p2p-ld/nwb-linkml
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nwb-linkml/nwb_linkml/pyproject.toml

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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
]
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"
progress with using pydantic models
2023-08-18 08:11:14 +00:00
linkml-runtime = "^1.5.6"
upload to pypi
2023-09-06 05:10:10 +00:00
nwb_schema_language = "^0.1.1"
working schema language import
2023-08-19 05:09:28 +00:00
rich = "^13.5.2"
some vague sketching on mapping namespaces
2023-08-21 06:00:58 +00:00
linkml = "^1.5.7"
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 = [
"ignore:Deprecated NumPy 1.24:DeprecationWarning",
"ignore:parse_obj:pydantic.PydanticDeprecatedSince20"
]
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