add common workspace dir

Author: jcschaff

pyvcell/vcml/__init__.py

@@ -39,6 +39,7 @@
 )
 from pyvcell.vcml.vcml_reader import VcmlReader
 from pyvcell.vcml.vcml_writer import VcmlWriter
+from pyvcell.vcml.workspace import get_workspace_dir, set_workspace_dir
 
 __all__ = [
     "VCMLDocument",
@@ -79,4 +80,6 @@
     "load_vcml_file",
     "load_sbml_file",
     "load_antimony_file",
+    "get_workspace_dir",
+    "set_workspace_dir",
 ]

pyvcell/vcml/workspace.py

@@ -0,0 +1,17 @@
+from os import PathLike
+from pathlib import Path
+
+workspace_dir: Path = Path.cwd() / "workspace"
+
+
+def set_workspace_dir(path: PathLike[str]) -> None:
+    """Set the workspace directory for VCell simulations."""
+    global workspace_dir
+    workspace_dir = Path(path)
+
+
+def get_workspace_dir() -> Path:
+    """Get the current workspace directory for VCell simulations."""
+    if not workspace_dir.exists():
+        workspace_dir.mkdir(parents=True, exist_ok=True)
+    return workspace_dir

tests/conftest.py

@@ -4,6 +4,7 @@
     solver_output_simid_jobid,
     temp_sim_946368938_path,
     zarr_path,
+    temp_workspace
 )
 from tests.fixtures.model_fixtures import (  # noqa: F401
     sbml_spatial_bunny_3d_path,

tests/fixtures/data_fixtures.py

@@ -1,10 +1,13 @@
+import shutil
 import tarfile
 import tempfile
 from collections.abc import Generator
 from pathlib import Path
 
 import pytest
 
+from pyvcell.vcml import get_workspace_dir, set_workspace_dir
+
 ROOT_DIR = Path(__file__).parent.parent.parent
 FIXTURE_DATA_DIR = ROOT_DIR / "tests" / "fixtures" / "data"
 
@@ -37,3 +40,16 @@ def temp_sim_946368938_path() -> Generator[Path, None, None]:
 @pytest.fixture
 def fielddata_file_path() -> Path:
     return FIXTURE_DATA_DIR / "SimID_1232918682_0_test2_lsm_DEMO_species0_cyt_0_5_Volume.fdat"
+
+
+@pytest.fixture(scope="function", autouse=True)
+def temp_workspace() -> Generator[Path, None, None]:
+    with tempfile.TemporaryDirectory() as temp_dir:
+        temp_dir_path = Path(temp_dir)
+        temp_dir_path.mkdir(parents=True, exist_ok=True)
+        saved_workspace_dir = get_workspace_dir()
+        set_workspace_dir(temp_dir_path)
+
+        yield temp_dir_path
+
+        set_workspace_dir(saved_workspace_dir)