Merge pull request #96 from databio/dev

Release 0.14.0

Author: khoroshevskyi

.github/workflows/black.yml

@@ -6,6 +6,6 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@20.8b1
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+      - uses: psf/black@stable

.github/workflows/cli-coverage.yml

@@ -8,7 +8,7 @@ jobs:
   cli-coverage-report:
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.12"]
         os: [ ubuntu-latest ] # can't use macOS when using service containers or container jobs
     runs-on: ${{ matrix.os }}
     services:
@@ -28,7 +28,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
       - name: Install uv
         run: pip install uv

.github/workflows/python-publish.yml

@@ -13,7 +13,7 @@ jobs:
       id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python
       uses: actions/setup-python@v5
       with:

.github/workflows/run-pytest.yml

@@ -12,7 +12,7 @@ jobs:
   pytest:
     strategy:
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.10", "3.13"]
         os: [ubuntu-latest] # can't use macOS when using service containers or container jobs
     runs-on: ${{ matrix.os }}
     services:

bbconf/_version.py

@@ -1 +1 @@
-__version__ = "0.13.0"
+__version__ = "0.14.0"

bbconf/bbagent.py

@@ -1,36 +1,36 @@
 import logging
+import statistics
 from functools import cached_property
 from pathlib import Path
-from typing import List, Union, Dict
-import numpy as np
-import statistics
+from typing import Dict, List, Union
 
+import numpy as np
 from sqlalchemy.orm import Session
-from sqlalchemy.sql import distinct, func, select, and_, or_
+from sqlalchemy.sql import and_, distinct, func, or_, select
 
 from bbconf.config_parser.bedbaseconfig import BedBaseConfig
 from bbconf.db_utils import (
     Bed,
     BedMetadata,
     BedSets,
+    BedStats,
+    Files,
+    GeoGsmStatus,
     License,
-    UsageBedSetMeta,
     UsageBedMeta,
+    UsageBedSetMeta,
     UsageFiles,
     UsageSearch,
-    GeoGsmStatus,
-    BedStats,
-    Files,
 )
 from bbconf.models.base_models import (
-    StatsReturn,
-    UsageModel,
-    FileStats,
-    UsageStats,
     AllFilesInfo,
-    FileInfo,
     BinValues,
+    FileInfo,
+    FileStats,
     GEOStatistics,
+    StatsReturn,
+    UsageModel,
+    UsageStats,
 )
 from bbconf.modules.bedfiles import BedAgentBedFile
 from bbconf.modules.bedsets import BedAgentBedSet