diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml index 18b8ee2..3371720 100644 --- a/.github/workflows/run-pytest.yml +++ b/.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: diff --git a/.gitignore b/.gitignore index 19c66fc..3a554a2 100644 --- a/.gitignore +++ b/.gitignore @@ -137,3 +137,6 @@ test/bedqc/* openSignalMatrix out2023/* + +# test data +test/test_data/* \ No newline at end of file diff --git a/bedboss/bedboss.py b/bedboss/bedboss.py index 3a7e9fa..2537c4f 100644 --- a/bedboss/bedboss.py +++ b/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) diff --git a/bedboss/bedmaker/bedmaker.py b/bedboss/bedmaker/bedmaker.py index d908c8e..6f902ff 100755 --- a/bedboss/bedmaker/bedmaker.py +++ b/bedboss/bedmaker/bedmaker.py @@ -164,6 +164,7 @@ def __init__( name="bedmaker", outfolder=self.logs_dir, recover=True, + multi=True, ) else: self.pm = pm diff --git a/test/test_bedboss.py b/test/test_bedboss.py index 038fa40..d17359d 100644 --- a/test/test_bedboss.py +++ b/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" diff --git a/test/test_dependencies/bedbase_config_test.yaml b/test/test_dependencies/bedbase_config_test.yaml index 24b680c..696aae2 100644 --- a/test/test_dependencies/bedbase_config_test.yaml +++ b/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