From e87be03e9eb52825794e630a9fbf022f0a0a77b2 Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Wed, 9 Oct 2024 16:54:26 -0700
Subject: [PATCH] Handle local parameters (again).

Two aspects to the fix:
* Load in the 'param promoted' version of the SBML.
* Use the new 'separator' argument of validate_target_xpaths from biosimulators_utils to get IDs like "J0_n" instead of just "n".
---
 .github/workflows/ci.yml        | 1 +
 biosimulators_tellurium/core.py | 6 ++++--
 requirements.txt                | 6 +++---
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9d4a62b..f7b8056 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -125,6 +125,7 @@ jobs:
           fi
 
           echo "version=$version" >> $GITHUB_OUTPUT
+          echo "version=$version"
 
       - id: get-docker-image-tag
         name: Determine Docker image tag
diff --git a/biosimulators_tellurium/core.py b/biosimulators_tellurium/core.py
index 0754333..9dac704 100644
--- a/biosimulators_tellurium/core.py
+++ b/biosimulators_tellurium/core.py
@@ -431,7 +431,8 @@ def preprocess_sed_task(task, variables, config=None, simulator_config=None):
                                   warning_summary='Model `{}` may be invalid.'.format(model.id))
 
         # read model
-        road_runner = roadrunner.RoadRunner(model.source)
+        road_runner = roadrunner.RoadRunner()
+        road_runner = roadrunner.RoadRunner(road_runner.getParamPromotedSBML(model.source))
 
         # get algorithm to execute
         algorithm_substitution_policy = get_algorithm_substitution_policy(config=config)
@@ -583,7 +584,7 @@ def get_model_change_target_tellurium_change_map(model_etree, changes, alg_kisao
     Returns:
         :obj:`dict`: dictionary that maps the targets of changes to their corresponding tellurium identifiers
     """
-    change_targets_to_sbml_ids = validation.validate_target_xpaths(changes, model_etree, attr='id')
+    change_targets_to_sbml_ids = validation.validate_target_xpaths(changes, model_etree, attr='id', separator="_")
 
     species_ids = model.getFloatingSpeciesIds() + model.getBoundarySpeciesIds()
     component_ids = species_ids + model.getGlobalParameterIds() + model.getCompartmentIds()
@@ -889,3 +890,4 @@ def exec_sed_doc_with_tellurium(doc, working_dir, base_out_path, rel_out_path=No
 
     # Return a data structure with the results of the reports
     return report_results, log
+
diff --git a/requirements.txt b/requirements.txt
index 965b78d..6d9c617 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
-biosimulators_utils[logging] >= 0.1.187
-kisao >= 2.33
-libroadrunner >= 2.5.0
+biosimulators_utils[logging] >= 0.2.3
+kisao >= 2.34
+libroadrunner >= 2.7.0
 lxml
 numpy
 pandas