try mac disk space

.github/workflows/ci.yaml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         # os: [macos-latest, ubuntu-latest]
-        os: [ubuntu-latest]
+        os: [macos-latest]
         python-version: ["3.10"]
 
     steps:

src/phold/io/sub_db_outputs.py

@@ -41,19 +41,19 @@ def create_sub_db_outputs(
         "function",
         "product",
         "annotation_method",
-        "function_with_highest_bitscore_percentage",
-        "top_bitscore_percentage_not_unknown",
-        "top_bitscore_percentage_not_unknown",
-        "head_and_packaging_bitscore_percentage",
-        "integration_and_excision_bitscore_percentage",
-        "tail_bitscore_percentage",
-        "moron_auxiliary_metabolic_gene_and_host_takeover_bitscore_percentage",
-        "DNA_RNA_and_nucleotide_metabolism_bitscore_percentage",
-        "connector_bitscore_percentage",
-        "transcription_regulation_bitscore_percentage",
-        "lysis_bitscore_percentage",
-        "other_bitscore_percentage",
-        "unknown_function_bitscore_percentage",
+        "function_with_highest_bitscore_proportion",
+        "top_bitscore_proportion_not_unknown",
+        "top_bitscore_proportion_not_unknown",
+        "head_and_packaging_bitscore_proportion",
+        "integration_and_excision_bitscore_proportion",
+        "tail_bitscore_proportion",
+        "moron_auxiliary_metabolic_gene_and_host_takeover_bitscore_proportion",
+        "DNA_RNA_and_nucleotide_metabolism_bitscore_proportion",
+        "connector_bitscore_proportion",
+        "transcription_regulation_bitscore_proportion",
+        "lysis_bitscore_proportion",
+        "other_bitscore_proportion",
+        "unknown_function_bitscore_proportion",
     ]
 
     acr_merged_output_path: Path = Path(sub_db_tophits_dir) / "acr_cds_predictions.tsv"

tests/test_integration.py

@@ -6,6 +6,7 @@
 
 # import
 import os
+os.environ["KMP_DUPLICATE_LIB_OK"] = "True"
 
 import shutil
 
@@ -48,15 +49,9 @@ def remove_directory(dir_path):
     if os.path.exists(dir_path):
         shutil.rmtree(dir_path)
 
-
-@pytest.fixture(scope="session")
-def tmp_dir(tmpdir_factory):
-    return tmpdir_factory.mktemp("tmp")
-
-@pytest.fixture(autouse=True)
-def workingdir(tmp_dir, monkeypatch):
-    """set the working directory for all tests"""
-    monkeypatch.chdir(tmp_dir)
+# @pytest.fixture(scope="session")
+# def tmp_dir(tmpdir_factory):
+#     return tmpdir_factory.mktemp("tmp")
 
 # the server can be down
 run_remote = False
@@ -88,8 +83,6 @@ def test_install():
 def test_run_genbank():
     """test phold run with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
-    cmd = f"phold install -d {database_dir}"
-    exec_command(cmd)
     cmd = f"phold run -i {input_gbk} -o {run_gbk_dir} -t {threads} --cpu -d {database_dir} -f"
     exec_command(cmd)