Merge branch 'develop' into adjoint_event

python/examples/example_splines_swameye/ExampleSplinesSwameye2003.ipynb

@@ -101,11 +101,11 @@
    "source": [
     "# If running as a GitHub action, just do the minimal amount of work required to check whether the code is working\n",
     "if os.getenv(\"GITHUB_ACTIONS\") is not None:\n",
-    "    n_starts = 15\n",
+    "    n_starts = 25\n",
     "    pypesto_optimizer = pypesto.optimize.FidesOptimizer(\n",
     "        verbose=logging.WARNING, options=dict(maxiter=10)\n",
     "    )\n",
-    "    pypesto_engine = pypesto.engine.SingleCoreEngine()"
+    "    pypesto_engine = pypesto.engine.MultiProcessEngine()"
    ]
   },
   {

python/sdist/amici/de_export.py

@@ -58,8 +58,8 @@
     generate_flux_symbol,
     smart_subs_dict,
     strip_pysb,
-    symbol_with_assumptions,
     toposort_symbols,
+    unique_preserve_order,
 )
 from .logging import get_logger, log_execution_time, set_log_level
 
@@ -2844,16 +2844,12 @@ def _process_heavisides(
         :returns:
             dxdt with Heaviside functions replaced by amici helper variables
         """
-
-        # expanding the rhs will in general help to collect the same
-        # heaviside function
-        dt_expanded = dxdt.expand()
         # track all the old Heaviside expressions in tmp_roots_old
         # replace them later by the new expressions
         heavisides = []
         # run through the expression tree and get the roots
-        tmp_roots_old = self._collect_heaviside_roots(dt_expanded.args)
-        for tmp_old in tmp_roots_old:
+        tmp_roots_old = self._collect_heaviside_roots(dxdt.args)
+        for tmp_old in unique_preserve_order(tmp_roots_old):
             # we want unique identifiers for the roots
             tmp_new = self._get_unique_root(tmp_old, roots)
             # `tmp_new` is None if the root is not time-dependent.

python/sdist/amici/import_utils.py

@@ -734,5 +734,20 @@ def strip_pysb(symbol: sp.Basic) -> sp.Basic:
         return symbol
 
 
+def unique_preserve_order(seq: Sequence) -> list:
+    """Return a list of unique elements in Sequence, keeping only the first
+    occurrence of each element
+
+    Parameters:
+        seq: Sequence to prune
+
+    Returns:
+        List of unique elements in ``seq``
+    """
+    seen = set()
+    seen_add = seen.add
+    return [x for x in seq if not (x in seen or seen_add(x))]
+
+
 sbml_time_symbol = symbol_with_assumptions("time")
 amici_time_symbol = symbol_with_assumptions("t")

python/sdist/amici/sbml_import.py

@@ -38,7 +38,6 @@
     DEModel,
     _default_simplify,
     smart_is_zero_matrix,
-    symbol_with_assumptions,
 )
 from .import_utils import (
     RESERVED_SYMBOLS,
@@ -54,6 +53,7 @@
     sbml_time_symbol,
     smart_subs,
     smart_subs_dict,
+    symbol_with_assumptions,
     toposort_symbols,
 )
 from .logging import get_logger, log_execution_time, set_log_level

tests/benchmark-models/test_petab_benchmark.py

@@ -1,5 +1,5 @@
 """Tests for simulate_petab on PEtab benchmark problems."""
-
+import os
 from pathlib import Path
 
 import amici
@@ -13,13 +13,13 @@
 ATOL: float = 1e-3
 RTOL: float = 1e-2
 
-benchmark_path = (
-    Path(__file__).parent.parent.parent
-    / "Benchmark-Models-PEtab"
-    / "Benchmark-Models"
-)
+repo_root = Path(__file__).parent.parent.parent
+benchmark_path = repo_root / "Benchmark-Models-PEtab" / "Benchmark-Models"
+if not benchmark_path.exists():
+    benchmark_path = Path(os.environ["BENCHMARK_COLLECTION"])
+
 # reuse compiled models from test_benchmark_collection.sh
-benchmark_outdir = Path(__file__).parent.parent.parent / "test_bmc"
+benchmark_outdir = repo_root / "test_bmc"
 models = [
     str(petab_path.stem)
     for petab_path in benchmark_path.glob("*")

tests/benchmark-models/test_petab_model.py

@@ -9,6 +9,7 @@
 import logging
 import os
 import sys
+from pathlib import Path
 
 import amici
 import numpy as np
@@ -100,7 +101,7 @@ def parse_cli_args():
 
 def main():
     """Simulate the model specified on the command line"""
-
+    script_dir = Path(__file__).parent.absolute()
     args = parse_cli_args()
     loglevel = logging.DEBUG if args.verbose else logging.INFO
     logger.setLevel(loglevel)
@@ -168,10 +169,7 @@ def main():
 
     times["np"] = sum(problem.parameter_df[petab.ESTIMATE])
 
-    pd.Series(times).to_csv(
-        f"./tests/benchmark-models/{args.model_name}_benchmark.csv"
-    )
-
+    pd.Series(times).to_csv(script_dir / f"{args.model_name}_benchmark.csv")
     for rdata in rdatas:
         assert (
             rdata.status == amici.AMICI_SUCCESS
@@ -201,9 +199,7 @@ def main():
                 ax.get_figure().savefig(fig_path, dpi=150)
 
     if args.check:
-        references_yaml = os.path.join(
-            os.path.dirname(__file__), "benchmark_models.yaml"
-        )
+        references_yaml = script_dir / "benchmark_models.yaml"
         with open(references_yaml) as f:
             refs = yaml.full_load(f)