sqlite: add SQLite persistence for projects, runs, and mutants#35
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sqlite: add SQLite persistence for projects, runs, and mutants#35
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Introduce --sqlite[=<path>] flag (default: mutation.db) on both the mutate and analyze subcommands, backed by a new db module. mutate: - Opens/creates the database, applies schema (projects, runs, mutants with indexes and CHECK constraints), and seeds the Bitcoin Core project row via INSERT OR IGNORE. - Creates a runs row capturing commit_hash, tool_version, and optional pr_number before generation begins. - mutate_file now returns Vec<MutantData> (unified diff, SHA-256 patch_hash, file_path, operator) alongside the existing file writes. - Mutants are batch-inserted in chunks of 100 within transactions; duplicate (run_id, patch_hash) pairs are silently ignored. analyze: - New --sqlite <path> + --run_id <id> flags trigger DB-based analysis. - Reads all mutants for the run, applies each diff via `git apply` (temp file), runs the supplied --command, updates status to killed/survived/error, then restores the file with git restore. - --command is required in DB mode; --run_id without --sqlite is rejected with a clear error. Other: - get_commit_hash() added to git_changes (git rev-parse HEAD). - MutationError gains a Rusqlite(#[from] rusqlite::Error) variant. - rusqlite 0.32 (bundled) and sha2 0.10 added as dependencies. - Running without --sqlite preserves existing behaviour exactly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add a config_json TEXT column to the runs table. When --range is
supplied together with --sqlite, the range bounds are written as
{"range":[start,end]} into that column, making the exact scope of
every run reproducible and queryable.
Schema migration: ensure_schema now issues
ALTER TABLE runs ADD COLUMN config_json TEXT
after the CREATE TABLE statement and silently ignores the
"duplicate column name" error so existing databases are upgraded
non-destructively without requiring a full schema recreation.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
restore_file discarded the bool returned by run_command, so a failed `git restore` was silently ignored and left the file in a mutated state. All subsequent mutants targeting the same file then failed with "patch does not apply" because the `-` line in their diff no longer matched the actual file content. Two fixes: - restore_file now returns an error when `git restore` exits non-zero. - run_db_analysis resets the file to HEAD at the start of each mutant iteration (soft pre-restore with a warning on failure) so a single bad restore cannot poison the rest of the run. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Replace the hand-crafted minimal diff in generate_diff with an actual `git diff --no-index` invocation against a temp file. This produces a proper unified diff with 3 context lines that `git apply` can reliably locate and apply, fixing silent patch failures during DB-based analysis. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Allows narrowing a run's mutants to a single source file, enabling per-file analysis with different test commands on multi-file PRs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Fixes #11