1351 pymio interface for sde sir type models #1371
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…interface-for-sde-sir-type-models
MaxBetzDLR
added
the
loc::python interface
2 tasks
MaxBetzDLR
added
the
model::sde
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1371 +/- ##
==========================================
- Coverage 97.28% 97.24% -0.05%
==========================================
Files 174 174
Lines 15153 15153
==========================================
- Hits 14742 14735 -7
- Misses 411 418 +7 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
jubicker
reviewed
Sep 26, 2025
|
|
||
|
|
||
| def run_sde_sir_simulation(): | ||
| """Runs the c++ SDE SIR model""" |
There was a problem hiding this comment.
Suggested change
| """Runs the c++ SDE SIR model""" | |
| """Runs SDE SIR model""" |
| def run_sde_sir_simulation(): | ||
| """Runs the c++ SDE SIR model""" | ||
|
|
||
| # Define population of age groups |
There was a problem hiding this comment.
I don't understand the comment. This is the total population, right? Does the SDE model even have age groups?
| # Define population of age groups | ||
| population = 10000 | ||
|
|
||
| days = 5. # number of days to simulate |
There was a problem hiding this comment.
Suggested change
| days = 5. # number of days to simulate | |
| tmax = 5. # simulation time frame |
| days = 5. # number of days to simulate | ||
| dt = 0.1 | ||
|
|
||
| # Initialize Parameters |
There was a problem hiding this comment.
Suggested change
| # Initialize Parameters | |
| # Initialize model |
| # Initialize Parameters | ||
| model = Model() | ||
|
|
||
| # Compartment transition duration |
There was a problem hiding this comment.
Suggested change
| # Compartment transition duration | |
| # Mean time in Infected compartment |
|
|
||
| def test_check_constraints_parameters(self): | ||
| model = Model() | ||
| # valid |
There was a problem hiding this comment.
This is not a very well-formulated comment
| vals = result[i] | ||
| self.assertEqual(len(vals), 3) | ||
| # Non-negativity | ||
| self.assertTrue(np.all(np.array(vals) >= -1e-10)) |
| ############################################################################# | ||
| # Copyright (C) 2020-2025 MEmilio | ||
| # | ||
| # Authors: |
| def setUp(self): | ||
| # Initialize model similar to the sde_sirs_simple example | ||
| self.population = 10000 | ||
| self.days = 5.0 |
There was a problem hiding this comment.
Suggested change
| self.days = 5.0 | |
| self.tmax = 5.0 |
| vals = result[i] | ||
| self.assertEqual(len(vals), 3) | ||
| # Non-negativity | ||
| self.assertTrue(np.all(np.array(vals) >= -1e-8)) |
There was a problem hiding this comment.
Is there a reason you use e-8 here and e-10 for the SSIR example?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes and Information
Please briefly list the changes (main added features, changed items, or corrected bugs) made:
If need be, add additional information and what the reviewer should look out for in particular:
Merge Request - Guideline Checklist
Please check our git workflow. Use the draft feature if the Pull Request is not yet ready to review.
Checks by code author
Checks by code reviewer(s)
Closes #1351