pymetadata 0.3.1__tar.gz → 0.5.9__tar.gz

pymetadata-0.5.9/.bumpversion.toml

@@ -0,0 +1,19 @@
+[tool.bumpversion]
+current_version = "0.5.9"
+commit = true
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+tag = true
+sign_tags = false
+tag_name = "{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "./src/pymetadata/__init__.py"

pymetadata-0.5.9/.github/workflows/main.yml

@@ -0,0 +1,83 @@
+name: CI-CD
+
+on: [push]
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        exclude:
+          - os: windows-latest
+            python-version: "3.10"
+          - os: windows-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.12"
+          - os: windows-latest
+            python-version: "3.14"
+          - os: macos-latest
+            python-version: "3.10"
+          - os: macos-latest
+            python-version: "3.11"
+          - os: macos-latest
+            python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.14"
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install uv and set the python version
+      uses: astral-sh/setup-uv@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
+    - name: Test with tox
+      run:
+        uvx --with tox-uv tox -e py${{ matrix.python-version }}
+
+  release:
+    needs: test
+    if: startsWith(github.ref, 'refs/tags')
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.13"]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/<your-pypi-project-name>
+    permissions:
+      id-token: write
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get tag
+      id: tag
+      run: echo "version=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install hatch twine
+
+    - name: Build package
+      # run: python setup.py sdist bdist_wheel
+      run: hatch build
+    - name: Check the package
+      run: twine check dist/*
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages-dir: dist
+    - name: Create GitHub release
+      uses: softprops/action-gh-release@v1
+      with:
+        body_path: "release-notes/${{ github.ref_name }}.md"
+        draft: false
+        prerelease: false

pymetadata-0.5.9/.github/workflows/mypy.yml

@@ -0,0 +1,21 @@
+name: MyPy
+on: [push]
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ "3.13" ]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+      - name: Test with tox
+        run:
+          uvx --with tox-uv tox -e mypy

pymetadata-0.5.9/.github/workflows/ruff.yml

@@ -0,0 +1,8 @@
+name: Ruff
+on: [push]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3

pymetadata-0.5.9/.gitignore

@@ -0,0 +1,29 @@
+uv.lock
+.vscode
+*.pyc
+*~
+.DS_Store
+.eggs/
+dist
+build
+.idea
+cover/
+.tox/
+.venv
+.cache/
+.coverage
+coverage.xml
+.benchmark
+src/pymetadata.egg-info/
+src/pymetadata/resources/cache
+
+
+wheels
+__pycache__
+.pytest_cache
+.Rhistory
+*.tsv#
+*.xlsx#
+
+# OWL ontologies
+*.owl.gz

pymetadata-0.5.9/.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+# This is run as a precondition to commits, run manually via `pre-commit run`
+
+# When adding new hooks, it may make sense to once run
+# `pre-commit run --all-files` as by default only changed files are checked
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-yaml
+    description: Check yaml files for parseable syntax
+  - id: check-added-large-files
+    description: Prevent large files from being committed
+  - id: check-merge-conflict
+    description: Check for files that contain merge conflict strings
+  - id: check-symlinks
+    description: Check for symlinks which do not point to anything
+  - id: trailing-whitespace
+    description: Trim trailing whitespaces
+  - id: end-of-file-fixer
+    description: Fix empty lines at ends of files
+  - id: detect-private-key
+    description: Detects the presence of private keys
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.6
+  hooks:
+    # Run the linter.
+    - id: ruff
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]

pymetadata-0.5.9/.python-version

@@ -0,0 +1 @@
+3.13

pymetadata-0.5.9/.ruff.toml

@@ -0,0 +1,50 @@
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+target-version = "py313"
+
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = []
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"
+
+[lint.pydocstyle]
+convention = "google"  # Accepts: "google", "numpy", or "pep257".

pymetadata-0.5.9/.zenodo.json

@@ -0,0 +1,22 @@
+{
+  "upload_type": "software",
+  "title": "pymetadata are python utilities for working with metadata",
+  "creators": [
+    {
+      "orcid": "0000-0003-1725-179X",
+      "affiliation": "Humboldt-University Berlin, Institute for Theoretical Biology, Berlin",
+      "name": "König, Matthias"
+    }
+  ],
+  "description": "<p><code>pymetadata</code> is a collection of python utilities for working with metadata in the context of COMBINE standards with source code available from available from <a href=\"https://github.com/matthiaskoenig/pymetadata\">https://github.com/matthiaskoenig/pymetadata</a></p><p>Features include among others<ul><li>annotation classes and helpers</li></ul></p><p>If you have any questions or issues please <a href=\"https://github.com/matthiaskoenig/pymetadata/issues\">open an issue</a></p><h2>Funding</h2><p>Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).</p>",
+  "access_right": "open",
+  "license": "MIT",
+  "keywords": [
+	"modeling",
+	"standardization",
+	"COMBINE",
+	"metadata",
+	"archive",
+	"annotation"
+  ]
+}

pymetadata-0.5.9/LICENSE

@@ -0,0 +1,7 @@
+Copyright (c) 2025 Matthias König
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

pymetadata-0.5.9/PKG-INFO

@@ -0,0 +1,99 @@
+Metadata-Version: 2.4
+Name: pymetadata
+Version: 0.5.9
+Summary: pymetadata are python utilities for working with metadata.
+Author-email: Matthias König <konigmatt@googlemail.com>
+Maintainer-email: Matthias König <konigmatt@googlemail.com>
+License-File: LICENSE
+Keywords: COMBINE,annotation,archive,metadata,modeling,standardization
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Requires-Dist: depinfo>=2.2.0
+Requires-Dist: fastobo>=0.12.3
+Requires-Dist: jinja2>=3.1.5
+Requires-Dist: lxml>=5.3
+Requires-Dist: pronto>=2.5.8
+Requires-Dist: pydantic>=2.10.4
+Requires-Dist: requests>=2.32.3
+Requires-Dist: rich>=13.9.4
+Requires-Dist: xmltodict>=0.14.2
+Provides-Extra: dev
+Requires-Dist: bump-my-version>=1.2.4; extra == 'dev'
+Requires-Dist: mypy>=1.18.2; extra == 'dev'
+Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
+Requires-Dist: pytest-cov>=7.0.0; extra == 'dev'
+Requires-Dist: pytest>=8.4.2; extra == 'dev'
+Requires-Dist: ruff>=0.14.0; extra == 'dev'
+Requires-Dist: tox>=4.31.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+![pymetadata logo](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
+
+# pymetadata: python utilities for metadata and COMBINE archives
+[![GitHub Actions CI/CD Status](https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg)](https://github.com/matthiaskoenig/pymetadata/actions/workflows/main.yml)
+[![Version](https://img.shields.io/pypi/v/pymetadata.svg)](https://pypi.org/project/pymetadata/)
+[![Python Versions](https://img.shields.io/pypi/pyversions/pymetadata.svg)](https://pypi.org/project/pymetadata/)
+[![MIT License](https://img.shields.io/pypi/l/pymetadata.svg)](https://opensource.org/licenses/MIT)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
+
+pymetadata is a collection of python utilities for working with
+metadata in the context of COMBINE standards with source code available from
+[https://github.com/matthiaskoenig/pymetadata](https://github.com/matthiaskoenig/pymetadata).
+
+Features include among others
+
+- COMBINE archive version 1 support (OMEX)
+- annotation classes and helpers
+- SBO, KISAO and ECO ontology enums
+
+If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/pymetadata/issues).
+
+# Documentation
+Documentation is still work in progress. For an example usage of the COMBINE archive
+see [omex_example.py](src/pymetadata/examples/omex_example.py).
+
+# How to cite
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
+
+
+# License
+- Source Code: [MIT](https://opensource.org/license/MIT)
+- Documentation: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)
+
+# Funding
+Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
+
+# Installation
+`pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
+can be installed via
+
+```bash
+pip install pymetadata
+```
+
+# Cache path
+`pymetadata` caches some information for faster retrieval. The cache path is set to
+
+```python
+CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
+```
+
+To use a custom cache path use
+
+```python
+import pymetadata
+pymetadata.CACHE_PATH = <cache_path>
+```
+
+© 2021-2025 Matthias König

pymetadata-0.5.9/README.md

@@ -0,0 +1,59 @@
+![pymetadata logo](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
+
+# pymetadata: python utilities for metadata and COMBINE archives
+[![GitHub Actions CI/CD Status](https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg)](https://github.com/matthiaskoenig/pymetadata/actions/workflows/main.yml)
+[![Version](https://img.shields.io/pypi/v/pymetadata.svg)](https://pypi.org/project/pymetadata/)
+[![Python Versions](https://img.shields.io/pypi/pyversions/pymetadata.svg)](https://pypi.org/project/pymetadata/)
+[![MIT License](https://img.shields.io/pypi/l/pymetadata.svg)](https://opensource.org/licenses/MIT)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
+
+pymetadata is a collection of python utilities for working with
+metadata in the context of COMBINE standards with source code available from
+[https://github.com/matthiaskoenig/pymetadata](https://github.com/matthiaskoenig/pymetadata).
+
+Features include among others
+
+- COMBINE archive version 1 support (OMEX)
+- annotation classes and helpers
+- SBO, KISAO and ECO ontology enums
+
+If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/pymetadata/issues).
+
+# Documentation
+Documentation is still work in progress. For an example usage of the COMBINE archive
+see [omex_example.py](src/pymetadata/examples/omex_example.py).
+
+# How to cite
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
+
+
+# License
+- Source Code: [MIT](https://opensource.org/license/MIT)
+- Documentation: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)
+
+# Funding
+Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
+
+# Installation
+`pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
+can be installed via
+
+```bash
+pip install pymetadata
+```
+
+# Cache path
+`pymetadata` caches some information for faster retrieval. The cache path is set to
+
+```python
+CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
+```
+
+To use a custom cache path use
+
+```python
+import pymetadata
+pymetadata.CACHE_PATH = <cache_path>
+```
+
+© 2021-2025 Matthias König

pymetadata-0.5.9/RELEASE.md

@@ -0,0 +1,45 @@
+# Release information
+
+## make release
+* update ontologies via `ontology.update_ontology_files()`
+* update release notes in `release-notes` with commit
+* make sure all tests run (`tox -p`)
+* check formating and linting (`ruff check`)
+* test bump version (`uvx bump-my-version bump [major|minor|patch] --dry-run -vv`)
+* bump version (`uvx bump-my-version bump [major|minor|patch]`)
+* `git push --tags` (triggers release)
+* `git push`
+* test installation in virtualenv from pypi
+```bash
+uv venv --python 3.13
+uv pip install pymetadata
+```
+
+# Install dev dependencies:
+```bash
+# install core dependencies
+uv sync
+# install dev dependencies
+uv pip install -r pyproject.toml --extra dev
+```
+
+## Setup tox testing
+See information on https://github.com/tox-dev/tox-uv
+```bash
+uv tool install tox --with tox-uv
+```
+Run single tox target
+```bash
+tox r -e py312
+```
+Run all tests in parallel
+```bash
+tox run-parallel
+```
+
+# Setup pre-commit
+```bash
+uv pip install pre-commit
+pre-commit install
+pre-commit run
+```

pymetadata-0.5.9/docs/composite_annotations.md

@@ -0,0 +1,36 @@
+# Working with composite annotations.
+
+Composite annotations are semantic annotations that are comprised of multiple annotation
+terms linked using  standard  qualifiers  (also  known  as  “relations”  or  “predicates”)
+to  indicate  the  meaning  of  annotation.
+Composite annotations are used when a single knowledge resource term is not available to
+sufficiently define a model or data element.  For model-component annotations,
+composite annotations have two primary components:
+1. the physical property represented by the annotated item (e.g., chemical concentration,
+fluid volume) and
+2. the physical entity, process, force, or dependency that bears the property (e.g., a pool
+of ATP in the cytoplasm, blood in a cardiac cavity, the glucokinase reaction).
+
+
+
+**entity**
+OPB: https://bioportal.bioontology.org/ontologies/OPB
+Ontology of Physics for Biology
+
+Molecular weight: OPB_01146; constant parameter
+Concentration of chemical: OPB_00340
+
+OBP: fluid volume; plasma;
+similar to blood volume in vessel
+portion of plasma (portion of blood)
+
+dose
+OBP: mass amount of chemical;
+
+aborption rate: "Material flow rate"
+Property first; entity second
+
+
+**Properties of processes**
+- describe process: source, sink & mediator; flow of material from one pool to another
+- to describe the source: stomach; sink

pymetadata-0.5.9/docs/images/favicon/about.txt

@@ -0,0 +1,6 @@
+This favicon was generated using the following graphics from Twitter Twemoji:
+
+- Graphics Title: 1f363.svg
+- Graphics Author: Copyright 2020 Twitter, Inc and other contributors (https://github.com/twitter/twemoji)
+- Graphics Source: https://github.com/twitter/twemoji/blob/master/assets/svg/1f363.svg
+- Graphics License: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

pymetadata-0.5.9/docs/images/favicon/site.webmanifest

@@ -0,0 +1 @@
+{"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}

pymetadata-0.5.9/pyproject.toml

@@ -0,0 +1,70 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pymetadata"
+dynamic = ["version"]
+description = "pymetadata are python utilities for working with metadata."
+readme = "README.md"
+requires-python = ">=3.10"
+authors = [
+	{name="Matthias König", email="konigmatt@googlemail.com"}
+]
+maintainers = [
+	{name="Matthias König", email="konigmatt@googlemail.com"}
+]
+classifiers = [
+	"Development Status :: 4 - Beta",
+	"Intended Audience :: Science/Research",
+	"License :: OSI Approved :: MIT License",
+	"Operating System :: OS Independent",
+	"Programming Language :: Python :: 3.10",
+	"Programming Language :: Python :: 3.11",
+	"Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+	"Programming Language :: Python :: Implementation :: CPython",
+	"Topic :: Scientific/Engineering",
+	"Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+keywords = [
+	"modeling",
+	"standardization",
+	"COMBINE",
+	"metadata",
+	"archive",
+	"annotation",
+]
+dependencies = [
+    "depinfo>=2.2.0",
+	"lxml>=5.3",
+	"rich>=13.9.4",
+	"requests>=2.32.3",
+	"pronto>=2.5.8",
+	"fastobo>=0.12.3",
+	"jinja2>=3.1.5",
+	"xmltodict>=0.14.2",
+	"pydantic>=2.10.4",
+]
+
+[project.optional-dependencies]
+dev = [
+    "bump-my-version>=1.2.4",
+	"ruff>=0.14.0",
+	"pre-commit>=4.0.1",
+	"mypy>=1.18.2",
+    "tox>=4.31.0",
+    "pytest>=8.4.2",
+    "pytest-cov>=7.0.0",
+]
+
+[project_urls]
+Homepage = "https://github.com/matthiaskoenig/pymetadata"
+Repository = "https://github.com/matthiaskoenig/pymetadata"
+Documentation = "https://github.com/matthiaskoenig/pymetadata"
+Issues = "https://github.com/matthiaskoenig/pymetadata/issues"
+Download = "https://pypi.org/project/pymetadata"
+
+[tool.hatch.version]
+path = "./src/pymetadata/__init__.py"

pymetadata-0.5.9/release-notes/0.0.10.md

@@ -0,0 +1,6 @@
+# Release notes for pymetadata 0.0.10
+
+- ontology enums (Fix #8)
+- removed ontology downloads
+- fixed mypy issues (Fix #1)
+- checks on additional branches (Fix #9)

pymetadata-0.5.9/release-notes/0.0.11.md

@@ -0,0 +1,3 @@
+# Release notes for pymetadata 0.0.11
+
+- typehints added

pymetadata-0.5.9/release-notes/0.0.12.md

@@ -0,0 +1,3 @@
+# Release notes for pymetadata 0.0.12
+
+- minor bugfixes

pymetadata-0.5.9/release-notes/0.0.13.md

@@ -0,0 +1,3 @@
+# Release notes for pymetadata 0.0.13
+
+- fixing slowdown due to large enums

pymetadata-0.5.9/release-notes/0.0.14.md

@@ -0,0 +1,8 @@
+# Release notes for pymetadata 0.0.14
+
+- Fix #9, enable check on all branches & macos tests
+- Simplified dependencies
+- Fix #13, zenodo metadata added
+- Fix #14, updated KISAO
+- Fix #7, rich logging
+- Fix #12, removed libchebi dependency