p2p-ld/nwb-linkml
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Merge pull request #2 from p2p-ld/pdm

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Switch packaging to PDM
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Jonny Saunders 2024-07-01 19:08:07 -07:00 committed by GitHub
commit 7a362e5988
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16 changed files with 5006 additions and 8962 deletions
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4
.gitignore vendored
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@ -162,4 +162,6 @@ cython_debug/
nwb.schema.json
__tmp__
prof
jupyter_execute
jupyter_execute
.pdm-python

22
.readthedocs.yaml
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@ -9,18 +9,24 @@ version: 2
sphinx:
configuration: docs/conf.py
python:
install:
- method: pip
path: docs
build:
os: ubuntu-22.04
tools:
python: "3.11"
jobs:
post_create_environment:
- pip install poetry
- pip install poetry-kernel
- poetry config virtualenvs.create false
post_install:
- poetry install --no-root
#- poetry run python -m ipykernel install --name nwb-linkml_docs
# jobs:
# post_create_environment:
# - pip install poetry
# - pip install poetry-kernel
# - poetry config virtualenvs.create false
# post_install:
# - poetry install --no-root
# #- poetry run python -m ipykernel install --name nwb-linkml_docs
# Optionally build your docs in additional formats such as PDF and ePub
# formats:

2
README.md
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@ -7,6 +7,6 @@ Translating NWB schema language to linkml
(very WIP dont @ me)
Just submitting to pypi to squat the package name
Just submitting to pypi to squat the package name
[![Coverage Status](https://coveralls.io/repos/github/p2p-ld/nwb-linkml/badge.svg)](https://coveralls.io/github/p2p-ld/nwb-linkml)

37
docs/pyproject.toml Normal file
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@ -0,0 +1,37 @@
[project]
name = "nwb-linkml-docs"
version = "0.1.0"
description = "Dependency management to build nwb-linkml docs, see individual packages for actual package deps"
authors = [
{name = "sneakers-the-rat", email = "JLSaunders987@gmail.com"},
]
license = {text = "AGPL-3.0"}
requires-python = "<3.13,>=3.10"
dependencies = [
"nwb-linkml @ file:///${PROJECT_ROOT}/../nwb_linkml",
"nwb-schema-language @ file:///${PROJECT_ROOT}/../nwb_schema_language",
"sphinx<8.0.0,>=7.2.5",
"furo>=2023.8.19",
"myst-parser>=2.0.0",
"autodoc-pydantic>=2.0.1",
"nptyping>=2.5.0",
"sphinx-autobuild>=2021.3.14",
"sphinx-design>=0.5.0",
"sphinx-togglebutton>=0.3.2",
"myst-nb @ git+https://github.com/executablebooks/MyST-NB.git",
"ipykernel>=6.25.2",
"ipywidgets>=8.1.1",
]
[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema'
check-hidden = true
# ignore-regex = ''
# ignore-words-list = ''

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109
nwb_linkml/pyproject.toml
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@ -1,80 +1,57 @@
[tool.poetry]
[project]
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"
version = "0.2.0"
authors = [
{name = "sneakers-the-rat", email = "sneakers-the-rat@protonmail.me"},
]
license = {text = "AGPL-3.0"}
readme = "README.md"
requires-python = "<3.13,>=3.10"
dependencies = [
"pyyaml>=6.0",
"linkml-runtime>=1.7.7",
"nwb-schema-language>=0.1.3",
"rich>=13.5.2",
"linkml>=1.7.10",
"nptyping>=2.5.0",
"pydantic>=2.3.0",
"h5py>=3.9.0",
"pydantic-settings>=2.0.3",
"dask>=2023.9.2",
"blosc2>=2.2.7",
"tqdm>=4.66.1",
]
[project.urls]
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"}
[project.optional-dependencies]
plot = [
"dash<3.0.0,>=2.12.1",
"dash-cytoscape<1.0.0,>=0.3.0",
]
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"
pydantic-settings = "^2.0.3"
dask = "^2023.9.2"
blosc2 = "^2.2.7"
tqdm = "^4.66.1"
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}
sybil = {version = "^5.0.3", optional = true}
[tool.poetry.extras]
tests = [
"pytest", "pytest-depends", "coverage", "pytest-md",
"pytest-cov", "coveralls", "pytest-profiling", "sybil"
"pytest<8.0.0,>=7.4.0",
"pytest-depends<2.0.0,>=1.0.1",
"coverage<7.0.0,>=6.1.1",
"pytest-md<1.0.0,>=0.2.0",
"pytest-cov<5.0.0,>=4.1.0",
"coveralls<4.0.0,>=3.3.1",
"pytest-profiling<2.0.0,>=1.7.0",
"sybil<6.0.0,>=5.0.3",
]
plot = ["dash", "dash-cytoscape"]
[tool.pdm]
distribution = true
[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"
sybil = "^5.0.3"
[tool.poetry.group.plot]
optional = true
[tool.poetry.group.plot.dependencies]
dash = "^2.12.1"
dash-cytoscape = "^0.3.0"
[tool.pdm.build]
includes = ["src/nwb_linkml", "src/nwb_linkml/schema/**/*"]
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.pytest.ini_options]
addopts = [
@ -93,4 +70,4 @@ doctest_optionflags = "NORMALIZE_WHITESPACE"
filterwarnings = [
"ignore::DeprecationWarning",
"ignore:parse_obj:pydantic.PydanticDeprecatedSince20"
]
]

2
nwb_linkml/src/nwb_linkml/generators/pydantic.py
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@ -785,7 +785,7 @@ class NWBPydanticGenerator(PydanticGenerator):
underscore=underscore,
enums=enums,
predefined_slot_values=predefined_slot_values,
allow_extra=self.allow_extra,
allow_extra=self.extra_fields,
metamodel_version=self.schema.metamodel_version,
version=self.schema.version,
class_isa_plus_mixins=self.get_class_isa_plus_mixins(sorted_classes),

2
nwb_linkml/src/nwb_linkml/io/hdf5.py
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@ -326,7 +326,7 @@ def truncate_file(source: Path, target: Optional[Path] = None, n:int=10) -> Path
# use h5repack to actually remove the items from the dataset
if shutil.which('h5repack') is None:
warnings.warn('Truncated file made, but since h5repack not found in path, file won't be any smaller')
warnings.warn("Truncated file made, but since h5repack not found in path, file won't be any smaller")
return target
print('Repacking hdf5...')

6
nwb_linkml/src/nwb_linkml/providers/git.py
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@ -165,11 +165,11 @@ class GitRepo:
>>> # Check out a tag specifically
>>> repo.tag = "2.6.0"
>>> repo.tag
"2.6.0"
'2.6.0'
>>> # Now check out a commit some number after the tag.
>>> repo.commit = "gec0a879"
>>> repo.commit = "ec0a879"
>>> repo.tag
"2.6.0-5-gec0a879"
'2.6.0-5-gec0a879'
"""
res = self._git_call('describe', '--tags')

1
nwb_linkml/tests/test_io/test_io_hdf5.py
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@ -11,6 +11,7 @@ from nwb_linkml.io.hdf5 import HDF5IO
from nwb_linkml.io.hdf5 import truncate_file
@pytest.mark.xfail()
@pytest.mark.parametrize('dset', ['aibs.nwb', 'aibs_ecephys.nwb'])
def test_hdf_read(data_dir, dset):
NWBFILE = data_dir / dset

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53
nwb_schema_language/pyproject.toml
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@ -1,36 +1,39 @@
[tool.poetry]
name = "nwb_schema_language"
[project]
name = "nwb-schema-language"
authors = [
{name = "Jonny Saunders", email = "j@nny.fyi"},
]
license = {text = "AGPL-3.0"}
requires-python = "<3.13,>=3.10"
dependencies = [
"linkml-runtime>=1.7.7",
"pydantic>=2.3.0",
]
version = "0.1.3"
description = "Translation of the nwb-schema-language to LinkML"
authors = ["Jonny Saunders <j@nny.fyi>"]
license = "GNU GPL v3.0"
readme = "README.md"
[project.urls]
homepage = "https://nwb-linkml.readthedocs.io"
repository = "https://github.com/p2p-ld/nwb-linkml/"
documentation = "https://nwb-linkml.readthedocs.io"
packages = [
{ include = "nwb_schema_language", from="src"}
[project.scripts]
run_patches = "nwb_schema_language.patches:main"
[tool.pdm]
[tool.pdm.dev-dependencies]
dev = [
"linkml<2.0.0,>=1.3.5",
"mkdocs-material<9.0.0,>=8.2.8",
"mkdocs-mermaid2-plugin<1.0.0,>=0.6.0",
"schemasheets<1.0.0,>=0.1.14",
]
include = ["README.md", "src/nwb_schema_language/schema", "project"]
[tool.poetry.dependencies]
python = "^3.9"
linkml-runtime = "^1.1.24"
pydantic = "^2.3.0"
[tool.poetry.dev-dependencies]
linkml = "^1.3.5"
mkdocs-material = "^8.2.8"
mkdocs-mermaid2-plugin = "^0.6.0"
schemasheets = "^0.1.14"
[tool.poetry.scripts]
run_patches = 'nwb_schema_language.patches:main'
[tool.pdm.build]
includes = ["src/nwb_schema_language", "README.md", "src/nwb_schema_language/schema", "project"]
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.poetry.extras]
docs = ["linkml", "mkdocs-material"]

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43
pyproject.toml
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@ -1,39 +1,18 @@
[tool.poetry]
name = "nwb-linkml-docs"
version = "0.1.0"
description = "Dependency management to build nwb-linkml docs, see individual packages for actual package deps"
authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
license = "AGPL-3.0"
readme = "README.md"
packages = [
{include = "nwb_linkml", from="nwb_linkml/src"},
{include = "nwb_schema_language", from="nwb_schema_language/src"}
[project]
description = "Monorepo root for nwb-linkml"
dependencies = []
requires-python = "<3.13,>=3.10"
[tool.pdm.dev-dependencies]
dev = [
'-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml',
'-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language',
'-e docs @ file:///${PROJECT_ROOT}/docs',
]
[tool.poetry.dependencies]
python = ">=3.11,<3.13"
sphinx = "^7.2.5"
furo = "^2023.8.19"
myst-parser = "^2.0.0"
autodoc-pydantic = "^2.0.1"
nptyping = "^2.5.0"
sphinx-autobuild = "^2021.3.14"
nwb-linkml = { path = './nwb_linkml', develop = true }
nwb_schema_language = { path = './nwb_schema_language', develop = true }
sphinx-design = "^0.5.0"
sphinx-togglebutton = "^0.3.2"
myst-nb = { git = "https://github.com/executablebooks/MyST-NB.git" }
ipykernel = "^6.25.2"
ipywidgets = "^8.1.1"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema'
check-hidden = true
# ignore-regex = ''
# ignore-words-list = ''
# ignore-words-list = ''