metahq-core 0.1.2__tar.gz → 1.0.0rc1__tar.gz

metahq_core-1.0.0rc1/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Krishnan Lab
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

{metahq_core-0.1.2 → metahq_core-1.0.0rc1}/PKG-INFO

@@ -1,17 +1,16 @@
 Metadata-Version: 2.4
 Name: metahq-core
-Version: 0.1.2
+Version: 1.0.0rc1
 Summary: Core API for the meta-hq CLI.
 Author-email: Parker Hicks <parker.hicks@cuanschutz.edu>, Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
-Keywords: CLI,Data Curation,Database,Public Biomedical Data
+License-File: LICENSE
+Keywords: Data Curation,Database,Public Biomedical Data
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.11
+Requires-Python: >=3.12
 Requires-Dist: duckdb>=1.4.0
 Requires-Dist: networkx>=3.0
 Requires-Dist: numpy>=2.3.0
@@ -21,13 +20,20 @@ Requires-Dist: pydantic>=2.0.0
 Requires-Dist: pymongo>=4.13.0
 Requires-Dist: pyyaml>=5.1
 Requires-Dist: rank-bm25>=0.2.2
+Requires-Dist: rich>=13.0.0
 Provides-Extra: dev
 Requires-Dist: black; extra == 'dev'
 Requires-Dist: flake8; extra == 'dev'
 Requires-Dist: isort; extra == 'dev'
+Requires-Dist: mkdocs-click; extra == 'dev'
+Requires-Dist: mkdocs-material; extra == 'dev'
+Requires-Dist: mkdocs>=1.6.1; extra == 'dev'
+Requires-Dist: mkdocstrings[python]; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pymdown-extensions; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
 Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: vulture; extra == 'dev'
 Provides-Extra: test
 Requires-Dist: pytest-benchmark; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
@@ -37,9 +43,10 @@ Description-Content-Type: text/markdown
 # metahq-core
 
 ![Core Tests](https://github.com/krishnanlab/meta-hq/workflows/Core%20Tests/badge.svg)
-![Python](https://img.shields.io/badge/python-3.11+-blue.svg)
+![Python](https://img.shields.io/badge/python-3.12+-blue.svg)
 ![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)
 ![pypi](https://img.shields.io/pypi/v/metahq-core.svg)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
 Backend package for `metahq-cli` also available on PyPI. Currently this package
 is solely intended to be used through the MetaHQ CLI.

{metahq_core-0.1.2 → metahq_core-1.0.0rc1}/README.md

@@ -1,9 +1,10 @@
 # metahq-core
 
 ![Core Tests](https://github.com/krishnanlab/meta-hq/workflows/Core%20Tests/badge.svg)
-![Python](https://img.shields.io/badge/python-3.11+-blue.svg)
+![Python](https://img.shields.io/badge/python-3.12+-blue.svg)
 ![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)
 ![pypi](https://img.shields.io/pypi/v/metahq-core.svg)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
 Backend package for `metahq-cli` also available on PyPI. Currently this package
 is solely intended to be used through the MetaHQ CLI.

{metahq_core-0.1.2 → metahq_core-1.0.0rc1}/pyproject.toml

@@ -3,18 +3,16 @@ name = "metahq-core"
 dynamic = ["version"]
 description = "Core API for the meta-hq CLI."
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 authors = [
     {name = "Parker Hicks", email = "parker.hicks@cuanschutz.edu"},
     {name = "Faisal Alquaddoomi", email = "faisal.alquaddoomi@cuanschutz.edu"},
 ]
-keywords = ["CLI", "Database", "Data Curation", "Public Biomedical Data"]
+keywords = ["Database", "Data Curation", "Public Biomedical Data"]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
@@ -29,6 +27,7 @@ dependencies = [
     "pyyaml>=5.1",
     "duckdb>=1.4.0",
     "rank-bm25>=0.2.2",
+    "rich>=13.0.0",
 ]
 
 [project.optional-dependencies]
@@ -39,6 +38,12 @@ dev = [
     "isort",
     "flake8",
     "mypy",
+    "mkdocs>=1.6.1",
+    "pymdown-extensions",
+    "mkdocstrings[python]",
+    "mkdocs-material",
+    "mkdocs-click",
+    "vulture",
 ]
 
 test = [
@@ -71,7 +76,7 @@ profile = "black"
 multi_line_output = 3
 
 [tool.mypy]
-python_version = "3.11"
+python_version = "3.12"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true

metahq_core-1.0.0rc1/src/metahq_core/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0-rc.1"

{metahq_core-0.1.2 → metahq_core-1.0.0rc1}/src/metahq_core/curations/annotation_converter.py

@@ -17,10 +17,10 @@ import polars as pl
 from metahq_core.curations.labels import Labels
 from metahq_core.curations.propagator import Propagator, propagate_controls
 from metahq_core.logger import setup_logger
-from metahq_core.ontology.loader import RelationsLoader
+from metahq_core.relations_loader import RelationsLoader
 from metahq_core.util.helpers import merge_list_values
 from metahq_core.util.progress import progress_wrapper
-from metahq_core.util.supported import get_ontology_families
+from metahq_core.util.supported import get_default_log_dir, get_ontology_families
 
 if TYPE_CHECKING:
     import logging
@@ -69,7 +69,7 @@ class AnnotationsConverter:
         control_col="MONDO:0000000",
         logger=None,
         loglevel=20,
-        logdir=Path("."),
+        logdir=get_default_log_dir(),
         verbose=False,
     ):
         self.anno: Annotations = anno
@@ -276,8 +276,8 @@ class AnnotationsConverter:
             relatives=["ancestors", "descendants"],
             verbose=self.verbose,
         )
-        up_mat, cols, up_ids = propagator.propagate_up(verbose=self.verbose)
-        down_mat, _, _ = propagator.propagate_down(verbose=self.verbose)
+        up_mat, cols, up_ids = propagator.propagate_up()
+        down_mat, _, _ = propagator.propagate_down()
 
         neg_mask = (up_mat == 0) & (down_mat == 0)
         up_mat[neg_mask] = -1