Update dependencies and fix breakages from pyomo 6.10

[ParticularlyPythonicBS]

• Updated dependencies to latest versions
• Replaced sparse_iterkeys() with sparse_keys() to comply with pyomo 6.10 deprecation
• Wrapped critical sparse_keys() calls in set() in temoa/components/technology.py to ensure a stable lookups

Summary by CodeRabbit

• Improvements

  • Increased consistency and stability across capacity, commodity, cost, emissions, time, limits, reserves, and technology processing by unifying internal index handling.
  • Minor reliability and performance improvements that reduce intermittent index-related inconsistencies.

• Bug Fixes

  • Improved detection and messaging for invalid capacity-factor configurations.

• Tests

  • Updated legacy full-run test to align with revised internal index handling.

[coderabbitai]

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Walkthrough

Replaced Pyomo's sparse_iterkeys() calls with sparse_keys() across the codebase. Only the enumeration API for sparse parameters/sets changed; tuple unpacking, filters, arithmetic, and control flow in the affected loops remain unchanged.

Changes

Cohort / File(s)	Summary
Core internal polling temoa/_internal/table_data_puller.py	Switched sparse_iterkeys() → sparse_keys() in polling loops for construction_input, cost tables, and emissions; iteration API changed but loop logic preserved.
Components — capacity / technology / time / limits / costs / emissions / geography / reserves / commodities temoa/components/capacity.py, temoa/components/technology.py, temoa/components/time.py, temoa/components/limits.py, temoa/components/costs.py, temoa/components/emissions.py, temoa/components/geography.py, temoa/components/reserves.py, temoa/components/commodities.py	Replaced sparse-key iteration API across many component modules (efficiency, existing_capacity, cost_/emission_, reserve margins, time segments, etc.). Some sites now materialize key sets via set(...sparse_keys()). No other logic or filters were changed.
Model checking & validators temoa/model_checking/network_model_data.py, temoa/model_checking/pricing_check.py, temoa/model_checking/validators.py	Replaced sparse_iterkeys() with sparse_keys() when enumerating demand, linked techs, costs, efficiencies, and reserve margins; downstream validation logic unchanged.
Tests tests/test_full_runs.py	Updated test to compute expected efficiency index size from efficiency_param.sparse_keys() instead of sparse_iterkeys().

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Refactoring repo and restructuring temoa initialize and rules #158: Overlaps with refactors replacing Pyomo sparse-index iteration across many component modules; directly related to the same API change.
• Fixing materials flows in myopic mode (take 2) #279: Modifies the same polling functions in temoa/_internal/table_data_puller.py; closely related to flow/cost/emissions polling logic.
• Making naming and casing more consistent: Part 1 #180: Makes similar edits to poll_flow_results, poll_cost_results, and poll_emissions in table_data_puller.py; changes overlap at the code level.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 60.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Update dependencies and fix breakages from pyomo 6.10' directly describes the main changes: dependency updates and fixing issues caused by Pyomo 6.10 compatibility, which aligns with the primary changes throughout the PR.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch update_pyomo_and_fix

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Actionable comments posted: 1

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (2)

temoa/components/capacity.py (1)

652-654: ⚠️ Potential issue | 🟡 Minor

Inconsistent API: sparse_iterkeys() not updated to sparse_keys().

This line still uses the deprecated sparse_iterkeys() while all other occurrences in this file and across the PR have been updated to sparse_keys(). This should be updated for consistency with the Pyomo 6.10 migration.

Proposed fix

- for r, _e, t, v in model.emission_end_of_life.sparse_iterkeys():+ for r, _e, t, v in model.emission_end_of_life.sparse_keys():

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.
In `@temoa/components/capacity.py` around lines 652 - 654, The loop uses the
deprecated iterator method model.emission_end_of_life.sparse_iterkeys(); replace
this call with the updated API model.emission_end_of_life.sparse_keys() in the
for loop that checks (r, t, v) in model.retirement_periods and updates
model.used_techs.add(t) so the code consistently uses Pyomo 6.10's sparse_keys()
method.

temoa/components/technology.py (1)

448-456: ⚠️ Potential issue | 🟡 Minor

Inconsistent API: sparse_iterkeys() not updated to sparse_keys().

This line still uses the deprecated sparse_iterkeys() while all other occurrences in this file and across the PR have been updated to sparse_keys(). This should be updated for consistency with the Pyomo 6.10 migration.

Proposed fix

- for r, t, v in model.existing_capacity.sparse_iterkeys():+ for r, t, v in model.existing_capacity.sparse_keys():

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.
In `@temoa/components/technology.py` around lines 448 - 456, The loop uses the
deprecated model.existing_capacity.sparse_iterkeys() API; update it to
model.existing_capacity.sparse_keys() in the loop that unpacks (r, t, v) and
computes cap using value(model.existing_capacity[r, t, v]) so behavior is
unchanged. Locate the for-loop referencing sparse_iterkeys() in the technology
component (around the block that logs non-positive existing capacity) and
replace sparse_iterkeys() with sparse_keys() while keeping the unpacking and
subsequent logic (variables r, t, v, cap, logger.warning, continue) intact.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@temoa/components/technology.py`:
- Around line 63-64: There are duplicate loops iterating
model.existing_capacity.sparse_keys() and setting
model.is_survival_curve_process[r, t, v] = False twice; remove the redundant
loop so each (r, t, v) is initialized only once (keep a single loop that
iterates model.existing_capacity.sparse_keys() and assigns
model.is_survival_curve_process[r, t, v] = False). Apply the same removal for
the other duplicated occurrences noted (the similar duplicate around the indices
handling), ensuring only one initialization loop exists for
model.is_survival_curve_process per key source.
---
Outside diff comments:
In `@temoa/components/capacity.py`:
- Around line 652-654: The loop uses the deprecated iterator method
model.emission_end_of_life.sparse_iterkeys(); replace this call with the updated
API model.emission_end_of_life.sparse_keys() in the for loop that checks (r, t,
v) in model.retirement_periods and updates model.used_techs.add(t) so the code
consistently uses Pyomo 6.10's sparse_keys() method.
In `@temoa/components/technology.py`:
- Around line 448-456: The loop uses the deprecated
model.existing_capacity.sparse_iterkeys() API; update it to
model.existing_capacity.sparse_keys() in the loop that unpacks (r, t, v) and
computes cap using value(model.existing_capacity[r, t, v]) so behavior is
unchanged. Locate the for-loop referencing sparse_iterkeys() in the technology
component (around the block that logs non-positive existing capacity) and
replace sparse_iterkeys() with sparse_keys() while keeping the unpacking and
subsequent logic (variables r, t, v, cap, logger.warning, continue) intact.

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ℹ️ Review info

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📥 Commits

Reviewing files that changed from the base of the PR and between 5baa092 and 1383bd3.

⛔ Files ignored due to path filters (2)

• stubs/pyomo/core/base/param.pyi is excluded by !stubs/**
• uv.lock is excluded by !**/*.lock

📒 Files selected for processing (14)

• temoa/_internal/table_data_puller.py
• temoa/components/capacity.py
• temoa/components/commodities.py
• temoa/components/costs.py
• temoa/components/emissions.py
• temoa/components/geography.py
• temoa/components/limits.py
• temoa/components/reserves.py
• temoa/components/technology.py
• temoa/components/time.py
• temoa/model_checking/network_model_data.py
• temoa/model_checking/pricing_check.py
• temoa/model_checking/validators.py
• tests/test_full_runs.py