Move general datetime indexing functions from pyrenew-hew to PyRenew #709
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Codecov Report✅ All modified and coverable lines are covered by tests.
Additional details and impacted files@@ Coverage Diff @@
## main #709 +/- ##
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- Coverage 26.08% 14.82% -11.26%
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Files 26 22 -4
Lines 2427 1862 -565
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- Hits 633 276 -357
+ Misses 1794 1586 -208
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…yrenew-hew into mem_refactor_datetime_indexing
- Replace date-to-model-time list comprehensions with align_observation_times() - Fix Saturday edge case in to_forecast_data() to correctly add 7 days when start date is already a Saturday - Replace complex ceiling division with get_first_week_on_or_after_t0() utility - Add test for Saturday edge case - Update test assertion to allow up to 7 days offset for MMWR week alignment 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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- Rename date properties (e.g., dates_observed_ed_visits → ed_dates) - Rename first/last date properties (e.g., first_ed_visits_date → ed_first_date) - Rename observation data (e.g., data_observed_disease_ed_visits → ed_visit_count) - Rename time indices (e.g., model_t_obs_ed_visits → ed_obs_time) - Remove model_ prefix from time variables (e.g., model_t_first_latent_infection → t_first_infection) - Rename array indices (e.g., which_obs_ed_visits → ed_obs_idx) - Change to singular form (e.g., ww_observed_subpops → ww_obs_subpop) - Update all tests accordingly - All 49 tests passing
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…or_datetime_indexing
…yrenew-hew into mem_refactor_datetime_indexing
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Hey @cdc-mitzimorris , The % uv sync --upgrade-package pyrenew commit it and I think the CI will work (at least the local python tests did on my machine). |
cdc-mitzimorris
requested review from
damonbayer,
dylanhmorris and
sbidari
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Pull Request Overview
This PR moves general datetime indexing and time handling utilities from the pyrenew-hew package to the PyRenew core library to enable code reuse across projects. It replaces custom datetime manipulation logic with standardized functions from PyRenew's time module.
Key changes:
- Replaces custom date validation and time indexing functions with imports from
pyrenew.time - Updates hospital admissions date calculation logic to use centralized utilities
- Adds comprehensive test coverage for edge cases in datetime handling
Reviewed Changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| tests/test_pyrenew_hew_data.py | Adds extensive test coverage for datetime edge cases and refactors existing tests to use datetime.date objects |
| pyrenew_hew/pyrenew_hew_model.py | Updates hospital admissions calculation to use get_first_week_on_or_after_t0 utility function |
| pyrenew_hew/pyrenew_hew_data.py | Removes custom datetime functions and replaces with imports from pyrenew.time module |
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…or_datetime_indexing
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2 participants
This PR is the companion to CDCgov/PyRenew#600 which adds general utilities for handing time indexing and time slicing to PyRenew by identifying code which was implemented in pyrenew-hew and is a good candidate for reuse.