Atlas adds a regression test for a Python bug fix by running the discipline in the only order that proves anything: red first, then green. Atlas writes the failing pytest case with the write tool, runs it with the bash tool to show it reproduces the bug, applies the fix with edit, and re-runs the same pytest command. Because the bash tool records the process exit code in its metadata alongside the output, the failing and passing states are unambiguous rather than inferred from a wall of traceback text.
Why does a Python regression test have to fail before the fix?
A regression test that never failed proves nothing. Atlas enforces red first, then green: the pytest case is written against the observed wrong behavior, run with the bash tool to confirm a non-zero exit code, and only then is the fix applied. In 2026 that ordering is the entire value of the test.
The trap is easy to fall into. A developer fixes a rounding bug in src/billing/invoices.py, then writes tests/test_invoices.py afterwards, and the test passes on the first pytest run. Nobody ever learns whether the assertion would have caught the original bug, and a year later a refactor reintroduces it and the suite stays green. Atlas runs the sequence the other way. The pytest case asserts on the wrong behavior you actually observed, the bash tool proves it reproduces, and the fix flips the exit code from failing to passing. Atlas snapshots file changes as git patches so edits can be diffed and rolled back, so experimenting with the reproduction costs nothing.
How does Atlas prove a pytest case actually failed?
Atlas runs pytest through the bash tool, and the bash tool records the process exit code in its metadata alongside the output. A Python developer reading the transcript in 2026 sees an unambiguous non-zero exit before the fix and a zero exit after, rather than guessing from a truncated traceback.
Exit codes matter here more than they look like they should. pytest prints a great deal, and a suite that errors during collection can look, in a scrolled log, a lot like a suite that failed an assertion, which in turn can look like a suite that passed with warnings. The Atlas bash tool sidesteps the ambiguity by carrying the real exit code in tool metadata. That also protects the agent from fooling itself: an agent that misreads its own output will happily declare victory, and an exit code will not let it. Output over 2000 lines or 50 KB is truncated and the full log is saved to a file, so long Python tracebacks stay readable.
How does Atlas apply the Python fix without breaking neighboring code?
Atlas applies the fix with edit, whose replacer cascade requires an exact-enough oldString and refuses ambiguous multi-match replacements. In a Python file where the same 3 line pattern appears in 4 methods, edit will not silently pick one, which is exactly the failure a regression test cannot catch.
The refusal is the feature. An agent that fuzzily matched a Decimal rounding line and changed the wrong occurrence would produce a passing regression test and a new bug somewhere else in the package. Atlas would rather stop and ask. On top of that, Atlas computes a unified diff for every file edit and surfaces it for approval before writing, so the one-line change to src/billing/invoices.py is reviewed before it exists, and every Atlas tool call is permission-gated against allow, ask, and deny rules before it runs. When the fix is larger than a single replacement, apply_patch handles it, still as a reviewable diff.
What do I run after the Python fix turns the test green?
Re-run the same pytest command with the bash tool and confirm the exit code is now 0, then run the wider suite to check for collateral damage. Run ruff format over the changed files, and if the regression test needed a new library, install it with uv so pyproject.toml stays accurate.
Re-running the identical command is deliberate. A different invocation is a different experiment, and the whole claim being made is that this exact command failed and now passes. After that, the wider pytest run matters because a fix that satisfies one assertion by changing a shared helper can quietly break three other modules in the package. ruff format is the formatter, so the diff a reviewer reads is behavior. uv is the package manager, so a test dependency is declared rather than assumed present in the virtualenv. Atlas reads git branches, status, and diffs, and can stage and create commits on your behalf.
Can I roll back a Python fix if the wider pytest suite goes red?
Yes. Atlas snapshots file changes as git patches so edits can be diffed and rolled back, and Atlas reads git branches, status, and diffs. If the wider pytest run shows collateral damage in 2 other modules, the Python fix and its regression test can be reverted together and re-approached.
Rollback is the safety net that makes red-first cheap to attempt. A Python developer chasing a subtle bug will often write two or three candidate reproductions before one actually fails for the right reason, and each attempt touches tests/ and sometimes the source. Because Atlas snapshots file changes as git patches, discarding a dead end is a revert rather than an archaeology exercise. The reproduction that survives, the fix that flips the bash exit code from non-zero to zero, and the passing wider suite are then staged together, which is what a reviewer wants to see: the failing case and its fix in one commit.
Step by step
- 01Run atlas in a repo with a pyproject.toml or requirements.txt and let it read your package layout, virtualenv, and installed dependencies.
- 02Reproduce the bug once with the bash tool and capture the exact failing command and output.
- 03Write the regression test with the write tool, asserting on the observed wrong behavior, and approve the diff in the permission prompt.
- 04Run the new pytest case with the bash tool and confirm it fails; the tool records the process exit code in its metadata alongside the output.
- 05Apply the fix with edit, whose replacer cascade requires an exact-enough oldString and refuses ambiguous multi-match replacements.
- 06Re-run the same pytest command with the bash tool and confirm the exit code is now zero.
- 07Run the wider pytest suite to check for collateral damage in other modules of the package.
- 08Run ruff format over the changed files, install any new test dependency with uv, and let Atlas stage the fix and the regression test as one commit.
Frequently asked questions
- how to write a regression test in python that fails before the fix
- Have Atlas reproduce the bug with the bash tool, write the pytest case asserting on the observed wrong behavior with the write tool, and run it to confirm a non-zero exit code. Only then apply the fix with edit and re-run the same command.
- how does atlas know a test failed and not just printed errors
- The Atlas bash tool records the process exit code in its metadata alongside the output, so a failing pytest run and a passing one are distinguishable without parsing the traceback text. Output over 2000 lines or 50 KB is truncated with the full log saved to a file.
- can an ai agent edit the wrong occurrence of a line in python
- The Atlas edit tool's replacer cascade requires an exact-enough oldString and refuses ambiguous multi-match replacements, so a pattern that appears in four methods will not be silently changed in the wrong one. Larger changes go through apply_patch as a reviewable diff.
- should i run the whole pytest suite after a bug fix
- Yes. In the Atlas workflow you re-run the same pytest command to confirm the regression test now passes, then run the wider suite to check for collateral damage, because a fix that touches a shared helper can break other modules in the package.
- how do i undo a python fix an ai agent applied
- Atlas snapshots file changes as git patches so edits can be diffed and rolled back, and Atlas reads git branches, status, and diffs. A fix that turns the wider pytest suite red can be reverted along with its regression test.
- does atlas run pytest itself or do i have to
- Atlas runs pytest through the bash tool as a permission-gated tool call. It runs the test to prove it fails, applies the fix with edit, and re-runs the same command to prove it passes.
- python regression test workflow with an ai coding agent
- Reproduce with bash, write the failing pytest case with write, confirm the non-zero exit code, fix with edit, re-run the same command for a zero exit code, run the wider suite, then run ruff format and commit. uv handles any new dependency.
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