fix: parse checkpoint and localcheckpoint rule lines

[nh13]

Summary

• Snakemake logs checkpoint rules as checkpoint X: / localcheckpoint X: instead of rule X: / localrule X:
• RULE_START_PATTERN only matched rule/localrule, making checkpoint jobs invisible to all log-based parsers — timing was lost or misattributed to whatever rule preceded the checkpoint in the log
• Update regex to (?:local)?(?:rule|checkpoint) (\w+): and add checkpoint prefixes to LogLineParser fast-path checks

Test plan

• 8 new tests: running/completed/failed/all-jobs parsing + LogLineParser for checkpoint lines
• Includes a regression test verifying checkpoint doesn't steal the next rule's timing
• Full suite (986 tests) passes
• ruff, mypy clean

Closes #43

Summary by CodeRabbit

• New Features

  • Extended parser to recognize and handle Snakemake checkpoint rules (including local variants) alongside regular rules.

• Tests

  • Introduced comprehensive test suites for checkpoint parsing, including job status tracking and rule-association validation.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: e8c1f42b-3e48-4518-8e5e-9667990f7b66

📥 Commits

Reviewing files that changed from the base of the PR and between 684359e and 7f20192.

📒 Files selected for processing (3)

• snakesee/parser/line_parser.py
• snakesee/parser/patterns.py
• tests/test_parser.py

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📝 Walkthrough

Walkthrough

The parser now recognizes checkpoint rules (checkpoint and localcheckpoint) alongside standard rules. Pattern matching and line-parsing logic were expanded to detect and process checkpoint declarations, with comprehensive test coverage added for checkpoint behavior validation.

Changes

Cohort / File(s)	Summary
Pattern Matching snakesee/parser/patterns.py	Updated RULE_START_PATTERN regex to match both rule/localrule and checkpoint/localcheckpoint declarations using alternation: (?:local)?(?:rule|checkpoint) (\w+):
Parser Logic snakesee/parser/line_parser.py	Broadened rule-start detection in parse_line() to recognize four prefixes ("rule ", "localrule ", "checkpoint ", "localcheckpoint ") when first character is in ("r","l","c"). Same downstream behavior: flush pending error, extract name, reset context, emit RULE_START event.
Test Coverage tests/test_parser.py	Added checkpoint-specific log fixtures and test suites validating parser behavior for checkpoint jobs in running/completed/failed lists with correct metadata (rule, job_id, wildcards), and confirming LogLineParser emits RULE_START for checkpoint lines without consuming subsequent rule context.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Poem

🐰 Checkpoints now dance in parser's sight,
No longer hidden from the code's keen eye,
Rules and checkpoints together align,
Statistics bloom as they should design, ✨
A rabbit's hop toward parsing just right!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: updating the parser to recognize checkpoint and localcheckpoint rule lines, matching the primary objective of fixing the checkpoint parsing issue.
Description check	✅ Passed	The PR description clearly explains the problem, the solution implemented, and provides comprehensive testing details including test counts and verification that the full suite passes.
Linked Issues check	✅ Passed	The changes directly address issue #43 by enabling checkpoint rule recognition in logs, which resolves the root cause of incorrect historical statistics for checkpoint rules.
Out of Scope Changes check	✅ Passed	All changes are focused on checkpoint parsing: pattern updates, parser logic, and comprehensive tests—all directly related to the linked issue objective.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch nh/fix-checkpoint-parsing

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.47%. Comparing base (684359e) to head (7f20192).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #53      +/-   ##
==========================================
+ Coverage   88.25%   88.47%   +0.21%     
==========================================
  Files          48       48              
  Lines        4692     4684       -8     
==========================================
+ Hits         4141     4144       +3     
+ Misses        551      540      -11     

Files with missing lines	Coverage Δ
snakesee/parser/line_parser.py	98.70% <100.00%> (+4.23%)	⬆️
snakesee/parser/patterns.py	100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

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