Fixed #30

.github/workflows/run-pytest.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.10"]
+        python-version: ["3.8", "3.12"]
         os: [ubuntu-latest]
 
     steps:

.gitignore

@@ -137,3 +137,6 @@ test/bedqc/*
 openSignalMatrix
 
 out2023/*
+
+# test data
+test/test_data/*

bedboss/bedboss.py

@@ -134,7 +134,10 @@ def run_all(
         chrom_sizes=chrom_sizes,
         pm=pm,
     )
-    other_metadata.update(classification_meta)
+    if not other_metadata:
+        other_metadata = classification_meta
+    else:
+        other_metadata.update(classification_meta)
 
     bed_digest = bedstat(
         bedfile=output_bed,
@@ -293,6 +296,7 @@ def main(test_args: dict = None) -> NoReturn:
         outfolder=pm_out_folder,
         version=__version__,
         args=args,
+        multi=args_dict.get("multy", False),
     )
     if args_dict["command"] == "all":
         run_all(pm=pm, **args_dict)

bedboss/bedmaker/bedmaker.py

@@ -164,6 +164,7 @@ def __init__(
                 name="bedmaker",
                 outfolder=self.logs_dir,
                 recover=True,
+                multi=True,
             )
         else:
             self.pm = pm

test/test_bedboss.py

@@ -61,17 +61,14 @@ def test_qc(bedfile, tmpdir):
             "command": "qc",
             "bedfile": bedfile,
             "outfolder": tmpdir,
+            "multy": True,
         }
     )
     assert qc_passed is None
 
 
 @pytest.mark.skipif(
-    not db_setup() or not dependencies_installed,
-    reason=pytest_db_skip_reason,
-)
-@pytest.mark.skipif(
-    not db_setup() or not dependencies_installed,
+    not dependencies_installed,
     reason=pytest_db_skip_reason,
 )
 @pytest.mark.parametrize(
@@ -92,6 +89,7 @@ def test_make(bedfile, tmpdir):
             "output_bigbed": os.path.join(tmpdir, "bigbed"),
             "outfolder": tmpdir,
             "no_db_commit": True,
+            "multy": True,
         }
     )
     assert os.path.isfile(os.path.join(tmpdir, "bed", "sample1.bed.gz"))
@@ -129,9 +127,9 @@ def test_stat(self, bedfile, bigbed_file, genome, output_temp_dir):
                 "bigbed": bigbed_file,
                 "no_db_commit": True,
                 "skip_qdrant": True,
+                "multy": True,
             }
         )
-        assert True
 
     case_name = "sample1"
 
@@ -199,9 +197,9 @@ def test_boss(self, input_file, genome, input_type, output_temp_dir):
                 "no_db_commit": True,
                 "outfolder": output_temp_dir,
                 "skip_qdrant": True,
+                "multy": True,
             }
         )
-        assert True
 
     case_name = "sample1"
 

test/test_dependencies/bedbase_config_test.yaml

@@ -13,7 +13,7 @@ database:
   name: bedbase
   #name: pep-db
   dialect: postgresql
-  driver: psycopg2
+  driver: psycopg
 server:
   host: 0.0.0.0
   port: 8000