metahq-core 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

metahq_core/__init__.py

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.1.2"

metahq_core/ontology/loader.py

@@ -12,9 +12,11 @@ The values of these DataFrames answer the following questions with a
 Author: Parker Hicks
 Date: 2025-11-17
 
-Last updated: 2025-11-17 by Parker Hicks
+Last updated: 2025-11-21 by Parker Hicks
 """
 
+from pathlib import Path
+
 import polars as pl
 
 from metahq_core.logger import setup_logger
@@ -33,11 +35,11 @@ class RelationsLoader:
 
     """
 
-    def __init__(self, file, logger=None, loglevel=20):
+    def __init__(self, file, logger=None, loglevel=20, logdir=Path(".")):
         self.relations: pl.LazyFrame = self.setup(file)
 
         if logger is None:
-            logger = setup_logger(__name__, level=loglevel)
+            logger = setup_logger(__name__, level=loglevel, log_dir=logdir)
         self.logger = logger
 
     def setup(self, file) -> pl.LazyFrame:

metahq_core/util/supported.py

@@ -1,13 +1,15 @@
 """
 This script stores file path constants and functions to retrieve those paths.
 
+Functions beginning with an underscore are intended to be called through the
+`supported` function or are just helpers.
+
 Author: Parker Hicks
 Date: 2025-04-15
 
-Last updated: 2025-11-21 by Parker Hicks
+Last updated: 2025-11-24 by Parker Hicks
 """
 
-import sys
 from pathlib import Path
 from typing import Literal
 
@@ -53,13 +55,23 @@ def _ecodes() -> dict[str, str]:
     }
 
 
+def _formats() -> list[str]:
+    """Returns supported save formats."""
+    return ["parquet", "tsv", "csv", "json"]
+
+
 def _levels() -> list[str]:
     """Return supported annotation levels."""
     return ["sample", "series"]
 
 
+def _log_levels() -> list[str]:
+    """Return supported logger levels."""
+    return ["notset", "debug", "info", "warning", "error", "critical"]
+
+
 def _modes() -> list[str]:
-    return ["direct", "propagate", "label"]
+    return ["annotate", "label"]
 
 
 # tmp fix. Need to find out why these are included in anno
@@ -101,7 +113,7 @@ def _technologies() -> list[str]:
     return ["microarray", "rnaseq"]
 
 
-def age_groups() -> list[str]:
+def _age_groups() -> list[str]:
     """Return supported age groups."""
     return [
         "fetus",
@@ -163,7 +175,7 @@ def get_config_file():
 
 
 def get_config_file_no_check():
-    """Only used to intialize MetaHQ."""
+    """Only used to initialize MetaHQ."""
     return get_metahq_home() / "config.yaml"
 
 
@@ -182,7 +194,7 @@ def get_log_dir() -> Path:
     return get_config()["logs"]
 
 
-def get_default_log_dir():
+def get_default_log_dir() -> Path:
     """Returns path to default logging directory."""
     return get_metahq_home()
 
@@ -365,7 +377,9 @@ def _supported() -> dict[str, list[str]]:
     """Returns mapping between all supported entities and their items."""
     return {
         "attributes": _attributes(),
+        "age_groups": _age_groups(),
         "ecodes": list(_ecodes().keys()),
+        "formats": _formats(),
         "levels": _levels(),
         "modes": _modes(),
         "ontologies": _ontologies(),
@@ -373,6 +387,7 @@ def _supported() -> dict[str, list[str]]:
         "series_metadata": _series_metadata(),
         "species": list(species_map().keys()),
         "technologies": _technologies(),
+        "log_levels": _log_levels(),
     }
 
 

{metahq_core-0.1.0.dist-info → metahq_core-0.1.2.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: metahq-core
-Version: 0.1.0
+Version: 0.1.2
 Summary: Core API for the meta-hq CLI.
 Author-email: Parker Hicks <parker.hicks@cuanschutz.edu>, Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
-Keywords: cli,core,tool
+Keywords: CLI,Data Curation,Database,Public Biomedical Data
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
@@ -32,3 +32,20 @@ Provides-Extra: test
 Requires-Dist: pytest-benchmark; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: pytest>=8.0; extra == 'test'
+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)
+![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)
+![pypi](https://img.shields.io/pypi/v/metahq-core.svg)
+
+Backend package for `metahq-cli` also available on PyPI. Currently this package
+is solely intended to be used through the MetaHQ CLI.
+
+## Install
+
+```bash
+pip install metahq-core
+```

{metahq_core-0.1.0.dist-info → metahq_core-0.1.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 metahq_core/README.md,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-metahq_core/__init__.py,sha256=kUR5RAFc7HCeiqdlX36dZOHkUI5wI6V_43RpEcD8b-0,22
+metahq_core/__init__.py,sha256=YvuYzWnKtqBb-IqG8HAu-nhIYAsgj9Vmc_b9o7vO-js,22
 metahq_core/logger.py,sha256=06QrC5msnehVLZ40T8oBFIUrlmBB-ysNiF5zo7Ms4fw,1319
 metahq_core/query.py,sha256=B8oyh_vKps02QXW3MgBQmZgCK20tdy2bUB4tTmNfBXk,18526
 metahq_core/search.py,sha256=XEyZqqAIE5GPK-kUw2YQFnntvcsjMmZkAR_xjRJjuYI,9549
@@ -16,7 +16,7 @@ metahq_core/export/labels.py,sha256=pvS5_WIa2Aau7s4rpnSAm7OlD57Ht6Qln8-91GbNNao,
 metahq_core/ontology/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 metahq_core/ontology/base.py,sha256=DtdIb18aerwi3sX_B6opmkaoSuO_sVEKFTWbEY3MZHg,11545
 metahq_core/ontology/graph.py,sha256=47S_kfO6h6Np6i2g90Zizehq9yZiE4sXbuZzukyoDVE,8430
-metahq_core/ontology/loader.py,sha256=FsjpjfKu2uvPA0p0OOvaWQOVaTTqUnvVVHev42GhMGk,4627
+metahq_core/ontology/loader.py,sha256=epSiBAjiJa2KFe4Tfm3dxtjPcPgxTIHwOpN3VV03iTI,4687
 metahq_core/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 metahq_core/util/alltypes.py,sha256=zYrBKvtkAhR7lmqDlGp7BOh2bUNI-toQfd7o7isDCxw,721
 metahq_core/util/checkers.py,sha256=_7Aw2bO1PNg-9TPYOwKwvTqFtmb5vMyYU-omfUID_DE,508
@@ -24,7 +24,7 @@ metahq_core/util/exceptions.py,sha256=FlYUN8g4lNB3OSwQ20dfnSDmgX8NKZV5Yx7xERurrW
 metahq_core/util/helpers.py,sha256=sak1A7gp2qvnbhCBYHNQ5IUxIZeljgyRSu5U7C8a7bU,949
 metahq_core/util/io.py,sha256=3JY04VjxuWA1TSx59iIQaON1LG-ZZp2zxSLkuFDoHWg,3075
 metahq_core/util/progress.py,sha256=NF158KVFO9pO3vrsl7OrPAhYtd-cXaXRavL0iOV5XeM,2128
-metahq_core/util/supported.py,sha256=Gx4BRPcThEkapUnoos4DfMBzN55tupZSQSz-2V9W0kQ,10517
-metahq_core-0.1.0.dist-info/METADATA,sha256=B_AdZZCACKVjIsR7QUyaC9CeNRu68_YnxS8m0HeNKac,1275
-metahq_core-0.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-metahq_core-0.1.0.dist-info/RECORD,,
+metahq_core/util/supported.py,sha256=RRMCaNh5xKBL8zNDW_7oR7v0bWRXyhI4FgWmiUH4_i4,10995
+metahq_core-0.1.2.dist-info/METADATA,sha256=lcjV5sxKOWdTV69O1FSgWbVN-fa4DJu7Cy1YcTCT5RI,1836
+metahq_core-0.1.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+metahq_core-0.1.2.dist-info/RECORD,,