Centralize default model path generation (#3002)

Currently, there are several places where default model directory paths are generated. Centralize that.

Running the test suite or building the documentation creates model directories all over the place. Reduce that.

Allow overriding the model base dir via environment variable.

Closes #2994.

Author: dweindl

CHANGELOG.md

@@ -79,6 +79,9 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 * The import function `sbml2amici`, `pysb2amici`, and `antimony2amici` now
   return an instance of the generated model class if called with `compile=True`
   (default).
+* The default directory for model import changed, and a base directory
+  can now be specified via the `AMICI_MODELS_ROOT` environment variable.
+  See `amici.get_model_dir` for details.
 
 ## v0.X Series
 

python/sdist/amici/__init__.py

@@ -76,6 +76,53 @@ def _imported_from_setup() -> bool:
     return False
 
 
+def get_model_root_dir() -> Path:
+    """Get the default root directory for AMICI models.
+
+    :return:
+        The model root directory.
+        This defaults to `{base_dir}/{amici_version}`.
+        If the environment variable `AMICI_MODELS_ROOT` is set,
+        it is used as `base_dir`, otherwise `amici_models` in the current
+        working directory.
+    """
+    try:
+        base_dir = Path(os.environ["AMICI_MODELS_ROOT"])
+    except KeyError:
+        base_dir = Path("amici_models")
+
+    return base_dir / __version__
+
+
+def get_model_dir(model_id: str | None = None, jax: bool = False) -> Path:
+    """Get the default directory for the model with the given ID.
+
+    :param model_id:
+        The model ID.
+    :param jax:
+        Whether to get the model directory for a JAX model.
+        If `True`, a suffix `_jax` is appended to the `model_id`.
+    :return:
+        The model directory.
+        This defaults to `{root_dir}/{model_id}`, where `root_dir` is
+        determined via :func:`get_model_root_dir`.
+        If `model_id` is `None`, a temporary directory is created in
+        `{base_dir}/{amici_version}` and returned.
+    """
+    base_dir = get_model_root_dir()
+
+    suffix = "_jax" if jax else ""
+
+    if model_id is None:
+        import tempfile
+
+        return Path(
+            tempfile.mkdtemp(dir=base_dir / __version__), suffix=suffix
+        )
+
+    return base_dir / __version__ / (model_id + suffix)
+
+
 # Initialize AMICI paths
 #: absolute root path of the amici repository or Python package
 amici_path = _get_amici_path()

python/sdist/amici/de_export.py

@@ -30,6 +30,7 @@
     amiciModulePath,
     amiciSrcPath,
     amiciSwigPath,
+    get_model_dir,
     splines,
 )
 from ._codegen.cxx_functions import (
@@ -1311,7 +1312,7 @@ def set_paths(self, output_dir: str | Path | None = None) -> None:
 
         """
         if output_dir is None:
-            output_dir = os.path.join(os.getcwd(), f"amici-{self.model_name}")
+            output_dir = get_model_dir(self.model_name)
 
         self.model_path = os.path.abspath(output_dir)
         self.model_swig_path = os.path.join(self.model_path, "swig")

python/sdist/amici/petab/petab_import.py

@@ -55,7 +55,7 @@ def import_petab_problem(
 
     :param model_output_dir:
         Directory to write the model code to. It will be created if it doesn't
-        exist. Defaults to current directory.
+        exist. Defaults to :func:`amici.get_model_dir`.
 
     :param model_name:
         Name of the generated model module. Defaults to the ID of the model
@@ -99,20 +99,11 @@ def import_petab_problem(
 
     # generate folder and model name if necessary
     if model_output_dir is None:
-        if petab_problem.model.type_id == MODEL_TYPE_PYSB:
-            raise ValueError("Parameter `model_output_dir` is required.")
-
-        from .sbml_import import _create_model_output_dir_name
-
-        model_output_dir = _create_model_output_dir_name(
-            petab_problem.sbml_model, model_name, jax=jax
-        )
+        model_output_dir = amici.get_model_dir(model_name, jax=jax).absolute()
     else:
-        model_output_dir = os.path.abspath(model_output_dir)
+        model_output_dir = Path(model_output_dir).absolute()
 
-    # create folder
-    if not os.path.exists(model_output_dir):
-        os.makedirs(model_output_dir)
+    model_output_dir.mkdir(parents=True, exist_ok=True)
 
     # check if compilation necessary
     if compile_ or (

python/sdist/amici/petab/sbml_import.py

@@ -2,7 +2,6 @@
 import math
 import os
 import re
-import tempfile
 from _collections import OrderedDict
 from itertools import chain
 from pathlib import Path
@@ -604,29 +603,3 @@ def _get_fixed_parameters_sbml(
                 continue
 
     return list(sorted(fixed_parameters))
-
-
-def _create_model_output_dir_name(
-    sbml_model: "libsbml.Model",
-    model_name: str | None = None,
-    jax: bool = False,
-) -> Path:
-    """
-    Find a folder for storing the compiled amici model.
-    If possible, use the sbml model id, otherwise create a random folder.
-    The folder will be located in the `amici_models` subfolder of the current
-    folder.
-    """
-    BASE_DIR = Path("amici_models").absolute()
-    BASE_DIR.mkdir(exist_ok=True)
-    # try model_name
-    suffix = "_jax" if jax else ""
-    if model_name:
-        return BASE_DIR / (model_name + suffix)
-
-    # try sbml model id
-    if sbml_model_id := sbml_model.getId():
-        return BASE_DIR / (sbml_model_id + suffix)
-
-    # create random folder name
-    return Path(tempfile.mkdtemp(dir=BASE_DIR))

python/sdist/amici/pysb_import.py

@@ -252,7 +252,7 @@ def pysb2amici(
         constant_parameters = []
 
     model_name = model_name or model.name
-
+    output_dir = output_dir or amici.get_model_dir(model_name)
     set_log_level(logger, verbose)
     ode_model = ode_model_from_pysb_importer(
         model,

python/sdist/amici/sbml_import.py

@@ -28,7 +28,7 @@
 
 import amici
 
-from . import has_clibs
+from . import get_model_dir, has_clibs
 from .constants import SymbolId
 from .de_export import (
     DEExporter,
@@ -317,6 +317,7 @@ def sbml2amici(
 
         :param output_dir:
             Directory where the generated model package will be stored.
+            Defaults to :func:`amici.get_model_dir`.
 
         :param constant_parameters:
             list of SBML Ids identifying constant parameters
@@ -398,6 +399,8 @@ def sbml2amici(
             hardcode_symbols=hardcode_symbols,
         )
 
+        output_dir = output_dir or get_model_dir(model_name)
+
         exporter = DEExporter(
             ode_model,
             model_name=model_name,

python/tests/conftest.py

@@ -2,6 +2,7 @@
 
 import copy
 import importlib
+import os
 import sys
 from pathlib import Path
 
@@ -12,7 +13,8 @@
 
 pytest_plugins = ["amici.testing.fixtures"]
 
-EXAMPLES_DIR = Path(__file__).parents[2] / "doc" / "examples"
+REPO_ROOT = Path(__file__).parents[2]
+EXAMPLES_DIR = REPO_ROOT / "doc" / "examples"
 TEST_DIR = Path(__file__).parent
 MODEL_STEADYSTATE_SCALED_XML = (
     EXAMPLES_DIR / "getting_started" / "model_steadystate_scaled.xml"
@@ -21,6 +23,8 @@
     EXAMPLES_DIR / "example_presimulation" / "model_presimulation.xml"
 )
 
+os.environ.setdefault("AMICI_MODELS_ROOT", str(REPO_ROOT.absolute()))
+
 
 @pytest.fixture(scope="session")
 def sbml_example_presimulation_module():

tests/benchmark_models/conftest.py

@@ -5,6 +5,7 @@
 import benchmark_models_petab
 import petab.v1 as petab
 import pytest
+from amici import get_model_root_dir
 from amici.petab.petab_import import import_petab_problem
 from petab.v1.lint import measurement_table_has_timepoint_specific_mappings
 
@@ -14,8 +15,7 @@
 
 from test_petab_benchmark import problems
 
-repo_root = script_dir.parent.parent
-benchmark_outdir = repo_root / "test_bmc"
+benchmark_outdir = get_model_root_dir() / "test_bmc"
 
 
 @pytest.fixture(scope="session", params=problems, ids=problems)

tests/benchmark_models/test_petab_benchmark.py

@@ -20,7 +20,7 @@
 import petab.v1 as petab
 import pytest
 import yaml
-from amici import SensitivityMethod
+from amici import SensitivityMethod, get_model_root_dir
 from amici.adapters.fiddy import simulate_petab_to_cached_functions
 from amici.logging import get_logger
 from amici.petab.petab_import import import_petab_problem
@@ -44,8 +44,7 @@
 )
 
 script_dir = Path(__file__).parent.absolute()
-repo_root = script_dir.parent.parent
-benchmark_outdir = repo_root / "test_bmc"
+benchmark_outdir = get_model_root_dir() / "test_bmc"
 debug_path = script_dir / "debug"
 if debug:
     debug_path.mkdir(exist_ok=True, parents=True)