Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Rename templates during stratification #338

Merged
merged 3 commits into from
Jun 13, 2024
Merged

Rename templates during stratification #338

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
5af7378
Rename templates during stratification
bgyori Jun 11, 2024
5f742fe
Handle None template names
bgyori Jun 11, 2024
638c85e
Improve controller stratification naming and fix test
bgyori Jun 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 9 additions & 3 deletions mira/metamodel/ops.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -176,6 +176,8 @@ def stratify(
for stratum, stratum_idx in stratum_index_map.items():
template_strata = []
new_template = deepcopy(template)
new_template.name = \
f"{template.name if template.name else 't'}_{stratum}"
# We have to make sure that we only add the stratum to the
# list of template strata if we stratified any of the non-controllers
# in this first for loop
Expand Down Expand Up @@ -227,6 +229,7 @@ def stratify(
# We now apply the stratum assigned to each controller in this particular
# tuple to the controller
for controller, c_stratum in zip(stratified_controllers, c_strata_tuple):
stratified_template.name += f"_{c_stratum}"
controller.with_context(do_rename=modify_names, inplace=True,
**{key: c_stratum})
template_strata.append(c_stratum if param_renaming_uses_strata_names
Expand Down Expand Up @@ -297,7 +300,8 @@ def stratify(
observables[observable_key].expression = SympyExprStr(expr)

# Generate a conversion between each concept of each strata based on the network structure
for (source_stratum, target_stratum), concept in itt.product(structure, concept_map.values()):
for idx, ((source_stratum, target_stratum), concept) in \
enumerate(itt.product(structure, concept_map.values())):
if concept.name in exclude_concepts:
continue
# Get stratum names from map if provided, otherwise use the stratum
Expand All @@ -317,14 +321,16 @@ def stratify(
curie_to_name_map=strata_curie_to_name,
**{key: target_stratum})
# todo will need to generalize for different kwargs for different conversions
template = conversion_cls(subject=subject, outcome=outcome)
template = conversion_cls(subject=subject, outcome=outcome,
name=f't{idx}_{source_stratum_name}_{target_stratum_name}')
template.set_mass_action_rate_law(param_name)
templates.append(template)
if not directed:
param_name = f"p_{target_stratum_name}_{source_stratum_name}"
if param_name not in parameters:
parameters[param_name] = Parameter(name=param_name, value=0.1)
reverse_template = conversion_cls(subject=outcome, outcome=subject)
reverse_template = conversion_cls(subject=outcome, outcome=subject,
name=f't{idx}_{target_stratum_name}_{source_stratum_name}')
reverse_template.set_mass_action_rate_law(param_name)
templates.append(reverse_template)

Expand Down
4 changes: 4 additions & 0 deletions tests/test_ops.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ def test_stratify_full(self):
)

expected_0 = ControlledConversion(
name="t_unvaccinated_unvaccinated",
subject=susceptible.with_context(vaccination_status="unvaccinated",
do_rename=True),
outcome=infected.with_context(vaccination_status="unvaccinated",
Expand All @@ -54,6 +55,7 @@ def test_stratify_full(self):
)
)
expected_1 = ControlledConversion(
name="t_unvaccinated_vaccinated",
subject=susceptible.with_context(vaccination_status="unvaccinated",
do_rename=True),
outcome=infected.with_context(vaccination_status="unvaccinated",
Expand All @@ -66,6 +68,7 @@ def test_stratify_full(self):
)
)
expected_2 = ControlledConversion(
name="t_vaccinated_unvaccinated",
subject=susceptible.with_context(vaccination_status="vaccinated",
do_rename=True),
outcome=infected.with_context(vaccination_status="vaccinated",
Expand All @@ -78,6 +81,7 @@ def test_stratify_full(self):
)
)
expected_3 = ControlledConversion(
name="t_vaccinated_vaccinated",
subject=susceptible.with_context(vaccination_status="vaccinated",
do_rename=True),
outcome=infected.with_context(vaccination_status="vaccinated",
Expand Down
Loading