minor code and test fixes

databio · Oct 17, 2023 · 45b538c · 45b538c
1 parent 23692f9
commit 45b538c
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Showing 10 changed files with 26 additions and 17 deletions.
diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
@@ -12,7 +12,7 @@ jobs:
   pytest:
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         os: [ubuntu-latest] # can't use macOS when using service containers or container jobs
     runs-on: ${{ matrix.os }}
     services:

diff --git a/bbconf/_version.py b/bbconf/_version.py
@@ -1 +1 @@
-__version__ = "0.4.0a5"
+__version__ = "0.4.0"
diff --git a/bbconf/bbconf.py b/bbconf/bbconf.py
@@ -37,6 +37,7 @@
     CFG_QDRANT_HOST_KEY,
     CFG_QDRANT_COLLECTION_NAME_KEY,
     DEFAULT_HF_MODEL,
+    DEFAULT_VEC2VEC_MODEL,
 )
 from bbconf.exceptions import MissingConfigDataError, BedBaseConfError
 from bbconf.helpers import raise_missing_key, get_bedbase_cfg
@@ -106,9 +107,10 @@ def __init__(self, config_path: str = None, database_only: bool = False):
                         f"{CFG_PATH_REGION2VEC_KEY} was not provided in config file!"
                     )
                 if not self.config[CFG_PATH_KEY].get(CFG_PATH_VEC2VEC_KEY):
-                    _LOGGER.error(
-                        f"{CFG_PATH_VEC2VEC_KEY} was not provided in config file!"
-                    )
+                    self.config[CFG_PATH_KEY][
+                        CFG_PATH_VEC2VEC_KEY
+                    ] = DEFAULT_VEC2VEC_MODEL
+
         except qdrant_client.http.exceptions.ResponseHandlingException as err:
             _LOGGER.error(f"error in Connection to qdrant! skipping... Error: {err}")
 
@@ -156,7 +158,9 @@ def _read_config_file(self, config_path: str) -> yacman.YAMLConfigManager:
 
     def search_bed_by_text(
         self, query: str
-    ) -> List[Dict[str, Union[int, float, Dict[str, str], List[float]]]]:
+    ) -> Tuple[
+        Union[List[int], List[List[int]]], Union[List[float], List[List[float]]]
+    ]:
         """
         Search for bed files by text query in the qdrant database
 

diff --git a/bbconf/const.py b/bbconf/const.py
@@ -93,3 +93,4 @@
 }
 
 DEFAULT_HF_MODEL = "sentence-transformers/all-MiniLM-L12-v2"
+DEFAULT_VEC2VEC_MODEL = "databio/v2v-ChIP-atlas-hg38-ATAC"
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,9 +2,11 @@
 
 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.
 
-## [0.3.0a1] - 2023-08-02
+## [0.4.0] - 2023-10-17
 ### Change
 - bbconf to use pipestat v0.4.1 and SQLModel
+- Added qdrant search, and insert methods
+- Fixed tests
 
 ## [0.3.0] - 2022-08-18
 ### Change

diff --git a/interactive_testing.py b/interactive_testing.py
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -1,7 +1,7 @@
 logmuse
 yacman>=0.9.1
-#pipestat>=0.6.0a1
-pipestat @ git+https://github.com/pepkit/pipestat@dev#egg=pipestat
+pipestat>=0.6.0a2
+#pipestat @ git+https://github.com/pepkit/pipestat@dev#egg=pipestat
 sqlalchemy<2.0.0
 qdrant_client
-# geniml
+# geniml
diff --git a/setup.py b/setup.py
@@ -41,9 +41,11 @@
     classifiers=[
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
+        "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",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
     keywords="",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -7,13 +7,13 @@
 @pytest.fixture
 def test_data_bed():
     s = "test_string"
-    return {"bedfile_name": s, "bedfile": {"path": s, "title": s}, "regions_no": 1}
+    return {"name": s, "bedfile": {"path": s, "title": s}, "regions_no": 1}
 
 
 @pytest.fixture
 def test_data_bedset():
     s = "test_string"
-    return {"bedset_name": s, "bedset_tar_archive_path": {"path": s, "title": s}}
+    return {"name": s, "bedset_tar_archive_path": {"path": s, "title": s}}
 
 
 @pytest.fixture

diff --git a/tests/test_bbconf.py b/tests/test_bbconf.py
@@ -6,11 +6,11 @@
 
 from bbconf import BedBaseConf, get_bedbase_cfg
 from bbconf.exceptions import *
-from sqlmodel import Session, SQLModel, create_engine
+from sqlmodel import SQLModel, create_engine
 from sqlmodel.main import default_registry
 
 
-DB_URL = "postgresql+psycopg2://postgres:docker@127.0.0.1:5432/pep-db"
+DB_URL = "postgresql+psycopg2://postgres:dockerpassword@127.0.0.1:5432/pipestat-test"
 
 
 class ContextManagerDBTesting:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -93,3 +93,4 @@
		}

		DEFAULT_HF_MODEL = "sentence-transformers/all-MiniLM-L12-v2"
		DEFAULT_VEC2VEC_MODEL = "databio/v2v-ChIP-atlas-hg38-ATAC"