"""Execute SED-ML."""
from pathlib import Path
from sbmlsim.combine.sedml.runner import execute_sedml
[docs]examples_dir = Path(__file__).parent / "l1v4"
# examples_dir = Path(__file__).parent / "l1v4_l1v3"
[docs]l1v4_l1v3_files = ["repeated-stochastic-runs/repeated-stochastic-runs.sedml"]
[docs]l1v4_files = [
# plotting
"algorithm_parameters.sedml",
# "axis.sedml",
# "axis_grids.sedml",
# "axis_minmax.sedml",
# "axis_minmax_smaller.sedml",
# "axis_minormax.sedml",
# "concentration_amount.sedml", # FIXME
# "concentration_amount_b.sedml" # FIXME
# "curve_types.sedml",
# "curve_types_errors.sedml",
# "heat_map_ls.sedml",
# "markertype.sedml",
# "linetype.sedml",
# "right_yaxis.sedml",
# "line_overlap_order.sedml",
# "repressilator_figure.xml",
# "repressilator.xml",
# "repressilator_urn.xml",
# "test_file_1.sedml",
# "test_line_fill.sedml",
# "stacked_bar.sedml",
# "test_3hbarstacked.sedml",
# "test_bar.sedml",
# "test_bar3stacked.sedml",
# "test_file.sedml",
# "test_hbar_stacked.sedml",
# "test_shaded_area.sedml",
# "test_shaded_area_overlap_order.sedml",
# "test_base_styles.sedml",
]
if __name__ == "__main__":
# ----------------------
# L1V4 Plotting
# ----------------------
[docs] working_dir = examples_dir
for sedml_file in l1v4_files:
# for sedml_file in l1v4_l1v3_files:
execute_sedml(
path=examples_dir / sedml_file,
working_dir=examples_dir / "sbmlsim",
output_path=examples_dir / "sbmlsim",
)
# ----------------------
# L1V4 Parameter Fitting
# ----------------------
# working_dir = base_path / "l1v4_parameter_fitting"
# for name, sedml_file in [
# # "Elowitz_Nature2000.xml",
# ]:
# execute_sedml(
# working_dir=working_dir,
# path=working_dir / sedml_file
# )