pymetadata 0.5.0__tar.gz → 0.5.2__tar.gz

{pymetadata-0.5.0 → pymetadata-0.5.2}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.5.0"
+current_version = "0.5.2"
 commit = true
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]

{pymetadata-0.5.0 → pymetadata-0.5.2}/.github/workflows/main.yml

@@ -1,30 +1,38 @@
 name: CI-CD
 
-on: [push]
+on: [ push, pull_request ]
 jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ["3.10", "3.11", "3.12", "3.13"]
+        exclude:
+          - os: windows-latest
+            python-version: "3.10"
+          - os: windows-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.13"
+          - os: macos-latest
+            python-version: "3.10"
+          - os: macos-latest
+            python-version: "3.11"
+          - os: macos-latest
+            python-version: "3.13"
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - name: Install uv and set the python version
+      uses: astral-sh/setup-uv@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip wheel
-        python -m pip install tox tox-gh-actions
-
-    # Update output format to enable automatic inline annotations.
+        enable-cache: true
     - name: Test with tox
       run:
-        tox --
+        uvx --with tox-uv tox -e py${{ matrix.python-version }}
 
   release:
     needs: test

pymetadata-0.5.2/.github/workflows/mypy.yml

@@ -0,0 +1,21 @@
+name: MyPy
+on: [ push, pull_request ]
+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-0.5.2/PKG-INFO

@@ -0,0 +1,115 @@
+Metadata-Version: 2.4
+Name: pymetadata
+Version: 0.5.2
+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 :: 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
+Requires-Dist: zeep>=4.3.1
+Provides-Extra: dev
+Requires-Dist: bump-my-version>=0.29.0; extra == 'dev'
+Requires-Dist: mypy>=1.9.0; extra == 'dev'
+Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
+Requires-Dist: ruff>=0.8.6; extra == 'dev'
+Provides-Extra: test
+Requires-Dist: pytest-cov>=5.0.0; extra == 'test'
+Requires-Dist: pytest>=8.1.1; extra == 'test'
+Requires-Dist: tox>=4.14.2; extra == 'test'
+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 and KISAO 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)
+
+# Contributing
+Contributions are always welcome! Please read the [contributing guidelines](https://github.com/matthiaskoenig/pymetadata/blob/develop/.github/CONTRIBUTING.rst) to get started.
+
+# 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
+```
+
+## Develop version
+The latest develop version can be installed via
+```bash
+pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop
+```
+
+Or via cloning the repository and installing via
+```bash
+git clone https://github.com/matthiaskoenig/pymetadata.git
+cd pymetadata
+pip install -e .
+```
+
+# 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-0.5.2/README.md

@@ -0,0 +1,74 @@
+![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 and KISAO 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)
+
+# Contributing
+Contributions are always welcome! Please read the [contributing guidelines](https://github.com/matthiaskoenig/pymetadata/blob/develop/.github/CONTRIBUTING.rst) to get started.
+
+# 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
+```
+
+## Develop version
+The latest develop version can be installed via
+```bash
+pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop
+```
+
+Or via cloning the repository and installing via
+```bash
+git clone https://github.com/matthiaskoenig/pymetadata.git
+cd pymetadata
+pip install -e .
+```
+
+# 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-0.5.0 → pymetadata-0.5.2}/RELEASE.md

@@ -5,39 +5,40 @@
 * update release notes in `release-notes` with commit
 * make sure all tests run (`tox run-parallel`)
 * check formating and linting (`ruff check`)
-* test bump version (`bump-my-version bump [major|minor|patch] --dry-run -vv`)
+* test bump version (`uv run bump-my-version bump [major|minor|patch] --dry-run -vv`)
 * bump version (`bump-my-version bump [major|minor|patch]`)
 * `git push --tags` (triggers release)
 * `git push`
 
 * test installation in virtualenv from pypi
 ```
-mkvirtualenv test --python=python3.13
-(test) pip install pymetadata
+uv venv --python 3.13
+uv pip install pymetadata
 ```
 
-## setup environment
-
-https://github.com/tox-dev/tox-uv
-uv tool install tox --with tox-uv
-tox r -e py312
-tox run-parallel
-
-
-# install dev dependencies:
+# Install dev dependencies:
 ```bash
-# install dependencies
+# install core dependencies
 uv sync
 # install dev dependencies
 uv pip install -r pyproject.toml --extra dev
-# install tox-uv support
+```
+
+## 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
+```
 
-# pre-commit
+# Setup pre-commit
 pip install pre-commit
 pre-commit install
-
 pre-commit run
-
-

{pymetadata-0.5.0 → pymetadata-0.5.2}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "pymetadata"
 dynamic = ["version"]
 description = "pymetadata are python utilities for working with metadata."
-readme = "README.rst"
+readme = "README.md"
 requires-python = ">=3.10"
 authors = [
 	{name="Matthias König", email="konigmatt@googlemail.com"}
@@ -54,7 +54,6 @@ dev = [
 	"ruff>=0.8.6",
 	"pre-commit>=4.0.1",
 	"mypy>=1.9.0",
-	"hatch"
 ]
 test = [
     "tox>=4.14.2",

pymetadata-0.5.2/release-notes/0.5.1.md

@@ -0,0 +1,10 @@
+# Release notes for pymetadata 0.5.1
+![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
+
+We are pleased to release the next version of pymetadata including the 
+following changes:
+
+## Features & fixes
+- Fix #52 windows paths
+
+Your pymetadata team

pymetadata-0.5.2/release-notes/0.5.2.md

@@ -0,0 +1,11 @@
+# Release notes for pymetadata 0.5.2
+![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
+
+We are pleased to release the next version of pymetadata including the 
+following changes:
+
+## Features & fixes
+- Speedup CI-CD with uv
+- Markdown README 
+
+Your pymetadata team

{pymetadata-0.5.0 → pymetadata-0.5.2}/src/pymetadata/__init__.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.5.0"
+__version__ = "0.5.2"
 
 
 program_name: str = "pymetadata"

{pymetadata-0.5.0 → pymetadata-0.5.2}/src/pymetadata/omex.py

@@ -574,6 +574,8 @@ class Omex:
             for file in files:
                 file_path = os.path.join(root, file)
                 location = f"./{os.path.relpath(file_path, directory)}"
+                # bugfix for windows paths
+                location = location.replace("\\", "/")
                 if location == "./manifest.xml":
                     # manifest is created from the internal manifest entries
                     continue

{pymetadata-0.5.0 → pymetadata-0.5.2}/tox.ini

@@ -1,13 +1,5 @@
-# --- tox -----------------------------------------------------------------------------------------------------------
 [tox]
-envlist = mypy, py3{10,11,12,13}
-
-[gh-actions]
-python =
-    3.10: py310
-    3.11: py311
-    3.12: py312
-    3.13: py313
+envlist = mypy, py3.{10,11,12,13}
 
 [testenv]
 package = wheel
@@ -18,15 +10,6 @@ deps=
 commands =
     pytest
 
-[testenv:mypy]
-skip_install = True
-
-deps=[]
-    mypy
-commands=
-    mypy {toxinidir}/src/pymetadata {toxinidir}/tests --config-file tox.ini
-
-
 [testenv:install]
 skip_install = True
 deps=
@@ -37,9 +20,13 @@ commands=
     python -m build {toxinidir}
     twine check {toxinidir}/dist/*
 
-################################################################################
-# Testing tools configuration                                                  #
-################################################################################
+[testenv:mypy]
+skip_install = True
+deps=[]
+    mypy
+commands=
+    mypy {toxinidir}/src/pymetadata {toxinidir}/tests --config-file tox.ini
+
 [pytest]
 testpaths =
     tests
@@ -47,7 +34,6 @@ markers =
     raises
 
 [mypy]
-# mypy src/pymetadata --config-file tox.ini
 warn_return_any = True
 follow_imports = silent
 disallow_untyped_defs = True

{pymetadata-0.5.0 → pymetadata-0.5.2}/uv.lock

@@ -749,7 +749,7 @@ wheels = [
 
 [[package]]
 name = "pymetadata"
-version = "0.4.4"
+version = "0.5.1"
 source = { editable = "." }
 dependencies = [
     { name = "depinfo" },

pymetadata-0.5.0/PKG-INFO

@@ -1,154 +0,0 @@
-Metadata-Version: 2.4
-Name: pymetadata
-Version: 0.5.0
-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 :: 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
-Requires-Dist: zeep>=4.3.1
-Provides-Extra: dev
-Requires-Dist: bump-my-version>=0.29.0; extra == 'dev'
-Requires-Dist: hatch; extra == 'dev'
-Requires-Dist: mypy>=1.9.0; extra == 'dev'
-Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
-Requires-Dist: ruff>=0.8.6; extra == 'dev'
-Provides-Extra: test
-Requires-Dist: pytest-cov>=5.0.0; extra == 'test'
-Requires-Dist: pytest>=8.1.1; extra == 'test'
-Requires-Dist: tox>=4.14.2; extra == 'test'
-Description-Content-Type: text/x-rst
-
-.. image:: https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png
-   :align: left
-   :alt: pymetadata logo
-
-pymetadata: python utilities for metadata and COMBINE archives
-==============================================================
-|icon1| |icon2| |icon3| |icon4| |icon5| |icon6|
-
-
-.. |icon1| image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
-   :target: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD
-   :alt: GitHub Actions CI/CD Status
-.. |icon2| image:: https://img.shields.io/pypi/v/pymetadata.svg
-   :target: https://pypi.org/project/pymetadata/
-   :alt: Current PyPI Version
-.. |icon3| image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
-   :target: https://pypi.org/project/pymetadata/
-   :alt: Supported Python Versions
-.. |icon4| image:: https://img.shields.io/pypi/l/pymetadata.svg
-   :target: https://opensource.org/licenses/MIT
-   :alt: MIT License
-.. |icon5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
-   :target: https://doi.org/10.5281/zenodo.5308801
-   :alt: Zenodo DOI
-.. |icon6| image:: http://www.mypy-lang.org/static/mypy_badge.svg
-   :target: http://mypy-lang.org/
-   :alt: mypy
-
-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 and KISAO 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 `src/pymetadata/examples/omex_example.py <src/pymetadata/examples/omex_example.py>`__.
-
-How to cite
-===========
-
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
-   :target: https://doi.org/10.5281/zenodo.5308801
-   :alt: Zenodo DOI
-
-Contributing
-============
-
-Contributions are always welcome! Please read the `contributing guidelines
-<https://github.com/matthiaskoenig/pymetadata/blob/develop/.github/CONTRIBUTING.rst>`__ to
-get started.
-
-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:: 
-
-    pip install pymetadata
-
-Develop version
----------------
-The latest develop version can be installed via::
-
-    pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop
-
-Or via cloning the repository and installing via::
-
-    git clone https://github.com/matthiaskoenig/pymetadata.git
-    cd pymetadata
-    pip install -e .
-
-
-To install for development use::
-
-    pip install -e .[development]
-
-
-Cache path
-==========
-`pymetadata` caches some information for faster retrieval. The cache path is set to::
-
-    CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
-
-To use a custom cache path use::
-
-    import pymetadata
-    pymetadata.CACHE_PATH = <cache_path>
-
-
-Checks
-==========
-- uv for project setup
-- ruff for linting, formating
-- mypy for type checking
-
-© 2021-2025 Matthias König

pymetadata-0.5.0/README.rst

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-.. image:: https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png
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-   :alt: pymetadata logo
-
-pymetadata: python utilities for metadata and COMBINE archives
-==============================================================
-|icon1| |icon2| |icon3| |icon4| |icon5| |icon6|
-
-
-.. |icon1| image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
-   :target: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD
-   :alt: GitHub Actions CI/CD Status
-.. |icon2| image:: https://img.shields.io/pypi/v/pymetadata.svg
-   :target: https://pypi.org/project/pymetadata/
-   :alt: Current PyPI Version
-.. |icon3| image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
-   :target: https://pypi.org/project/pymetadata/
-   :alt: Supported Python Versions
-.. |icon4| image:: https://img.shields.io/pypi/l/pymetadata.svg
-   :target: https://opensource.org/licenses/MIT
-   :alt: MIT License
-.. |icon5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
-   :target: https://doi.org/10.5281/zenodo.5308801
-   :alt: Zenodo DOI
-.. |icon6| image:: http://www.mypy-lang.org/static/mypy_badge.svg
-   :target: http://mypy-lang.org/
-   :alt: mypy
-
-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 and KISAO 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 `src/pymetadata/examples/omex_example.py <src/pymetadata/examples/omex_example.py>`__.
-
-How to cite
-===========
-
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
-   :target: https://doi.org/10.5281/zenodo.5308801
-   :alt: Zenodo DOI
-
-Contributing
-============
-
-Contributions are always welcome! Please read the `contributing guidelines
-<https://github.com/matthiaskoenig/pymetadata/blob/develop/.github/CONTRIBUTING.rst>`__ to
-get started.
-
-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:: 
-
-    pip install pymetadata
-
-Develop version
----------------
-The latest develop version can be installed via::
-
-    pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop
-
-Or via cloning the repository and installing via::
-
-    git clone https://github.com/matthiaskoenig/pymetadata.git
-    cd pymetadata
-    pip install -e .
-
-
-To install for development use::
-
-    pip install -e .[development]
-
-
-Cache path
-==========
-`pymetadata` caches some information for faster retrieval. The cache path is set to::
-
-    CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
-
-To use a custom cache path use::
-
-    import pymetadata
-    pymetadata.CACHE_PATH = <cache_path>
-
-
-Checks
-==========
-- uv for project setup
-- ruff for linting, formating
-- mypy for type checking
-
-© 2021-2025 Matthias König