diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..b575275f
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,9 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+- package-ecosystem: github-actions
+ directory: "/"
+ schedule:
+ interval: monthly
diff --git a/.github/workflows/check-dependencies.yaml b/.github/workflows/check-dependencies.yaml
index 3a43f463..fe121bb2 100644
--- a/.github/workflows/check-dependencies.yaml
+++ b/.github/workflows/check-dependencies.yaml
@@ -13,7 +13,7 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest]
- python-version: ["3.8", "3.9", "3.10"]
+ python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
exclude:
- os: windows-latest
python-version: "3.8"
@@ -26,17 +26,23 @@ jobs:
# install poetry
#----------------------------------------------
- name: Install Poetry
- # Pin to 1.3.2 to workaround https://github.com/python-poetry/poetry/issues/7611
- run: pipx install poetry==1.3.2
+ run: pipx install poetry
+
+ # We install poetry-dynamic-versioning into pipx because the automatic installallation
+ # by poetry 2.x triggers a Windows issue https://github.com/pypa/installer/issues/260
+ # and also does not work on Ubuntu in gh-actions.
+ - name: Install poetry-dynamic-versioning
+ run:
+ pipx inject poetry poetry-dynamic-versioning
#----------------------------------------------
# check-out repo and set-up python
#----------------------------------------------
- name: Check out repository
- uses: actions/checkout@v3
+ uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
with:
python-version: ${{ matrix.python-version }}
cache: 'poetry'
@@ -62,4 +68,5 @@ jobs:
run: Remove-Item poetry.lock -Force
- name: Run tests
- run: poetry run python -m unittest discover
\ No newline at end of file
+ shell: bash
+ run: poetry run python -m pytest --with-slow
\ No newline at end of file
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 973acf9c..7de84317 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -1,40 +1,50 @@
-# Built from:
-# https://docs.github.com/en/actions/guides/building-and-testing-python
-# https://github.com/actions/setup-python/
-
+# Action passes pedantic check with zizmor 1.3.0, https://woodruffw.github.io/zizmor/
name: Build and test linkml-runtime
on: [pull_request]
+permissions: {}
+
jobs:
test:
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest]
- python-version: ["3.8", "3.9", "3.10", "3.12"]
+ python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
exclude:
- os: windows-latest
python-version: "3.8"
-
runs-on: ${{ matrix.os }}
-
+ permissions:
+ contents: read
steps:
#----------------------------------------------
# install poetry
#----------------------------------------------
- name: Install Poetry
- run: pipx install poetry==1.4.0
-
+ run: |
+ pipx install poetry
+
+ # We install poetry-dynamic-versioning into pipx because the automatic installallation
+ # by poetry 2.x triggers a Windows issue https://github.com/pypa/installer/issues/260
+ # and also does not work on Ubuntu in gh-actions.
+ - name: Install poetry-dynamic-versioning
+ run:
+ pipx inject poetry poetry-dynamic-versioning
+
#----------------------------------------------
# check-out repo and set-up python
#----------------------------------------------
- name: Check out repository
- uses: actions/checkout@v3
+ uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+ with:
+ fetch-depth: 0
+ persist-credentials: false
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
with:
python-version: ${{ matrix.python-version }}
cache: 'poetry'
@@ -43,12 +53,14 @@ jobs:
# install your root project, if required
#----------------------------------------------
- name: Install library
- run: poetry install --no-interaction
+ run: |
+ poetry install --no-interaction
#----------------------------------------------
# coverage report
#----------------------------------------------
- name: Generate coverage results
+ shell: bash
run: |
poetry run coverage run -m pytest
poetry run coverage xml
@@ -58,7 +70,7 @@ jobs:
# upload coverage results
#----------------------------------------------
- name: Upload coverage report
- uses: codecov/codecov-action@v3
+ uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3
with:
name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }}
token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml
index a47376cb..0b30ce10 100644
--- a/.github/workflows/pypi-publish.yaml
+++ b/.github/workflows/pypi-publish.yaml
@@ -1,21 +1,21 @@
name: Publish Python Package
+# Publishes to PyPI triggered by creating a releases in GitHub UI
on:
release:
- types: [created]
+ types: [published]
jobs:
- build-n-publish:
- name: Build and publish Python 🐍 distributions 📦 to PyPI
+ build:
+ name: Build Python 🐍 distributions 📦 for publishing to PyPI
runs-on: ubuntu-latest
-
steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
- name: Set up Python
- uses: actions/setup-python@v2.2.2
+ uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
with:
- python-version: 3.8
+ python-version: 3.12
- name: Install Poetry
run: pipx install poetry
@@ -28,8 +28,40 @@ jobs:
poetry version $(git describe --tags --abbrev=0)
poetry build
- - name: Publish distribution 📦 to PyPI
- uses: pypa/gh-action-pypi-publish@v1.2.2
+ - name: Store built distribution
+ uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
with:
- user: __token__
- password: ${{ secrets.pypi_password }}
+ name: distribution-files
+ path: dist/
+
+ pypi-publish:
+ name: Build and publish Python 🐍 package 📦 to PyPI
+ needs: build
+ runs-on: ubuntu-latest
+ # Next 5 lines prepare for trusted publishing: https://docs.pypi.org/trusted-publishers/adding-a-publisher/
+ # environment:
+ # name: pypi-release
+ # url: https://pypi.org/p/linkml-runtime
+ # permissions:
+ # id-token: write # this permission is mandatory for trusted publishing
+ steps:
+ - name: Download built distribution
+ uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16
+ with:
+ name: distribution-files
+ path: dist
+
+ - name: Publish package 📦 to PyPI
+ if: github.event_name == 'release'
+ uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
+ with:
+ user: __token__
+ password: ${{ secrets.pypi_password }}
+ # verbose: true
+
+# Used actions: (updates managed by dependabot)
+# - https://github.com/actions/checkout
+# - https://github.com/actions/setup-python
+# - https://github.com/actions/upload-artifact
+# - https://github.com/actions/download-artifact
+# - https://github.com/pypa/gh-action-pypi-publish/
diff --git a/.github/workflows/test-upstream.yaml b/.github/workflows/test-upstream.yaml
index eb07758c..3a5d57bd 100644
--- a/.github/workflows/test-upstream.yaml
+++ b/.github/workflows/test-upstream.yaml
@@ -1,4 +1,4 @@
-name: Test with upstream linkml
+name: Test linkml-runtime with upstream linkml and run linkml tests
on:
pull_request_review:
types: [ submitted ]
@@ -8,6 +8,7 @@ jobs:
test_upstream:
if: github.event_name == 'workflow_dispatch' || github.event.review.state == 'APPROVED'
strategy:
+ fail-fast: false
matrix:
os: [ ubuntu-latest, windows-latest ]
python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
@@ -24,8 +25,8 @@ jobs:
steps:
- - name: checkout upstream
- uses: actions/checkout@v4
+ - name: checkout upstream linkml
+ uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
with:
repository: linkml/linkml
path: linkml
@@ -33,64 +34,54 @@ jobs:
fetch-depth: 0
- name: checkout linkml-runtime
- uses: actions/checkout@v4
+ uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
with:
- # don't specify repository like this or else we won't get pull request branches correctly
- # repository: linkml/linkml-runtime
path: linkml-runtime
fetch-depth: 0
- - name: Ensure tags if not run from main repo
+ - name: Ensure linkml-runtime tags if not run from main repo
if: github.repository != 'linkml/linkml-runtime'
working-directory: linkml-runtime
run: |
git remote add upstream https://github.com/linkml/linkml-runtime
git fetch upstream --tags
-
+
- name: set up python
- uses: actions/setup-python@v5
+ uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
with:
python-version: ${{ matrix.python-version }}
- name: Install poetry
run: pipx install poetry
- - name: Install dynamic versioning plugin
- run: poetry self add "poetry-dynamic-versioning[plugin]"
+ # We install poetry-dynamic-versioning into pipx because the automatic installallation
+ # by poetry 2.x triggers a Windows issue https://github.com/pypa/installer/issues/260
+ # and also does not work on Ubuntu in gh-actions.
+ - name: Install poetry-dynamic-versioning
+ run:
+ pipx inject poetry poetry-dynamic-versioning
- name: Load cached venv
id: cached-poetry-dependencies
- uses: actions/cache@v3
+ uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57
with:
path: linkml/.venv
key: venv-${{ matrix.python-version }}-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
- # make extra sure we're removing any old version of linkml-runtime that exists
- - name: uninstall potentially cached linkml-runtime
- working-directory: linkml
- run: poetry run pip uninstall linkml-runtime
-
- # we are not using linkml-runtime's lockfile, but simulating what will happen
- # when we merge this and update linkml's lockfile
- - name: add linkml-runtime to lockfile
- working-directory: linkml
- run: poetry add ../linkml-runtime
-
- # note that we run the installation step always, even if we restore a venv,
- # the cache will restore the old version of linkml-runtime, but the lockfile
- # will only store the directory dependency (and thus will reinstall it)
- # the cache will still speedup the rest of the installation
- - name: install linkml
+ # We are not using linkml-runtime's lockfile, but simulate what will happen
+ # when we merge this and update linkml's lockfile.
+ # By using poetry sync we remove any old stuff that exists in the cache.
+ - name: Refresh or install linkml & add linkml-runtime to check dependencies
working-directory: linkml
- run: poetry install --no-interaction -E tests
-
+ run: |
+ poetry sync --extras tests
+ poetry add ../linkml-runtime
+
- name: print linkml-runtime version
working-directory: linkml
run: poetry run python -c 'import linkml_runtime; from importlib.metadata import version; print(linkml_runtime.__file__); print(version("linkml_runtime"))'
- - name: run tests
+ - name: run linkml tests
+ shell: bash
working-directory: linkml
run: poetry run python -m pytest --with-slow
-
-
-
diff --git a/poetry.lock b/poetry.lock
index afd28039..b3739ad7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
[[package]]
name = "annotated-types"
@@ -6,6 +6,7 @@ version = "0.6.0"
description = "Reusable constraint types to use with typing.Annotated"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
{file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
@@ -20,6 +21,7 @@ version = "23.2.0"
description = "Classes Without Boilerplate"
optional = false
python-versions = ">=3.7"
+groups = ["main", "dev"]
files = [
{file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
{file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
@@ -39,6 +41,7 @@ version = "23.2.3"
description = "Composable complex class support for attrs and dataclasses."
optional = false
python-versions = ">=3.8"
+groups = ["dev"]
files = [
{file = "cattrs-23.2.3-py3-none-any.whl", hash = "sha256:0341994d94971052e9ee70662542699a3162ea1e0c62f7ce1b4a57f563685108"},
{file = "cattrs-23.2.3.tar.gz", hash = "sha256:a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f"},
@@ -64,6 +67,7 @@ version = "2024.2.2"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
+groups = ["main", "dev"]
files = [
{file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
{file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
@@ -75,6 +79,7 @@ version = "3.3.2"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
optional = false
python-versions = ">=3.7.0"
+groups = ["main", "dev"]
files = [
{file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
{file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
@@ -174,6 +179,7 @@ version = "8.1.7"
description = "Composable command line interface toolkit"
optional = false
python-versions = ">=3.7"
+groups = ["main"]
files = [
{file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
{file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
@@ -188,6 +194,8 @@ version = "0.4.6"
description = "Cross-platform colored terminal text."
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["main"]
+markers = "platform_system == \"Windows\" or sys_platform == \"win32\""
files = [
{file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
{file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
@@ -199,6 +207,7 @@ version = "6.5.0"
description = "Code coverage measurement for Python"
optional = false
python-versions = ">=3.7"
+groups = ["dev"]
files = [
{file = "coverage-6.5.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ef8674b0ee8cc11e2d574e3e2998aea5df5ab242e012286824ea3c6970580e53"},
{file = "coverage-6.5.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:784f53ebc9f3fd0e2a3f6a78b2be1bd1f5575d7863e10c6e12504f240fd06660"},
@@ -261,6 +270,7 @@ version = "0.7.7"
description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "curies-0.7.7-py3-none-any.whl", hash = "sha256:609de3e8cdf39f410e8f4d9f06eb7df379465860f4fb441bf0e79672430f8e2a"},
{file = "curies-0.7.7.tar.gz", hash = "sha256:a8d674029f906fb9c3564eafa0862ce96725932bd801fa751e076265b111cb34"},
@@ -285,6 +295,7 @@ version = "1.2.14"
description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["main"]
files = [
{file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"},
{file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"},
@@ -302,6 +313,8 @@ version = "1.2.0"
description = "Backport of PEP 654 (exception groups)"
optional = false
python-versions = ">=3.7"
+groups = ["main", "dev"]
+markers = "python_version < \"3.11\""
files = [
{file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
{file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
@@ -316,6 +329,7 @@ version = "0.9.1"
description = "Honey Badger reader - a generic file/url/string open and read tool"
optional = false
python-versions = ">=3.7"
+groups = ["main"]
files = [
{file = "hbreader-0.9.1-py3-none-any.whl", hash = "sha256:9a6e76c9d1afc1b977374a5dc430a1ebb0ea0488205546d4678d6e31cc5f6801"},
{file = "hbreader-0.9.1.tar.gz", hash = "sha256:d2c132f8ba6276d794c66224c3297cec25c8079d0a4cf019c061611e0a3b94fa"},
@@ -327,6 +341,7 @@ version = "3.6"
description = "Internationalized Domain Names in Applications (IDNA)"
optional = false
python-versions = ">=3.5"
+groups = ["main", "dev"]
files = [
{file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
{file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
@@ -334,21 +349,27 @@ files = [
[[package]]
name = "importlib-resources"
-version = "6.1.1"
+version = "6.4.5"
description = "Read resources from Python packages"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version < \"3.9\""
files = [
- {file = "importlib_resources-6.1.1-py3-none-any.whl", hash = "sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6"},
- {file = "importlib_resources-6.1.1.tar.gz", hash = "sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a"},
+ {file = "importlib_resources-6.4.5-py3-none-any.whl", hash = "sha256:ac29d5f956f01d5e4bb63102a5a19957f1b9175e45649977264a1416783bb717"},
+ {file = "importlib_resources-6.4.5.tar.gz", hash = "sha256:980862a1d16c9e147a59603677fa2aa5fd82b87f223b6cb870695bcfce830065"},
]
[package.dependencies]
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"]
+type = ["pytest-mypy"]
[[package]]
name = "iniconfig"
@@ -356,6 +377,7 @@ version = "2.0.0"
description = "brain-dead simple config-ini parsing"
optional = false
python-versions = ">=3.7"
+groups = ["main"]
files = [
{file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
{file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
@@ -367,6 +389,7 @@ version = "0.6.1"
description = "An ISO 8601 date/time/duration parser and formatter"
optional = false
python-versions = "*"
+groups = ["main"]
files = [
{file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"},
{file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"},
@@ -381,6 +404,7 @@ version = "0.1.9"
description = "Python library for denormalizing nested dicts or json objects to tables and back"
optional = false
python-versions = ">=3.7.0"
+groups = ["main"]
files = [
{file = "json_flattener-0.1.9-py3-none-any.whl", hash = "sha256:6b027746f08bf37a75270f30c6690c7149d5f704d8af1740c346a3a1236bc941"},
{file = "json_flattener-0.1.9.tar.gz", hash = "sha256:84cf8523045ffb124301a602602201665fcb003a171ece87e6f46ed02f7f0c15"},
@@ -396,6 +420,7 @@ version = "1.0.4"
description = "JSON as python objects - version 2"
optional = false
python-versions = ">=3.6"
+groups = ["main"]
files = [
{file = "jsonasobj2-1.0.4-py3-none-any.whl", hash = "sha256:12e86f86324d54fcf60632db94ea74488d5314e3da554c994fe1e2c6f29acb79"},
{file = "jsonasobj2-1.0.4.tar.gz", hash = "sha256:f50b1668ef478004aa487b2d2d094c304e5cb6b79337809f4a1f2975cc7fbb4e"},
@@ -410,6 +435,7 @@ version = "4.21.1"
description = "An implementation of JSON Schema validation for Python"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
{file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
@@ -433,6 +459,7 @@ version = "2023.12.1"
description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
{file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
@@ -448,6 +475,7 @@ version = "23.2"
description = "Core utilities for Python packages"
optional = false
python-versions = ">=3.7"
+groups = ["main"]
files = [
{file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
{file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
@@ -459,6 +487,8 @@ version = "1.3.10"
description = "Resolve a name to an object."
optional = false
python-versions = ">=3.6"
+groups = ["main"]
+markers = "python_version < \"3.9\""
files = [
{file = "pkgutil_resolve_name-1.3.10-py3-none-any.whl", hash = "sha256:ca27cc078d25c5ad71a9de0a7a330146c4e014c2462d9af19c6b828280649c5e"},
{file = "pkgutil_resolve_name-1.3.10.tar.gz", hash = "sha256:357d6c9e6a755653cfd78893817c0853af365dd51ec97f3d358a819373bbd174"},
@@ -470,6 +500,7 @@ version = "4.2.0"
description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
optional = false
python-versions = ">=3.8"
+groups = ["dev"]
files = [
{file = "platformdirs-4.2.0-py3-none-any.whl", hash = "sha256:0614df2a2f37e1a662acbd8e2b25b92ccf8632929bc6d43467e17fe89c75e068"},
{file = "platformdirs-4.2.0.tar.gz", hash = "sha256:ef0cc731df711022c174543cb70a9b5bd22e5a9337c8624ef2c2ceb8ddad8768"},
@@ -485,6 +516,7 @@ version = "1.4.0"
description = "plugin and hook calling mechanisms for python"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
{file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
@@ -500,6 +532,7 @@ version = "0.1.12"
description = "A python API for working with ID prefixes"
optional = false
python-versions = ">=3.7,<4.0"
+groups = ["main"]
files = [
{file = "prefixcommons-0.1.12-py3-none-any.whl", hash = "sha256:16dbc0a1f775e003c724f19a694fcfa3174608f5c8b0e893d494cf8098ac7f8b"},
{file = "prefixcommons-0.1.12.tar.gz", hash = "sha256:22c4e2d37b63487b3ab48f0495b70f14564cb346a15220f23919eb0c1851f69f"},
@@ -517,6 +550,7 @@ version = "0.2.2"
description = "A python library for retrieving semantic prefix maps"
optional = false
python-versions = ">=3.8,<4.0"
+groups = ["main"]
files = [
{file = "prefixmaps-0.2.2-py3-none-any.whl", hash = "sha256:4ac2bf3ddb9b27c40c978cf937e9bedb160050d24e8c679b94c9c885e1d73c72"},
{file = "prefixmaps-0.2.2.tar.gz", hash = "sha256:a36b1554154ef465271bde82dc91cd671e2d31dc1f50c2fd08ccb0d7d5791c33"},
@@ -532,6 +566,7 @@ version = "2.6.1"
description = "Data validation using Python type hints"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "pydantic-2.6.1-py3-none-any.whl", hash = "sha256:0b6a909df3192245cb736509a92ff69e4fef76116feffec68e93a567347bae6f"},
{file = "pydantic-2.6.1.tar.gz", hash = "sha256:4fd5c182a2488dc63e6d32737ff19937888001e2a6d86e94b3f233104a5d1fa9"},
@@ -551,6 +586,7 @@ version = "2.16.2"
description = ""
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "pydantic_core-2.16.2-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:3fab4e75b8c525a4776e7630b9ee48aea50107fea6ca9f593c98da3f4d11bf7c"},
{file = "pydantic_core-2.16.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8bde5b48c65b8e807409e6f20baee5d2cd880e0fad00b1a811ebc43e39a00ab2"},
@@ -642,6 +678,7 @@ version = "3.1.1"
description = "pyparsing module - Classes and methods to define and execute parsing grammars"
optional = false
python-versions = ">=3.6.8"
+groups = ["main"]
files = [
{file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
{file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
@@ -656,6 +693,7 @@ version = "8.0.1"
description = "pytest: simple powerful testing with Python"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "pytest-8.0.1-py3-none-any.whl", hash = "sha256:3e4f16fe1c0a9dc9d9389161c127c3edc5d810c38d6793042fb81d9f48a59fca"},
{file = "pytest-8.0.1.tar.gz", hash = "sha256:267f6563751877d772019b13aacbe4e860d73fe8f651f28112e9ac37de7513ae"},
@@ -678,6 +716,7 @@ version = "2015.11.4"
description = "Configures logging and allows tweaking the log level with a py.test flag"
optional = false
python-versions = "*"
+groups = ["main"]
files = [
{file = "pytest-logging-2015.11.4.tar.gz", hash = "sha256:cec5c85ecf18aab7b2ead5498a31b9f758680ef5a902b9054ab3f2bdbb77c896"},
]
@@ -691,8 +730,8 @@ version = "0.4.0"
description = "A pure Python implementation of the trie data structure."
optional = false
python-versions = "*"
+groups = ["main"]
files = [
- {file = "PyTrie-0.4.0-py3-none-any.whl", hash = "sha256:f687c224ee8c66cda8e8628a903011b692635ffbb08d4b39c5f92b18eb78c950"},
{file = "PyTrie-0.4.0.tar.gz", hash = "sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379"},
]
@@ -705,6 +744,7 @@ version = "6.0.1"
description = "YAML parser and emitter for Python"
optional = false
python-versions = ">=3.6"
+groups = ["main"]
files = [
{file = "PyYAML-6.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a"},
{file = "PyYAML-6.0.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:fd66fc5d0da6d9815ba2cebeb4205f95818ff4b79c3ebe268e75d961704af52f"},
@@ -765,6 +805,7 @@ version = "6.3.2"
description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
optional = false
python-versions = ">=3.7,<4.0"
+groups = ["main"]
files = [
{file = "rdflib-6.3.2-py3-none-any.whl", hash = "sha256:36b4e74a32aa1e4fa7b8719876fb192f19ecd45ff932ea5ebbd2e417a0247e63"},
{file = "rdflib-6.3.2.tar.gz", hash = "sha256:72af591ff704f4caacea7ecc0c5a9056b8553e0489dd4f35a9bc52dbd41522e0"},
@@ -786,6 +827,7 @@ version = "0.33.0"
description = "JSON Referencing + Python"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "referencing-0.33.0-py3-none-any.whl", hash = "sha256:39240f2ecc770258f28b642dd47fd74bc8b02484de54e1882b74b35ebd779bd5"},
{file = "referencing-0.33.0.tar.gz", hash = "sha256:c775fedf74bc0f9189c2a3be1c12fd03e8c23f4d371dce795df44e06c5b412f7"},
@@ -801,6 +843,7 @@ version = "2.31.0"
description = "Python HTTP for Humans."
optional = false
python-versions = ">=3.7"
+groups = ["main", "dev"]
files = [
{file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
{file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
@@ -822,6 +865,7 @@ version = "1.2.0"
description = "A persistent cache for python requests"
optional = false
python-versions = ">=3.8"
+groups = ["dev"]
files = [
{file = "requests_cache-1.2.0-py3-none-any.whl", hash = "sha256:490324301bf0cb924ff4e6324bd2613453e7e1f847353928b08adb0fdfb7f722"},
{file = "requests_cache-1.2.0.tar.gz", hash = "sha256:db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838"},
@@ -852,6 +896,7 @@ version = "0.18.0"
description = "Python bindings to Rust's persistent data structures (rpds)"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
files = [
{file = "rpds_py-0.18.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:5b4e7d8d6c9b2e8ee2d55c90b59c707ca59bc30058269b3db7b1f8df5763557e"},
{file = "rpds_py-0.18.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c463ed05f9dfb9baebef68048aed8dcdc94411e4bf3d33a39ba97e271624f8f7"},
@@ -960,6 +1005,7 @@ version = "1.16.0"
description = "Python 2 and 3 compatibility utilities"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+groups = ["main", "dev"]
files = [
{file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
{file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -971,6 +1017,7 @@ version = "2.4.0"
description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
optional = false
python-versions = "*"
+groups = ["main"]
files = [
{file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"},
{file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"},
@@ -982,6 +1029,8 @@ version = "2.0.1"
description = "A lil' TOML parser"
optional = false
python-versions = ">=3.7"
+groups = ["main"]
+markers = "python_version < \"3.11\""
files = [
{file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
@@ -993,10 +1042,12 @@ version = "4.9.0"
description = "Backported and Experimental Type Hints for Python 3.8+"
optional = false
python-versions = ">=3.8"
+groups = ["main", "dev"]
files = [
{file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
{file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
]
+markers = {dev = "python_version < \"3.11\""}
[[package]]
name = "url-normalize"
@@ -1004,6 +1055,7 @@ version = "1.4.3"
description = "URL normalization for Python"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+groups = ["dev"]
files = [
{file = "url-normalize-1.4.3.tar.gz", hash = "sha256:d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2"},
{file = "url_normalize-1.4.3-py2.py3-none-any.whl", hash = "sha256:ec3c301f04e5bb676d333a7fa162fa977ad2ca04b7e652bfc9fac4e405728eed"},
@@ -1018,6 +1070,7 @@ version = "2.2.1"
description = "HTTP library with thread-safe connection pooling, file post, and more."
optional = false
python-versions = ">=3.8"
+groups = ["main", "dev"]
files = [
{file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
{file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
@@ -1035,6 +1088,7 @@ version = "1.16.0"
description = "Module for decorators, wrappers and monkey patching."
optional = false
python-versions = ">=3.6"
+groups = ["main"]
files = [
{file = "wrapt-1.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4"},
{file = "wrapt-1.16.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e4fdb9275308292e880dcbeb12546df7f3e0f96c6b41197e0cf37d2826359020"},
@@ -1110,20 +1164,26 @@ files = [
[[package]]
name = "zipp"
-version = "3.17.0"
+version = "3.20.2"
description = "Backport of pathlib-compatible object wrapper for zip files"
optional = false
python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version < \"3.9\""
files = [
- {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
- {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+ {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+ {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
]
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
[metadata]
-lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "fddd54f2e38fdce32a4236c283d5f4e141f897e6d7ed4aac4ce5dbb40c37e428"
+lock-version = "2.1"
+python-versions = ">=3.8,<4.0"
+content-hash = "1a75128f421c3bf2aa66c393245df25c6d525a85ced17c2660147abe5bd25ede"
diff --git a/pyproject.toml b/pyproject.toml
index b50cba65..211d0beb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,23 +1,23 @@
-[tool.poetry]
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
+build-backend = "poetry_dynamic_versioning.backend"
+
+[project]
name = "linkml-runtime"
-version = "0.0.0"
description = "Runtime environment for LinkML, the Linked open data modeling language"
authors = [
- "Chris Mungall <cjmungall@lbl.gov>",
- "Harold Solbrig <solbrig@jhu.edu>",
- "Sierra Moxon <smoxon@lbl.gov>",
- "Bill Duncan <wdduncan@gmail.com>",
- "Harshad Hegde <hhegde@lbl.gov>"
+ {name = "Chris Mungall", email = "cjmungall@lbl.gov"},
+ {name = "Harold Solbrig", email = "solbrig@jhu.edu"},
+ {name = "Sierra Moxon", email = "smoxon@lbl.gov"},
+ {name = "Bill Duncan", email = "wdduncan@gmail.com"},
+ {name = "Harshad Hegde", email = "hhegde@lbl.gov"},
]
-
-readme = "README.md"
-
+license = "CC0-1.0"
homepage = "https://github.com/linkml/linkml-runtime"
repository = "https://github.com/linkml/linkml-runtime"
documentation = "https://github.com/linkml/linkml-runtime"
-
+readme = "README.md"
keywords = ["linkml", "metamodel", "schema visualization", "rdf", "owl", "yaml"]
-
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
@@ -32,40 +32,41 @@ classifiers = [
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
-
-packages = [
- { include = "linkml_runtime" }
+include = ["linkml_runtime"]
+requires-python = ">=3.8,<4.0"
+dynamic = ["version"]
+dependencies = [
+ "click",
+ "deprecated",
+ "hbreader",
+ "json-flattener >=0.1.9",
+ "jsonasobj2 ==1.*,>=1.0.0,>=1.0.4",
+ "jsonschema >=3.2.0",
+ "prefixcommons >=0.1.12",
+ "pyyaml",
+ "rdflib >=6.0.0",
+ "requests",
+ "prefixmaps >=0.1.4",
+ "curies >=0.5.4",
+ "pydantic >=1.10.2, <3.0.0",
]
+[project.scripts]
+comparefiles = "linkml_runtime.utils.comparefiles:cli"
+linkml-normalize = "linkml_runtime.processing.referencevalidator:cli"
+
+[tool.poetry]
+requires-poetry = ">=2.0"
+version = "0.0.0"
+
+[tool.poetry.requires-plugins]
+poetry-dynamic-versioning = ">=1.5.2"
+
[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "pep440"
-[tool.poetry.scripts]
-comparefiles = "linkml_runtime.utils.comparefiles:cli"
-linkml-normalize = "linkml_runtime.processing.referencevalidator:cli"
-
-[tool.poetry.dependencies]
-python = "^3.8"
-click = "*"
-deprecated = "*"
-hbreader = "*"
-json-flattener = ">=0.1.9"
-jsonasobj2 = "==1.*,>=1.0.0,>=1.0.4"
-jsonschema = ">=3.2.0"
-prefixcommons = ">=0.1.12"
-pyyaml = "*"
-rdflib = ">=6.0.0"
-requests = "*"
-prefixmaps = ">=0.1.4"
-curies = ">=0.5.4"
-pydantic = ">=1.10.2, <3.0.0"
-
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev.dependencies]
coverage = "^6.2"
requests-cache = "^1.2.0"
-
-[build-system]
-requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
-build-backend = "poetry_dynamic_versioning.backend"