pymetadata 0.4.0__tar.gz → 0.4.2__tar.gz

{pymetadata-0.4.0/src/pymetadata.egg-info → pymetadata-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pymetadata
-Version: 0.4.0
+Version: 0.4.2
 Summary: pymetadata are python utilities for working with metadata.
 Home-page: https://github.com/matthiaskoenig/pymetadata
 Download-URL: https://pypi.org/project/pymetadata
@@ -17,38 +17,37 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: depinfo>=1.7
-Requires-Dist: uuid>=1.30
-Requires-Dist: lxml>=4.9
-Requires-Dist: rich>=13.6
+Requires-Dist: lxml>=5.2
+Requires-Dist: rich>=13.7
 Requires-Dist: requests>=2.31
 Requires-Dist: zeep>=4.2.1
-Requires-Dist: pronto>=2.5.5
-Requires-Dist: fastobo>=0.12.2
-Requires-Dist: jinja2>=3.1.2
+Requires-Dist: pronto>=2.5.6
+Requires-Dist: fastobo>=0.12.3
+Requires-Dist: jinja2>=3.1
 Requires-Dist: xmltodict>=0.13.0
-Requires-Dist: pydantic>=2.4
+Requires-Dist: pydantic>=2.6
 Provides-Extra: development
-Requires-Dist: pip-tools>6.5.1; extra == "development"
-Requires-Dist: black>=22.1.0; extra == "development"
+Requires-Dist: pip-tools>=7.4.1; extra == "development"
+Requires-Dist: black>=24.3.0; extra == "development"
 Requires-Dist: bump2version>=1.0.1; extra == "development"
-Requires-Dist: isort>=5.10; extra == "development"
-Requires-Dist: tox>=3.25; extra == "development"
-Requires-Dist: flake8>=4.0.1; extra == "development"
+Requires-Dist: isort>=5.13.2; extra == "development"
+Requires-Dist: tox>=4.12.2; extra == "development"
+Requires-Dist: flake8>=7.0.0; extra == "development"
 Requires-Dist: flake8-mypy>=17.8.0; extra == "development"
-Requires-Dist: mypy>=0.931; extra == "development"
-Requires-Dist: pytest>=7.0.1; extra == "development"
-Requires-Dist: pytest-cov>=3.0.0; extra == "development"
+Requires-Dist: mypy>=1.9.0; extra == "development"
+Requires-Dist: pytest>=8.1.1; extra == "development"
+Requires-Dist: pytest-cov>=5.0.0; extra == "development"
 
 .. image:: https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png
    :align: left
@@ -56,36 +55,28 @@ Requires-Dist: pytest-cov>=3.0.0; extra == "development"
 
 pymetadata: python utilities for metadata and COMBINE archives
 ==============================================================
+|icon1| |icon2| |icon3| |icon4| |icon5| |icon6| |icon7|
 
-.. image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
+
+.. |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
-
-.. image:: https://img.shields.io/pypi/v/pymetadata.svg
+.. |icon2| image:: https://img.shields.io/pypi/v/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Current PyPI Version
-
-.. image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
+.. |icon3| image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Supported Python Versions
-
-.. image:: https://img.shields.io/pypi/l/pymetadata.svg
+.. |icon4| image:: https://img.shields.io/pypi/l/pymetadata.svg
    :target: http://opensource.org/licenses/LGPL-3.0
    :alt: GNU Lesser General Public License 3
-
-.. image:: https://codecov.io/gh/matthiaskoenig/pymetadata/branch/develop/graph/badge.svg
-   :target: https://codecov.io/gh/matthiaskoenig/pymetadata
-   :alt: Codecov
-
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
+.. |icon5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
    :target: https://doi.org/10.5281/zenodo.5308801
    :alt: Zenodo DOI
-
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+.. |icon6| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/ambv/black
    :alt: Black
-
-.. image:: http://www.mypy-lang.org/static/mypy_badge.svg
+.. |icon7| image:: http://www.mypy-lang.org/static/mypy_badge.svg
    :target: http://mypy-lang.org/
    :alt: mypy
 
@@ -140,11 +131,11 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 Funding
 =======
-Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
+Matthias König 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) 
-and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
+and is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
 "`QuaLiPerF <https://qualiperf.de>`__ (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).
+A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA), and 
 
 Installation
 ============
@@ -169,4 +160,4 @@ To install for development use::
 
     pip install -e .[development]
 
-© 2021-2022 Matthias König
+© 2021-2024 Matthias König

{pymetadata-0.4.0 → pymetadata-0.4.2}/README.rst

@@ -4,36 +4,28 @@
 
 pymetadata: python utilities for metadata and COMBINE archives
 ==============================================================
+|icon1| |icon2| |icon3| |icon4| |icon5| |icon6| |icon7|
 
-.. image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
+
+.. |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
-
-.. image:: https://img.shields.io/pypi/v/pymetadata.svg
+.. |icon2| image:: https://img.shields.io/pypi/v/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Current PyPI Version
-
-.. image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
+.. |icon3| image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Supported Python Versions
-
-.. image:: https://img.shields.io/pypi/l/pymetadata.svg
+.. |icon4| image:: https://img.shields.io/pypi/l/pymetadata.svg
    :target: http://opensource.org/licenses/LGPL-3.0
    :alt: GNU Lesser General Public License 3
-
-.. image:: https://codecov.io/gh/matthiaskoenig/pymetadata/branch/develop/graph/badge.svg
-   :target: https://codecov.io/gh/matthiaskoenig/pymetadata
-   :alt: Codecov
-
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
+.. |icon5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
    :target: https://doi.org/10.5281/zenodo.5308801
    :alt: Zenodo DOI
-
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+.. |icon6| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/ambv/black
    :alt: Black
-
-.. image:: http://www.mypy-lang.org/static/mypy_badge.svg
+.. |icon7| image:: http://www.mypy-lang.org/static/mypy_badge.svg
    :target: http://mypy-lang.org/
    :alt: mypy
 
@@ -88,11 +80,11 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 Funding
 =======
-Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
+Matthias König 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) 
-and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
+and is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
 "`QuaLiPerF <https://qualiperf.de>`__ (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).
+A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA), and 
 
 Installation
 ============
@@ -117,4 +109,4 @@ To install for development use::
 
     pip install -e .[development]
 
-© 2021-2022 Matthias König
+© 2021-2024 Matthias König

{pymetadata-0.4.0 → pymetadata-0.4.2}/setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.0
+current_version = 0.4.2
 commit = True
 tag = True
 parse = (?P<major>\d+)
@@ -28,10 +28,10 @@ classifiers =
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 	Operating System :: OS Independent
-	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
 	Programming Language :: Python :: Implementation :: CPython
 	Topic :: Scientific/Engineering
 	Topic :: Scientific/Engineering :: Bio-Informatics
@@ -49,22 +49,21 @@ keywords =
 
 [options]
 zip_safe = True
-python_requires = >=3.8
+python_requires = >=3.9
 install_requires = 
 	depinfo>=1.7
-	uuid>=1.30
-	lxml>=4.9
-	rich>=13.6
+	lxml>=5.2
+	rich>=13.7
 	requests>=2.31
 	zeep>=4.2.1
-	pronto>=2.5.5
-	fastobo>=0.12.2
-	jinja2>=3.1.2
+	pronto>=2.5.6
+	fastobo>=0.12.3
+	jinja2>=3.1
 	xmltodict>=0.13.0
-	pydantic>=2.4
+	pydantic>=2.6
 tests_require = 
-	tox>=3.27
-	pytest
+	tox>=4.14.2
+	pytest>=8.1.1
 packages = find:
 package_dir = 
 	= src
@@ -81,16 +80,16 @@ where = src
 
 [options.extras_require]
 development = 
-	pip-tools>6.5.1
-	black>=22.1.0
+	pip-tools>=7.4.1
+	black>=24.3.0
 	bump2version>=1.0.1
-	isort>=5.10
-	tox>=3.25
-	flake8>=4.0.1
+	isort>=5.13.2
+	tox>=4.12.2
+	flake8>=7.0.0
 	flake8-mypy>=17.8.0
-	mypy>=0.931
-	pytest>=7.0.1
-	pytest-cov>=3.0.0
+	mypy>=1.9.0
+	pytest>=8.1.1
+	pytest-cov>=5.0.0
 
 [bdist_wheel]
 universal = 1

{pymetadata-0.4.0 → pymetadata-0.4.2}/setup.py

@@ -4,4 +4,4 @@ from setuptools import setup  # type: ignore
 
 
 if __name__ == "__main__":
-    setup(version="0.4.0")
+    setup(version="0.4.2")

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/__init__.py

@@ -1,8 +1,9 @@
 """pymetadata - Python utilities for metadata."""
+
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.4.0"
+__version__ = "0.4.2"
 
 
 program_name: str = "pymetadata"

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/cache.py

@@ -1,4 +1,5 @@
 """Caching of information."""
+
 import json
 from json.encoder import JSONEncoder
 from pathlib import Path

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/chebi.py

@@ -1,4 +1,5 @@
 """Module for working with chebi."""
+
 from pathlib import Path
 from pprint import pprint
 from typing import Any, Dict

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/console.py

@@ -1,4 +1,5 @@
 """Rich console for logging."""
+
 from rich import pretty
 from rich.console import Console
 from rich.theme import Theme

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/core/annotation.py

@@ -2,6 +2,7 @@
 
 Core data structure to store annotations.
 """
+
 import re
 import urllib
 from pprint import pprint

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/core/creator.py

@@ -1,4 +1,5 @@
 """Creator information."""
+
 from typing import Optional
 
 

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/core/synonym.py

@@ -1,4 +1,5 @@
 """Synonym information."""
+
 from dataclasses import dataclass
 
 

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/core/xref.py

@@ -1,4 +1,5 @@
 """Module for crossreferences (xref)."""
+
 import re
 from dataclasses import dataclass
 from typing import Dict

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/examples/omex_example.py

@@ -1,4 +1,5 @@
 """Example for reading and writing omex archives."""
+
 import zipfile
 from pathlib import Path
 

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/identifiers/registry.py

@@ -4,6 +4,7 @@ Helper tools to work with identifiers registry.
 https://identifiers.org/
 https://docs.identifiers.org/articles/api.html
 """
+
 from __future__ import annotations
 
 import inspect
@@ -186,18 +187,6 @@ def ols_namespaces() -> Dict[str, Namespace]:
             description="MONDO",
             namespaceEmbeddedInLui=True,
         ),
-        Namespace(
-            id=None,
-            prefix="stato",
-            pattern=r"^STATO:\d+$",
-            name="STATO",
-            description="STATO is the statistical methods ontology. It contains "
-            "concepts and properties related to statistical methods, "
-            "probability distributions and other concepts related to "
-            "statistical analysis, including relationships to study "
-            "designs and plots.",
-            namespaceEmbeddedInLui=True,
-        ),
         Namespace(
             id=None,
             prefix="atol",
@@ -348,7 +337,7 @@ class Registry:
         registry_path: Optional[Path] = None,
     ) -> Dict[str, Namespace]:
         """Update registry from identifiers.org webservice."""
-        logger.warning(f"Update registry: '{Registry.URL}' -> '{registry_path}'")
+        logger.info(f"Update registry from '{Registry.URL}'")
         response = requests.get(Registry.URL)
         namespaces = response.json()["payload"]["namespaces"]
 
@@ -373,9 +362,6 @@ class Registry:
             ns_dict[ns.prefix] = ns
 
         if custom_namespaces is not None:
-            logger.warning(
-                f"Adding custom namespaces: {sorted(custom_namespaces.keys())}"
-            )
             for key, ns in custom_namespaces.items():
                 if key in ns_dict:
                     logger.error(

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/log.py

@@ -2,6 +2,7 @@
 
 Using rich for output formating.
 """
+
 import logging
 
 from rich.logging import RichHandler

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/metadata/kisao.py

@@ -481,6 +481,8 @@ _terms = {
     "KISAO_0000695": "parameters for",
     "KISAO_0000696": "steady state root-finding problem",
     "KISAO_0000697": "SDE solver",
+    "KISAO_0000698": "particle coordinates",
+    "KISAO_0000699": "DAE Solver",
     "KISAO_0000800": "systems property",
     "KISAO_0000801": "concentration control coefficient matrix (unscaled)",
     "KISAO_0000802": "control coefficient (scaled)",
@@ -2455,6 +2457,14 @@ class KISAO(str, Enum):
     KISAO_0000697 = "KISAO_0000697"
     SDE_SOLVER = "KISAO_0000697"
 
+    # particle coordinates
+    KISAO_0000698 = "KISAO_0000698"
+    PARTICLE_COORDINATES = "KISAO_0000698"
+
+    # DAE Solver
+    KISAO_0000699 = "KISAO_0000699"
+    DAE_SOLVER = "KISAO_0000699"
+
     # systems property
     KISAO_0000800 = "KISAO_0000800"
     SYSTEMS_PROPERTY = "KISAO_0000800"

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/omex.py

@@ -33,7 +33,7 @@ logger = log.get_logger(__name__)
 __all__ = ["EntryFormat", "ManifestEntry", "Manifest", "Omex"]
 
 
-IDENTIFIERS_PREFIX = "http://identifiers.org/combine.specifications:"
+IDENTIFIERS_PREFIX = "http://identifiers.org/combine.specifications/"
 PURL_PREFIX = "https://purl.org/NET/mediatypes/"
 
 

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/omex_v2.py

@@ -2,6 +2,7 @@
 
 See https://docs.google.com/document/d/1-UDgY5lQ6tv4mZILZzol-PvCoAYW8yr2Ydn1OxcHMjM/edit#
 """
+
 from typing import List, Optional
 
 from pydantic import BaseModel

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/ontologies/ols.py

@@ -4,6 +4,7 @@ This uses the EMBL-EBI Ontology Lookup Service
 https://www.ebi.ac.uk/ols4
 
 """
+
 import urllib.parse
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -79,13 +80,13 @@ class OLSQuery:
         cache: bool = CACHE_USE,
     ):
         """Initialize OLSQuery."""
-        self.ontologies = {
+        self.ontologies: Dict[str, OLSOntology] = {
             ontology.name: ontology for ontology in ontologies
-        }  # type: Dict[str, OLSOntology]
+        }
         self.cache_path = cache_path / "ols"
         self.cache = cache
 
-        if not self.cache_path.exists():
+        if cache and not self.cache_path.exists():
             self.cache_path.mkdir(parents=True)
 
     def get_iri(self, ontology: str, term: str) -> str:
@@ -136,11 +137,6 @@ class OLSQuery:
         # double urlencode iri for OLS
         urliri = urllib.parse.quote(iri, safe="")
         urliri = urllib.parse.quote(urliri, safe="")
-        # urliri = iri.replace(":", "%253A")
-        # urliri = urliri.replace("/", "%252F")
-
-        # term_id = term.split(":")[-1]
-        # url = ols_pattern.replace('{$id}', term_id)
         cache_path = self.cache_path / f"{urliri}.json"
         data: Dict[str, Any] = {}
         if self.cache:
@@ -176,7 +172,8 @@ class OLSQuery:
                 else:
                     data["errors"] = []
                     data["warnings"] = []
-                    write_json_cache(data=data, cache_path=cache_path)  # type: ignore
+                    if self.cache:
+                        write_json_cache(data=data, cache_path=cache_path)  # type: ignore
 
         return data
 

{pymetadata-0.4.0 → pymetadata-0.4.2}/src/pymetadata/ontologies/ontology.py

@@ -5,6 +5,7 @@ Special ontologies are provided as enums.
 
 Uses the OWL links provided on OLS4 to download the ontologies.
 """
+
 import gzip
 import importlib
 import re
@@ -290,7 +291,7 @@ def try_ontology_import(ontology_id: str) -> None:
 
 if __name__ == "__main__":
     # download latest versions
-    # update_ontology_files()
+    update_ontology_files()
 
     # test loading of OWL files
     # ofile: OntologyFile