From ca0effd84bdb2ec1cef2c36f7fdf37221889d9af Mon Sep 17 00:00:00 2001
From: Jonathan Karr <jonrkarr@gmail.com>
Date: Tue, 5 Jan 2021 03:59:53 -0500
Subject: [PATCH] updating to biosimulators-util 0.1.30; incrementing version

---
 Dockerfile                      | 2 +-
 biosimulators_amici/_version.py | 2 +-
 biosimulators_amici/core.py     | 5 ++++-
 requirements.txt                | 2 +-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index e647952..a23bee6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
 # Base OS
 FROM python:3.7.9-slim-buster
 
-ARG VERSION="0.1.2"
+ARG VERSION="0.1.3"
 ARG SIMULATOR_VERSION="0.11.11"
 
 # metadata
diff --git a/biosimulators_amici/_version.py b/biosimulators_amici/_version.py
index 10939f0..8ce9b36 100644
--- a/biosimulators_amici/_version.py
+++ b/biosimulators_amici/_version.py
@@ -1 +1 @@
-__version__ = '0.1.2'
+__version__ = '0.1.3'
diff --git a/biosimulators_amici/core.py b/biosimulators_amici/core.py
index 05866d2..39d1cc9 100644
--- a/biosimulators_amici/core.py
+++ b/biosimulators_amici/core.py
@@ -13,8 +13,10 @@
 from biosimulators_utils.sedml.data_model import (Task, ModelLanguage, UniformTimeCourseSimulation,  # noqa: F401
                                                   DataGeneratorVariable, DataGeneratorVariableSymbol)
 from biosimulators_utils.sedml import validation
+from biosimulators_utils.sedml.exec import exec_sed_doc
 from biosimulators_utils.utils.core import validate_str_value, parse_value
 import amici
+import functools
 import importlib.util
 import numpy
 import os.path
@@ -54,7 +56,8 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
         bundle_outputs (:obj:`bool`, optional): if :obj:`True`, bundle outputs into archives for reports and plots
         keep_individual_outputs (:obj:`bool`, optional): if :obj:`True`, keep individual output files
     """
-    exec_sedml_docs_in_archive(archive_filename, exec_sed_task, out_dir,
+    sed_doc_executer = functools.partial(exec_sed_doc, exec_sed_task)
+    exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir,
                                apply_xml_model_changes=True,
                                report_formats=report_formats,
                                plot_formats=plot_formats,
diff --git a/requirements.txt b/requirements.txt
index a103502..e95f762 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 amici
-biosimulators_utils >= 0.1.28
+biosimulators_utils >= 0.1.30
 numpy
 sympy >= 1.7