integrating changes from david's PR (#60)

Author: stitova-idm

docs/reference/virtual_environments.md

@@ -46,7 +46,7 @@ python -m pip install --upgrade pip
 Now, you have an environment where you can install the latest version of emodpy-workflow!!!
 
 ```
-pip install hiv-workflow –extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+pip install hiv-workflow 
 ```
 
 ### Deactivate a virtual environment

emodpy_workflow/scripts/run.py

@@ -57,7 +57,6 @@ def build_scenario_experiment(platform, samples, experiment_name, frame, suite_i
     experiment = Experiment(name=experiment_name,
                             simulations=TemplatedSimulations(base_task=task, builders={builder}), parent_id=suite_id)
     # doesn't work for now platform.num_cores = frame.num_cores  # TODO: this does set per-exp num_cores in comps (min/max cores is this) BUT it also does it on the sim config (breaks!)
-    platform.create_items(experiment)
     return experiment
 
 
@@ -138,6 +137,7 @@ def main(args):
                 'experiment_name': experiment_name
             }
             # add the experiment directory to the receipt if it exists on the platform
+            suite.add_experiment(experiment)
             try:
                 exp_directory = platform.get_directory(item=experiment)
                 frame_and_experiment_info['experiment_directory'] = exp_directory
@@ -149,7 +149,7 @@ def main(args):
     # https://github.com/InstituteforDiseaseModeling/idmtools/issues/1653
     suite.experiments.extend(experiments)
 
-    platform.run_items(experiments)
+    platform.run_items([suite])
     write_receipt(receipt=receipt, receipt_path=receipt_path)
 
     print('Done with model experiment creation.')

pyproject.toml

@@ -19,7 +19,7 @@ dependencies = [ #pandas and scikit-learn are dependencies of emodpy-hiv, so we
     "openpyxl==3.0.9",
     "scipy~=1.17",
     "seaborn~=0.13",
-    "urllib3<2.0"
+    "urllib3~=2.6"
 ]
 license = "MIT"
 classifiers=[