Merge pull request #114 from databio/schema_bug

Schema bug

Author: khoroshevskyi

bbconf/__init__.py

@@ -1,12 +1,15 @@
 import logging
+from importlib.metadata import version
 
 import coloredlogs
 
 from bbconf.bbagent import BedBaseAgent
 
 from .const import PKG_NAME
 
-__all__ = ["BedBaseAgent"]
+__version__ = version(__package__)
+
+__all__ = ["BedBaseAgent", "__version__"]
 
 _LOGGER = logging.getLogger(PKG_NAME)
 coloredlogs.install(

bbconf/models/bed_models.py

@@ -78,26 +78,28 @@ class BedStatsModel(BaseModel):
 
 
 class BedPEPHub(BaseModel):
-    sample_name: str = ""
-    genome: str = ""
-    organism: str = ""
-    species_id: str = ""
-    cell_type: str = ""
-    cell_line: str = ""
-    assay: str = Field("", description="Experimental protocol (e.g. ChIP-seq)")
-    library_source: str = Field(
+    sample_name: str | None = ""
+    genome: str | None = ""
+    organism: str | None = ""
+    species_id: str | None = ""
+    cell_type: str | None = ""
+    cell_line: str | None = ""
+    assay: str | None = Field("", description="Experimental protocol (e.g. ChIP-seq)")
+    library_source: str | None = Field(
         "", description="Library source (e.g. genomic, transcriptomic)"
     )
-    genotype: str = Field("", description="Genotype of the sample")
-    target: str = Field("", description="Target of the assay (e.g. H3K4me3)")
-    antibody: str = Field("", description="Antibody used in the assay")
-    treatment: str = Field(
+    genotype: str | None = Field("", description="Genotype of the sample")
+    target: str | None = Field("", description="Target of the assay (e.g. H3K4me3)")
+    antibody: str | None = Field("", description="Antibody used in the assay")
+    treatment: str | None = Field(
         "", description="Treatment of the sample (e.g. drug treatment)"
     )
-    tissue: str = Field("", description="Tissue type")
-    global_sample_id: str = Field("", description="Global sample identifier")
-    global_experiment_id: str = Field("", description="Global experiment identifier")
-    description: str = Field("", description="Description of the sample")
+    tissue: str | None = Field("", description="Tissue type")
+    global_sample_id: str | None = Field("", description="Global sample identifier")
+    global_experiment_id: str | None = Field(
+        "", description="Global experiment identifier"
+    )
+    description: str | None = Field("", description="Description of the sample")
 
     model_config = ConfigDict(extra="allow", populate_by_name=True)
 
@@ -107,35 +109,34 @@ class StandardMeta(BaseModel):
     Standardized Bed file metadata
     """
 
-    species_name: str = Field(
-        default="", description="Name of species. e.g. Homo sapiens.", alias="organism"
+    species_name: str | None = Field(
+        default=None,
+        description="Name of species. e.g. Homo sapiens.",
+        alias="organism",
     )
     species_id: str = ""
     genotype: str = Field("", description="Genotype of the sample")
     phenotype: str = Field("", description="Phenotype of the sample")
     description: str | None = ""
 
-    cell_type: str = Field(
-        "",
+    cell_type: str | None = Field(
+        None,
         description="specific kind of cell with distinct characteristics found in an organism. e.g. Neurons, Hepatocytes, Adipocytes",
     )
-    cell_line: str = Field(
-        "",
+    cell_line: str | None = Field(
+        None,
         description="population of cells derived from a single cell and cultured in the lab for extended use, e.g. HeLa, HepG2, k562",
     )
-    tissue: str = Field("", description="Tissue type")
+    tissue: str | None = Field(None, description="Tissue type")
 
-    library_source: str = Field(
-        "", description="Library source (e.g. genomic, transcriptomic)"
-    )
-    assay: str = Field(
-        "",
-        description="Experimental protocol (e.g. ChIP-seq)",
+    library_source: str | None = Field(
+        None, description="Library source (e.g. genomic, transcriptomic)"
     )
-    antibody: str = Field("", description="Antibody used in the assay")
-    target: str = Field("", description="Target of the assay (e.g. H3K4me3)")
-    treatment: str = Field(
-        "", description="Treatment of the sample (e.g. drug treatment)"
+    assay: str | None = Field(None, description="Experimental protocol (e.g. ChIP-seq)")
+    antibody: str | None = Field(None, description="Antibody used in the assay")
+    target: str | None = Field(None, description="Target of the assay (e.g. H3K4me3)")
+    treatment: str | None = Field(
+        None, description="Treatment of the sample (e.g. drug treatment)"
     )
 
     global_sample_id: list[str] | None = Field(
@@ -145,7 +146,7 @@ class StandardMeta(BaseModel):
         None, description="Global experiment identifier. e.g. GSE000"
     )  # excluded in training
 
-    original_file_name: str = Field("", description="Original file name")
+    original_file_name: str | None = Field(None, description="Original file name")
 
     model_config = ConfigDict(
         populate_by_name=True,

docs/changelog.md

@@ -2,6 +2,9 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+### [0.14.10] - 2026-04-05
+### Fixed:
+- version info bug
 
 ### [0.14.9] - 2026-02-26
 ### Changed:

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bbconf"
-version = "0.14.9"
+version = "0.14.10"
 description = "Configuration and data management tool for BEDbase"
 readme = "README.md"
 license = "BSD-2-Clause"
@@ -32,7 +32,7 @@ dependencies = [
     "zarr < 3.0.0",
     "pyyaml >= 6.0.1",
     "s3fs >= 2024.3.1",
-    "pandas < 3.0.0",
+    "pandas>2.0.0, < 3.0.0",
     "pybiocfilecache == 0.6.1",
     "umap-learn >= 0.5.8",
     "qdrant_client >= 1.16.1",