pymetadata 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

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/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-0.5.2.dist-info/METADATA

@@ -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-0.5.0.dist-info → pymetadata-0.5.2.dist-info}/RECORD

@@ -1,9 +1,9 @@
-pymetadata/__init__.py,sha256=-EZKeFfptRrccMcmwrtFlGJkpYRIFY0r47_VT7OzueQ,357
+pymetadata/__init__.py,sha256=35mfW854dCAnEdVYlCj4WPTTQiU-v_XXB7B0VnUPS6M,357
 pymetadata/cache.py,sha256=tQuMIcd1cOfO0dvODQMG92_IrHqgswPfshhFjtl7Pd0,1409
 pymetadata/chebi.py,sha256=EH8sYRx7af3Hi1O8x5Tvj_T9cawGVMtlYp_4B3L8tHY,2730
 pymetadata/console.py,sha256=ouDYOx_81ndvtMW5GVrut71uzPC5xlvibGu9N5YdbRA,332
 pymetadata/log.py,sha256=3uRVMYolalrS0PVWS_4qSme8RYhot3_W2ad1JopI88g,664
-pymetadata/omex.py,sha256=lXdWJQgX-_zDq1OX82zWEk_R1rlJX995jrCKOiQt8JM,29829
+pymetadata/omex.py,sha256=ZFsX9Xbh8sgT1UeBpKMgdrOh2PGTxrH2IAdYo_R9xc0,29927
 pymetadata/omex_v2.py,sha256=HZBg_wmQWixweOZG3qVj2zqG_o1x9Ljxy-JEP6-ZFhM,584
 pymetadata/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pymetadata/unichem.py,sha256=slxTabar1ZdZQUyTyRloiWKxD92ixnDGsJ2xk3alrTo,6878
@@ -36,7 +36,7 @@ pymetadata/ontologies/ontology.py,sha256=cnAgXzxPn3XxZ8FUAMuSAH0eOGio-YK1Enzy3Zu
 pymetadata/resources/chebi_webservice_wsdl.xml,sha256=0AEgcZ48bk4L6l3jO5-6BIVwfTr4yXnRZCtXue5NyHo,23846
 pymetadata/resources/ontologies/README.md,sha256=h1LIKpr42-s0RzwpCufkR_YJ2nWiwOapZX_frRXk3Qg,163
 pymetadata/resources/templates/ontology_enum.pytemplate,sha256=fK7SBTVfRzVk-z_6wiZ_9MDbTNSlEpGGellRoliGqac,1674
-pymetadata-0.5.0.dist-info/METADATA,sha256=R5xPvJVRW71mo79WwmUKkuGpx1lEZQqTZW070IynBrw,5725
-pymetadata-0.5.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-pymetadata-0.5.0.dist-info/licenses/LICENSE,sha256=bIHEDEMiQfVe9c81lFP7Q9hsCOmEuj2c_m50LuotsMM,1058
-pymetadata-0.5.0.dist-info/RECORD,,
+pymetadata-0.5.2.dist-info/METADATA,sha256=d39G-Arr7ZINSjkrXQg5JxHqurwMItj8dmwOAP0Vc0w,4943
+pymetadata-0.5.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+pymetadata-0.5.2.dist-info/licenses/LICENSE,sha256=bIHEDEMiQfVe9c81lFP7Q9hsCOmEuj2c_m50LuotsMM,1058
+pymetadata-0.5.2.dist-info/RECORD,,

pymetadata-0.5.0.dist-info/METADATA

@@ -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