.9.0"
dash = {version="^2.12.1", optional=true}
dash-cytoscape = {version="^0.3.0", optional=true}
pytest = { version="^7.4.0", optional=true}
pytest-depends = {version="^1.0.1", optional=true}
coverage = {version = "^6.1.1", optional = true}
pytest-md = {version = "^0.2.0", optional = true}
pytest-cov = {version = "^4.1.0", optional = true}
coveralls = {version = "^3.3.1", optional = true}
pytest-profiling = {version = "^1.7.0", optional = true}
pydantic-settings = "^2.0.3"
dask = "^2023.9.2"
blosc2 = "^2.2.7"
tqdm = "^4.66.1"


[tool.poetry.extras]
tests = [
    "pytest",       "pytest-depends", "coverage",  "pytest-md",
    "pytest-cov",   "coveralls",      "pytest-profiling"
]
plot = ["dash", "dash-cytoscape"]


[tool.poetry.group.tests]
optional = true

[tool.poetry.group.tests.dependencies]
pytest = "^7.4.0"
pytest-depends = "^1.0.1"
coverage = "^6.1.1"
pytest-md = "^0.2.0"
pytest-cov = "^4.1.0"
coveralls = "^3.3.1"
pytest-profiling = "^1.7.0"

[tool.poetry.group.plot]
optional = true

[tool.poetry.group.plot.dependencies]
dash = "^2.12.1"
dash-cytoscape = "^0.3.0"

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"


[tool.pytest.ini_options]
addopts = [
    "--cov=nwb_linkml",
    "--cov-append",
    "--cov-config=.coveragerc",
    "--doctest-modules",
    "--ignore=tests/__tmp__"
]
testpaths = [
    "tests",
    'nwb_linkml/tests'
]
doctest_optionflags = "NORMALIZE_WHITESPACE"
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore:parse_obj:pydantic.PydanticDeprecatedSince20"
]
starts 2023-08-12 02:52:35 +00:00			`[tool.poetry]`
Cleaned up old files, added some mysteriously delayed pydantic models, and submitted to pypi to keep the package name. 2023-08-25 07:52:12 +00:00			`name = "nwb-linkml"`
starts 2023-08-12 02:52:35 +00:00			`version = "0.1.0"`
			`description = "Translating NWB schema language to LinkML"`
			`authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]`
			`license = "GPL-3.0"`
			`readme = "README.md"`
[tests] - test adapter + results 2023-10-09 23:33:02 +00:00			`homepage = "https://nwb-linkml.readthedocs.io"`
			`repository = "https://github.com/p2p-ld/nwb-linkml/"`
			`documentation = "https://nwb-linkml.readthedocs.io"`
progress with using pydantic models 2023-08-18 08:11:14 +00:00			`packages = [`
refactor nwb_linkml to src layout 2023-09-06 02:25:20 +00:00			`{include = "nwb_linkml", from="src"},`
cant include package when out of working directory 2023-09-06 04:55:41 +00:00			`#{include = "nwb_schema_language", from="../nwb_schema_language/src"}`
progress with using pydantic models 2023-08-18 08:11:14 +00:00			`]`
trying to debug on CI by abusing warnings lol 2023-10-12 04:31:00 +00:00			`include = [`
			`'src/nwb_linkml/schema/*/'`
			`]`
starts 2023-08-12 02:52:35 +00:00
[tests] - test adapter + results 2023-10-09 23:33:02 +00:00
starts 2023-08-12 02:52:35 +00:00			`[tool.poetry.dependencies]`
pandas dataframe mimic 2023-09-23 07:08:59 +00:00			`python = ">=3.11,<3.13"`
starts 2023-08-12 02:52:35 +00:00			`pyyaml = "^6.0"`
holy hell it was a TYPE COERCION in the way linkml handles annotations and a version mismatch between CI and local https://github.com/linkml/linkml-model/pull/162 2023-10-12 05:30:26 +00:00			`linkml-runtime = "^1.6.0"`
updating nwb_schema_language to have proper single/multi fields for author/contact 2023-10-10 08:08:25 +00:00			`nwb_schema_language = "^0.1.3"`
working schema language import 2023-08-19 05:09:28 +00:00			`rich = "^13.5.2"`
holy hell it was a TYPE COERCION in the way linkml handles annotations and a version mismatch between CI and local https://github.com/linkml/linkml-model/pull/162 2023-10-12 05:30:26 +00:00			`linkml = "^1.6.1"`
Cleaner code generation, npytyping type hints for arrays - split off generated subclasses into "include" files, not sure if that's good, but in any case we have them separable now. - more work on cleanly un-nesting scalar and 1D-vector data into attributes and lists, respectively - brought the pydantic generator in-repo to do a bunch of overrides 2023-08-29 05:16:58 +00:00			`nptyping = "^2.5.0"`
update to pydantic 2 2023-08-31 22:36:58 +00:00			`pydantic = "^2.3.0"`
- Able to complete build all the way through to importing generated classes 2023-09-05 04:46:17 +00:00			`h5py = "^3.9.0"`
some baseline tests, fixing imports, coverage reports 2023-09-06 04:47:41 +00:00			`dash = {version="^2.12.1", optional=true}`
			`dash-cytoscape = {version="^0.3.0", optional=true}`
			`pytest = { version="^7.4.0", optional=true}`
			`pytest-depends = {version="^1.0.1", optional=true}`
			`coverage = {version = "^6.1.1", optional = true}`
			`pytest-md = {version = "^0.2.0", optional = true}`
			`pytest-cov = {version = "^4.1.0", optional = true}`
			`coveralls = {version = "^3.3.1", optional = true}`
perf enhancements to pydantic generation 2023-09-07 05:48:47 +00:00			`pytest-profiling = {version = "^1.7.0", optional = true}`
working on providers to cache generated models 2023-09-08 01:50:50 +00:00			`pydantic-settings = "^2.0.3"`
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00			`dask = "^2023.9.2"`
			`blosc2 = "^2.2.7"`
fix truncate hdf5 file to not try and write while iterating 2023-10-05 03:19:54 +00:00			`tqdm = "^4.66.1"`
Use dask instead of trying to make a dataframe compress arrays when serializing to json 2023-09-27 02:50:49 +00:00
Cleaned up old files, added some mysteriously delayed pydantic models, and submitted to pypi to keep the package name. 2023-08-25 07:52:12 +00:00
			`[tool.poetry.extras]`
some baseline tests, fixing imports, coverage reports 2023-09-06 04:47:41 +00:00			`tests = [`
perf enhancements to pydantic generation 2023-09-07 05:48:47 +00:00			`"pytest", "pytest-depends", "coverage", "pytest-md",`
Add ability to make JSON schema with numpy arrays! 2023-09-15 06:43:00 +00:00			`"pytest-cov", "coveralls", "pytest-profiling"`
some baseline tests, fixing imports, coverage reports 2023-09-06 04:47:41 +00:00			`]`
Cleaned up old files, added some mysteriously delayed pydantic models, and submitted to pypi to keep the package name. 2023-08-25 07:52:12 +00:00			`plot = ["dash", "dash-cytoscape"]`

starts 2023-08-12 02:52:35 +00:00
I believe that's a full translation or at least all the semantics are present. it's not pretty by any stretch of the imagination 2023-08-25 07:22:47 +00:00			`[tool.poetry.group.tests]`
			`optional = true`
starts 2023-08-12 02:52:35 +00:00
I believe that's a full translation or at least all the semantics are present. it's not pretty by any stretch of the imagination 2023-08-25 07:22:47 +00:00			`[tool.poetry.group.tests.dependencies]`
some vague sketching on mapping namespaces 2023-08-21 06:00:58 +00:00			`pytest = "^7.4.0"`
recursion works, more formal build method in adapters 2023-08-24 02:56:09 +00:00			`pytest-depends = "^1.0.1"`
some baseline tests, fixing imports, coverage reports 2023-09-06 04:47:41 +00:00			`coverage = "^6.1.1"`
			`pytest-md = "^0.2.0"`
			`pytest-cov = "^4.1.0"`
cant include package when out of working directory 2023-09-06 04:55:41 +00:00			`coveralls = "^3.3.1"`
perf enhancements to pydantic generation 2023-09-07 05:48:47 +00:00			`pytest-profiling = "^1.7.0"`
some vague sketching on mapping namespaces 2023-08-21 06:00:58 +00:00
I believe that's a full translation or at least all the semantics are present. it's not pretty by any stretch of the imagination 2023-08-25 07:22:47 +00:00			`[tool.poetry.group.plot]`
			`optional = true`

			`[tool.poetry.group.plot.dependencies]`
			`dash = "^2.12.1"`
			`dash-cytoscape = "^0.3.0"`

starts 2023-08-12 02:52:35 +00:00			`[build-system]`
			`requires = ["poetry-core"]`
			`build-backend = "poetry.core.masonry.api"`
some vague sketching on mapping namespaces 2023-08-21 06:00:58 +00:00

			`[tool.pytest.ini_options]`
huh coverage got disabled somehow 2023-10-06 01:10:04 +00:00			`addopts = [`
			`"--cov=nwb_linkml",`
			`"--cov-append",`
Regenerate nwb_schema_language models 2023-10-09 22:06:53 +00:00			`"--cov-config=.coveragerc",`
fix tests, cant assign to tuple 2023-10-10 01:59:53 +00:00			`"--doctest-modules",`
			`"--ignore=tests/__tmp__"`
huh coverage got disabled somehow 2023-10-06 01:10:04 +00:00			`]`
some baseline tests, fixing imports, coverage reports 2023-09-06 04:47:41 +00:00			`testpaths = [`
passing test directory??? 2023-09-06 05:29:48 +00:00			`"tests",`
			`'nwb_linkml/tests'`
some baseline tests, fixing imports, coverage reports 2023-09-06 04:47:41 +00:00			`]`
fix tests, cant assign to tuple 2023-10-10 01:59:53 +00:00			`doctest_optionflags = "NORMALIZE_WHITESPACE"`
			`filterwarnings = [`
install hdf5 2023-10-10 06:40:31 +00:00			`"ignore::DeprecationWarning",`
fix tests, cant assign to tuple 2023-10-10 01:59:53 +00:00			`"ignore:parse_obj:pydantic.PydanticDeprecatedSince20"`
			`]`