Centralize default model path generation

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

@@ -251,7 +251,7 @@ 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)

tests/petab_test_suite/test_petab_suite.py

@@ -63,10 +63,8 @@ def _test_case(case, model_type, version, jax):
     model_name = (
         f"petab_{model_type}_test_case_{case}_{version.replace('.', '_')}"
     )
-    model_output_dir = f"amici_models/{model_name}" + ("_jax" if jax else "")
     imported = import_petab_problem(
         petab_problem=problem,
-        model_output_dir=model_output_dir,
         model_name=model_name,
         compile_=True,
         jax=jax,