v1.22.1 - June 24, 2024

- Adding support for Custom_Node_Events and Custom_Coordinator_Events
- Updating a lot of documentation-related things
- Updating tests (fixes, improvements)

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.22.0
+current_version = 1.22.1
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)((?P<release>[\+a-z]+)\.(?P<build>\d+))?

docs/_templates/footer_end.html

@@ -0,0 +1,2 @@
+<p><a href="https://www.gatesfoundation.org/Privacy-and-Cookies-Notice">Privacy and Cookies Notice</a>&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;
+<a href="https://www.gatesfoundation.org/Terms-of-Use">Terms of Use</a></p>

docs/_templates/footer_start.html

@@ -0,0 +1,3 @@
+<p>emodpy is licensed under the <a href="https://creativecommons.org/licenses/by-sa/4.0/legalcode">Creative Commons
+    Attribution-ShareAlike 4.0 International License</a>.</p>
+<p>Send documentation feedback to <a href="mailto:idmsupport@gatesfoundation.org" target="_top">idmsupport@gatesfoundation.org</a>.</p>

docs/_templates/navbar-side.html

@@ -0,0 +1,12 @@
+{# Displays links to the top-level TOCtree elements, in the header navbar. #}
+<nav class="navbar-nav">
+  <p class="sidebar-header-items__title"
+     role="heading"
+     aria-level="1"
+     aria-label="{{ _('') }}">
+    {{ _("") }}
+  </p>
+  <ul class="bd-navbar-elements navbar-nav">
+    {{ generate_header_nav_html(n_links_before_dropdown=20, dropdown_text=theme_header_dropdown_text) }}
+  </ul>
+</nav>

docs/_templates/page.html

@@ -4,6 +4,20 @@
 
 {% block extrahead %}
 
+<script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':
+new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
+j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
+'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
+})(window,document,'script','dataLayer','GTM-NK4K647');</script>
+<!-- End Google Tag Manager -->
+
+<!-- Google Tag Manager (noscript) -->
+<noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-NK4K647"
+height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript>
+<!-- End Google Tag Manager (noscript) -->
+
+<link href="https://fonts.googleapis.com/css?family=Lato|Montserrat|Open+Sans" rel="stylesheet">
+
 <link href="https://fonts.googleapis.com/css?family=Lato|Montserrat|Open+Sans" rel="stylesheet">
 
 {% endblock %}

docs/conf.py

@@ -19,7 +19,7 @@
 import os
 import subprocess
 import sys
-import sphinx_rtd_theme
+#import sphinx_rtd_theme
 import configparser
 from datetime import datetime
 from urllib.request import urlretrieve
@@ -191,17 +191,48 @@
 # The theme to use for HTML and HTML Help pages.  See the docs for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'pydata_sphinx_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # docs.
 # #
-# html_theme_options = {
-# }
+html_theme_options = {
+    "collapse_navigation": False,
+    "navigation_depth": 3,
+    "show_prev_next": True,
+    "icon_links": [
+        {"name": "IDM docs", "url": "https://docs.idmod.org", "icon": "fas fa-home"},
+        {
+            "name": "GitHub",
+            "url": "https://github.com/institutefordiseasemodeling/emodpy",
+            "icon": "fab fa-github-square",
+        },
+    ],
+    "navbar_end": ["theme-switcher", "navbar-icon-links"],
+    "secondary_sidebar_items": ["navbar-side"],
+    "header_links_before_dropdown": 5,
+    "footer_start": ["copyright", "footer_start"],
+    "footer_end": ["theme-version", "footer_end"],
+}
+html_sidebars = {
+    "**": ["sidebar-nav-bs", "page-toc"],
+}
+html_logo = "images/idm-logo-transparent.png"
+html_favicon = "images/favicon.ico"
+html_static_path = ['_static']
+html_baseurl = "https://docs.idmod.org/projects/emodpy/en/latest"
+html_context = {
+    'rtd_url': 'https://docs.idmod.org/projects/emodpy/en/latest',
+    "versions_dropdown": {
+        "latest": "devel (latest)",
+        "stable": "current (stable)",
+    },
+    "default_mode": "light",
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+#html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # The name for this set of Sphinx documents.
 # "<project> v<release> docs" by default.
@@ -215,7 +246,7 @@
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 #
-html_logo = "images/IDM_white.png"
+#html_logo = "images/IDM_white.png"
 
 # The name of an image file (relative to this directory) to use as a favicon of
 # the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -231,7 +262,7 @@
 
 html_css_files = ['theme_overrides.css']
 
-html_js_files = ['show_block_by_os.js'] 
+#html_js_files = ['show_block_by_os.js']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -297,7 +328,7 @@
     search_project = os.environ["READTHEDOCS_PROJECT"]
     search_version = os.environ["READTHEDOCS_VERSION"]
 
-    rtd_sphinx_search_default_filter = f"subprojects:{search_project_parent}/{search_version}"
+    rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}"
 
     rtd_sphinx_search_filters = {
         "Search this project": f"project:{search_project}/{search_version}",

docs/index.rst

@@ -11,6 +11,9 @@ See :doc:`idmtools:api/idmtools_index` for a diagram showing how |IT_s| and each
 related packages are used in an end-to-end workflow using |EMOD_s| as the
 disease transmission model.
 
+Contents
+--------
+
 .. toctree::
    :maxdepth: 3
    :titlesonly:
@@ -35,14 +38,12 @@ disease transmission model.
    :titlesonly:
    :caption: Related documentation
 
-   emodpy Jupyter notebooks <https://docs.idmod.org/projects/jupyter-notebooks-emodpy/en/latest/>
    EMOD generic <https://docs.idmod.org/projects/emod-generic/en/latest/>
    emod-api <https://docs.idmod.org/projects/emod-api/en/latest/>
    idmtools <https://docs.idmod.org/projects/idmtools/en/latest/>
 
 
 .. not sure what to do with catalyst. Not included yet.
 
-.. nothing done with STAMP yet; not sure if it will be some sort of "plug-in" to the tools or totally standalone
 
 

docs/requirements.txt

@@ -1,6 +1,6 @@
 sphinxext.remoteliteralinclude~=0.4.0
 sphinx~=6.2.1
-sphinx-rtd-theme~=1.2.2
+pydata-sphinx-theme
 sphinxcontrib-napoleon~=0.7
 plantweb~=1.2.1
 sphinxcontrib-programoutput~=0.17
@@ -9,4 +9,5 @@ jupyterlab~=4.0.2
 myst-parser~=2.0.0
 readthedocs-sphinx-search~=0.3.1
 sphinx-copybutton~=0.5.2
-pygithub~=1.57
+pygithub~=1.57
+sphinxcontrib-jquery~=4.1

emodpy/__init__.py

@@ -1,4 +1,4 @@
 # flake8: noqa F821
 from emodpy.defaults.iemod_default import IEMODDefault
 
-__version__ = "1.22.0"
+__version__ = "1.22.1"

emodpy/emod_task.py

@@ -138,19 +138,26 @@ def create_campaign_from_callback(self, builder, params=None):
         adhoc_events = campaign.get_adhocs()
         if dev_mode:
             campaign.save()
-        # This might be a great place to reset the campaign object so users don't have to.
-        campaign.reset()
 
-        if len(adhoc_events) > 0:
+        if adhoc_events:
             # print("Found adhoc events in campaign. Needs some special processing behind the scenes.")
             logger.debug("Found adhoc events in campaign. Needs some special processing behind the scenes.")
             if "Custom_Individual_Events" in self.config.parameters:
                 self.config.parameters.Custom_Individual_Events = [x for x in adhoc_events.keys()]
             else:
                 reverse_map = {}
                 for user_name, builtin_name in adhoc_events.items():
-                    reverse_map[builtin_name] = user_name 
+                    reverse_map[builtin_name] = user_name
                 self.config.parameters["Event_Map"] = reverse_map
+        # checking attributes because if using older emod-api whose campaign doesn't have them,
+        # we don't want to fail, just move on.
+        if hasattr(campaign, "get_custom_coordinator_events") and "Custom_Coordinator_Events" in self.config.parameters:
+            self.config.parameters.Custom_Coordinator_Events = campaign.get_custom_coordinator_events()
+        if hasattr(campaign, "get_custom_node_events") and "Custom_Node_Events" in self.config.parameters:
+            self.config.parameters.Custom_Node_Events = campaign.get_custom_node_events()
+
+        # This might be a great place to reset the campaign object so users don't have to.
+        campaign.reset()
 
     def create_demog_from_callback(self, builder, from_sweep=False, params=None):
         if builder is None:

requirements.txt

@@ -3,11 +3,13 @@ click~=7.1
 idmtools~=1.7
 idmtools-platform-comps~=1.7
 idmtools-models~=1.7
-emod-api~=1.24
+emod-api~=1.30
 matplotlib
 astor
 astunparse
 bs4
 keyring
 pyCOMPS~=2.6
 requests==2.29.0
+xmlrunner~=1.7.7
+pytest==8.1.2

setup.py

@@ -65,5 +65,5 @@
     setup_requires=setup_requirements,
     test_suite='tests',
     extras_require=extras,
-    version='1.22.0'
+    version='1.22.1'
 )

tests/manifest.py

@@ -21,8 +21,7 @@
 output_dir = os.path.join(current_directory, "output")
 serialization_files_dir = os.path.join(output_dir, "serialization_files", "output")
 
-sft_id = "e5d5ab18-cfcf-ec11-92e9-f0921c167864"
-sft_id_file = os.path.join(current_directory, "stage_sif.id")
+sft_id_file = "stage_sif.id"
 
 demographics_folder = os.path.join(current_directory, "inputs", "demographics")
 if not os.path.isdir(demographics_folder):

tests/test_emod_task.py

@@ -141,15 +141,6 @@ def test_from_files(self):
                                                                 implicit_config_set_fns=self.demog.implicits),
                                                  config_out_path=self.config_path)
 
-        # workaround for https://github.com/InstituteforDiseaseModeling/emodpy/issues/358
-        import emod_api.schema_to_class as s2c
-        with open(self.config_path) as conf:
-            config_rod = json.load(conf, object_hook=s2c.ReadOnlyDict)
-        config_rod.parameters.Enable_Demographics_Builtin = 1
-        del config_rod.parameters["Demographics_Filenames"]
-        with open(self.config_path, "w") as outfile:
-            json.dump(config_rod, outfile, sort_keys=True, indent=4)
-
         task = EMODTask.from_files(
             eradication_path=self.eradication_path,
             config_path=self.config_path,
@@ -214,10 +205,10 @@ def test_from_files(self):
 
         del sim.task.config["parameters"]["Enable_Demographics_Builtin"]
         del sim.task.config["parameters"]["Demographics_Filenames"]
+        del config["Demographics_Filenames"]
         del config["Enable_Demographics_Builtin"]
 
         self.assertEqual(config, sim.task.config["parameters"])
-
         # Assert the right demo file is loaded in demographics.assets
         self.assertEqual(self.demo_path, sim.task.demographics.assets[0].absolute_path)
 
@@ -234,30 +225,26 @@ def test_from_files_config_only(self):
     def test_from_files_valid_customReport(self):
         self.prepare_input_files()
 
+        def set_param_fn(config, implicit_config_set_fns):
+            config.parameters.Enable_Demographics_Builtin = 0
+            config.parameters.Base_Infectivity_Constant = 1
+            config.parameters.Incubation_Period_Constant = 1
+            config.parameters.Infectious_Period_Constant = 1
+            config.parameters.Base_Infectivity_Distribution = 'CONSTANT_DISTRIBUTION'
+            config.parameters.Incubation_Period_Distribution = 'CONSTANT_DISTRIBUTION'
+            config.parameters.Infectious_Period_Distribution = 'CONSTANT_DISTRIBUTION'
+            config.parameters.x_Base_Population = 0.001
+            config.parameters.Simulation_Duration = 10
+            config.parameters.Start_Time = 0
+            for fn in implicit_config_set_fns:
+                    config = fn(config)
+            return config
+
         dfs.write_config_from_default_and_params(config_path=self.default_config_file,
                                                  set_fn=partial(set_param_fn,
                                                                 implicit_config_set_fns=self.demog.implicits),
                                                  config_out_path=self.config_path)
 
-        # workaround for https://github.com/InstituteforDiseaseModeling/emodpy/issues/358
-        import emod_api.schema_to_class as s2c
-        with open(self.config_path) as conf:
-            config_rod = json.load(conf, object_hook=s2c.ReadOnlyDict)
-        #config_rod.parameters.Enable_Demographics_Builtin = 1
-        #del config_rod.parameters["Demographics_Filenames"]
-        config_rod.parameters['Base_Infectivity_Constant'] = 1
-        config_rod.parameters['Incubation_Period_Constant'] = 1
-        config_rod.parameters['Infectious_Period_Constant'] = 1
-        config_rod.parameters['Base_Infectivity_Distribution'] = 'CONSTANT_DISTRIBUTION'
-        config_rod.parameters['Incubation_Period_Distribution'] = 'CONSTANT_DISTRIBUTION'
-        config_rod.parameters['Infectious_Period_Distribution'] = 'CONSTANT_DISTRIBUTION'
-        config_rod.parameters['x_Base_Population'] = 0.001
-        config_rod.parameters['Simulation_Duration'] = 10
-        config_rod.parameters['Start_Time'] = 0
-
-        with open(self.config_path, "w") as outfile:
-            json.dump(config_rod, outfile, sort_keys=True, indent=4)
-
         custom_reports_path = os.path.join(manifest.current_directory, "inputs", "custom_reports.json")
 
         task = EMODTask.from_files(
@@ -379,7 +366,6 @@ def build_demog_and_mig():
             return demog, mig_data
 
         self.prepare_schema_and_eradication()
-
 
         print(f"Telling emod-api to use {self.schema_path} as schema.")
         ob.schema_path = self.schema_path
@@ -662,5 +648,3 @@ def test_add_py_path(self):
         self.assertTrue(task.use_embedded_python)
 
         self.assertIn(f"--python-script-path './Assets/python;{pypackage_path};{virtual_path}'", str(task.command))
-
-

tests/test_experiment_simulations.py

@@ -19,6 +19,7 @@
 # current_directory = os.path.dirname(os.path.realpath(__file__))
 # BIN_PATH = os.path.join(current_directory, "..", "examples", "inputs", "bin")
 # INPUT_PATH = os.path.join(current_directory, "..", "examples", "serialization", "inputs")
+sif_path = manifest.sft_id_file
 
 
 @pytest.mark.comps
@@ -75,6 +76,7 @@ def test_mix_tasks_in_experiment(self):
                                    ep4_path=manifest.ep4_path)
         task.tags = {"idmtools": "idmtools-automation", "string_tag": "test", "number_tag": 123}
         task.set_parameter("Enable_Immunity", 0)
+        task.set_sif(sif_path)
 
         # User builder to create simulations
         num_sims = 3
@@ -92,6 +94,7 @@ def test_mix_tasks_in_experiment(self):
                                     demographics_paths=None,
                                     eradication_path=eradication_path,
                                     ep4_path=manifest.ep4_path)
+        task1.set_sif(sif_path)
         # create another TemplatedSimulations with this task1
         ts1 = TemplatedSimulations([builder], base_task=task1)
 
@@ -106,6 +109,9 @@ def test_mix_tasks_in_experiment(self):
         sims = experiment.simulations
         self.assertEqual(len(sims), 7)
 
+        self.assertTrue(experiment.succeeded, msg=f"Experiment {experiment.uid} failed.\n")
+        print(f"Experiment {experiment.uid} succeeded.")
+
     def test_create_suite(self):
         from idmtools.entities.suite import Suite
         from COMPS.Data import Suite as CompsSuite