pymetadata 0.5.2__tar.gz → 0.5.4__tar.gz
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- {pymetadata-0.5.2 → pymetadata-0.5.4}/.bumpversion.toml +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/CONTRIBUTING.rst +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/01-bug-report.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/workflows/main.yml +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/workflows/mypy.yml +2 -2
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/workflows/ruff.yml +2 -2
- pymetadata-0.5.4/.pre-commit-config.yaml +35 -0
- pymetadata-0.5.4/.python-version +1 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.ruff.toml +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/LICENSE +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/PKG-INFO +6 -7
- {pymetadata-0.5.2 → pymetadata-0.5.4}/README.md +5 -5
- {pymetadata-0.5.2 → pymetadata-0.5.4}/RELEASE.md +7 -6
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/composite_annotations.md +2 -2
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/site.webmanifest +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/pyproject.toml +0 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.17.md +0 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.18.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.19.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.20.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.21.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.22.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.1.0.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.1.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.10.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.2.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.3.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.4.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.5.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.6.md +2 -2
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.7.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.8.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.9.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.0.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.1.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.10.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.11.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.2.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.3.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.4.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.5.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.6.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.7.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.8.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.9.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.0.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.1.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.2.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.3.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.4.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.5.0.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.5.1.md +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.5.2.md +2 -2
- pymetadata-0.5.4/release-notes/0.5.3.md +11 -0
- pymetadata-0.5.4/release-notes/0.5.4.md +11 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/__init__.py +1 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/chebi.py +21 -29
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/annotation.py +4 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/cache_path_example.py +0 -1
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/identifiers/registry.py +11 -33
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/eco.py +1246 -1340
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/kisao.py +83 -26
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/sbo.py +131 -378
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/ontologies/ontology.py +6 -5
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/resources/templates/ontology_enum.pytemplate +0 -2
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/unichem.py +2 -2
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/core/test_annotation.py +5 -0
- pymetadata-0.5.4/uv.lock +1410 -0
- pymetadata-0.5.2/.pre-commit-config.yaml +0 -12
- pymetadata-0.5.2/.python-version +0 -1
- pymetadata-0.5.2/src/pymetadata/resources/chebi_webservice_wsdl.xml +0 -509
- pymetadata-0.5.2/uv.lock +0 -1180
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/02-question.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/03-feature-request.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/config.yml +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/SUPPORT.rst +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.gitignore +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/.zenodo.json +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/about.txt +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/android-chrome-192x192.png +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/android-chrome-512x512.png +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/apple-touch-icon.png +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon-16x16.png +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon-32x32.png +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon.ico +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon_io.zip +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/pymetadata-100x100-300dpi.png +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.10.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.11.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.12.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.13.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.14.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.15.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.16.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.2.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.3.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.4.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.5.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.6.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.7.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.8.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.9.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/cache.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/console.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/__init__.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/creator.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/synonym.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/xref.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/__init__.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/omex_example.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/test_from_files.omex +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/test_from_omex.omex +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/README.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/manifest.xml +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/models/omex_comp.xml +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/models/omex_comp_flat.xml +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/models/omex_minimal.xml +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/test.omex +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/identifiers/__init__.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/identifiers/miriam.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/log.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/__init__.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/omex.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/omex_v2.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/ontologies/__init__.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/ontologies/ols.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/py.typed +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/resources/ontologies/README.md +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/core/test_creator.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/BIOMD0000000001.omex +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CombineArchiveShowCase.omex +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CombineArchiveShowCase_manifest.xml +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CompModels.omex +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CompModels_manifest.xml +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/iCGB21FR.omex +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_chebi.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_ols.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_omex.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_ontology.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_registry.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_sbo_kisao.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_unichem.py +0 -0
- {pymetadata-0.5.2 → pymetadata-0.5.4}/tox.ini +0 -0
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pymetadata uses `pytest <http://docs.pytest.org/en/latest/>`_ for its
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unit-tests and new features should in general always come with new
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tests that make sure that the code runs as intended.
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tests that make sure that the code runs as intended.
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To run all tests do::
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description: Check yaml files for parseable syntax
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description: Prevent large files from being committed
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description: Detects the presence of private keys
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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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.
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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.
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Metadata-Version: 2.4
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Name: pymetadata
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Version: 0.5.
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Version: 0.5.4
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Summary: pymetadata are python utilities for working with metadata.
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Author-email: Matthias König <konigmatt@googlemail.com>
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Maintainer-email: Matthias König <konigmatt@googlemail.com>
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[](https://doi.org/10.5281/zenodo.5308801)
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pymetadata is a collection of python utilities for working with
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metadata in the context of COMBINE standards with source code available from
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metadata in the context of COMBINE standards with source code available from
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[https://github.com/matthiaskoenig/pymetadata](https://github.com/matthiaskoenig/pymetadata).
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# Documentation
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# Funding
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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).
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`pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
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`pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
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```bash
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metadata in the context of COMBINE standards with source code available from
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# Documentation
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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).
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# Installation
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`pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
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`pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
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**entity**
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{"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"}
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{"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"}
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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## Features
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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## Features
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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## Features
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
|
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## Features
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
|
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## Features
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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## Features
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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## Features
|
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
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|
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## Features
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# Release notes for pymetadata 0.3.9
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
|
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|
following changes:
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## Features
|
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# Release notes for pymetadata 0.4.0
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
|
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|
following changes:
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## Features
|
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# Release notes for pymetadata 0.4.1
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We are pleased to release the next version of pymetadata including the
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We are pleased to release the next version of pymetadata including the
|
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|
following changes:
|
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## Features
|
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# Release notes for pymetadata 0.4.2
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We are pleased to release the next version of pymetadata including the
|
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We are pleased to release the next version of pymetadata including the
|
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|
following changes:
|
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## Features & fixes
|
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# Release notes for pymetadata 0.4.3
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We are pleased to release the next version of pymetadata including the
|
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We are pleased to release the next version of pymetadata including the
|
|
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|
following changes:
|
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## Features & fixes
|
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# Release notes for pymetadata 0.4.4
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We are pleased to release the next version of pymetadata including the
|
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We are pleased to release the next version of pymetadata including the
|
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|
following changes:
|
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## Features & fixes
|
|
@@ -1,7 +1,7 @@
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# Release notes for pymetadata 0.5.0
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We are pleased to release the next version of pymetadata including the
|
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We are pleased to release the next version of pymetadata including the
|
|
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|
following changes:
|
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## Features & fixes
|
|
@@ -1,7 +1,7 @@
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# Release notes for pymetadata 0.5.1
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3
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-
We are pleased to release the next version of pymetadata including the
|
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+
We are pleased to release the next version of pymetadata including the
|
|
5
5
|
following changes:
|
|
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## Features & fixes
|
|
@@ -1,11 +1,11 @@
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# Release notes for pymetadata 0.5.2
|
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3
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We are pleased to release the next version of pymetadata including the
|
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We are pleased to release the next version of pymetadata including the
|
|
5
5
|
following changes:
|
|
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## Features & fixes
|
|
8
8
|
- Speedup CI-CD with uv
|
|
9
|
-
- Markdown README
|
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|
+
- Markdown README
|
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Your pymetadata team
|