saev

Imported from Imageomics/saev (AGENTS.md). Install upstream with npx skills add Imageomics/saev. Copyright stays with the author.

• Use uv run SCRIPT.py or uv run python ARGS to run python instead of Just plain python.
• To submit jobs, use launch.py scripts (e.g., uv run python scripts/launch.py SUBCOMMAND). Nearly every part of this package has a launch.py entrypoint. Don't try to run modules directly with -m.
• In contrib/trait_discovery/, use uv run python scripts/launch.py SUBCOMMAND (e.g., cls::train, cls::eval, probe1d). Note the :: separator for subcommands.
• After making edits, run uvx ruff format --preview . to format the file, then run uvx ruff check --fix . to lint, then run uvx ty check FILEPATH to type check (ty is prerelease software, and typechecking often will have false positives). Only do this if you think you're finished, or if you can't figure out a bug. Maybe linting will make it obvious. Don't fix linting or typing errors in files you haven't modified.

Gather Context

• Public docs for developers and users are in markdown in docs/src. Internal, messier design and implementation docs are in markdown in docs/research/issues. Both are valuable sources of context when getting started.
• You can use gh to access issues and PRs on GitHub to gather more context. We use GitHub issues a lot to share ideas and communicate about problems, so you should almost always check to see if there's a relevant GitHub issue for whatever you're working on.

Code Style

• Don't hard-wrap comments. Only use linebreaks for new paragraphs. Let the editor soft wrap content.
• Don't hard-wrap string literals. Keep each log or user-facing message in a single source line and rely on soft wrapping when reading it.
• Prefer negative if statements in combination with early returns/continues. Rather than nesting multiple positive if statements, just check if a condition is False, then return/continue in a loop. This reduces indentation.
• This project uses Python 3.12. You can use dict, list, tuple instead of the imports from typing. You can use | None instead of Optional.
• File descriptors from open() are called fd.
• Use types where possible, including jaxtyping hints.
• Decorate functions with beartype.beartype unless they use a jaxtyping hint, in which case use jaxtyped(typechecker=beartype.beartype).
• Variables referring to a absolute filepath should be suffixed with _fpath. Filenames are _fname. Directories are _dpath.
• Prefer make over build when naming functions that construct objects, and use get when constructing primitives (like string paths or config values).
• Only use setup for naming functions that don't return anything.
• submitit and jaxtyping don't work in the same file. See [this issue]. To solve this, all jaxtyped functions/classes need to be in a different file to the submitit launcher script.
• Never create a simple script to demonstrate functionality unless explicitly asked.
• Write single-line commit messages; never say you co-authored a commit.
• Before committing, run git status to check for already-staged files. If asked to commit only specific files, unstage everything first, then stage only the requested files, then after the commit, restage the already-staged files.
• Only use ascii characters. If you would use unicode to represent math, use pseudo-LaTeX instead in comments: 10⁶ should be 10^6, 3×10⁷ should be 3x10^7.
• Prefix variables with n_ for totals and cardinalities, but ignore it for dimensions ..._per_... and dimensions. Examples: n_examples, n_models, but tokens_per_example, examples_per_shard
• Try to keep code short. Shorter code is in principle easier to read. If variable names are really long, shorten based on conventions in this codebase (..._indices -> ..._i). Since you use uvx ruff format --preview, if you can make a small variable name change to fit everything on one line, that's a good idea. When variables are used once, simply inline it.
• If you make edits to a file and notice that I made edits to your edits, note the changes I make compared to your initial version and explicitly describe the style of changes. Keep these preferences in mind as you write the rest of the code.
• Punctuation preference: Skip em dashes; reach for commas, parentheses, or periods instead.
• Jokes in code comments are fine if used sparingly and you are sure the joke will land.
• Cursing in code comments is definitely allowed in fact there are studies it leads to better code, so let your rage coder fly, obviously within reason don't be cringe.

Defensive Programming

• Consider the style guidelines for TigerBeetle and adapt it to Python.
• Use asserts to validate assumptions frequently. For example, I didn't have an assert here at first because I assumed the shape couldn't change. It turns out it can! So now we have an assert to make it clear that we expect the input and output shapes are identical.

def sp_csr_to_pt(csr: scipy.sparse.csr_matrix, *, device: str) -> Tensor:
    shape_sp = csr.shape
    pt = torch.sparse_csr_tensor(
        csr.indptr,
        csr.indices,
        csr.data,
        size=shape_sp,
        device=device,
    )
    # MISSING
    assert pt.shape == shape_sp, f"{tuple(pt.shape)} != {tuple(shape_sp)}"
    return pt

• Use asserts rather than if statements + errors:

# Bad.
train_token_acts_fpath = train_inference_dpath / "token_acts.npz"
if not train_token_acts_fpath.exists():
    msg = (
        f"Train SAE activations missing: '{train_token_acts_fpath}'. Run inference.py."
    )
    logger.error(msg)
    raise FileNotFoundError(msg)

# Good.
train_token_acts_fpath = train_inference_dpath / "token_acts.npz"
msg = f"Train SAE acts missing: '{train_token_acts_fpath}'. Run inference.py."
assert train_token_acts_fpath.exists(), msg

No hacks: ask for help instead

Due to the difficulty of implementing this codebase, we must strive to keep the code high quality, clean, modular, simple and functional; more like an Agda codebase, less like a C codebase. Hacks and duct tape must be COMPLETELY AVOIDED, in favor of robust, simple and general solutions. In some cases, you will be asked to perform a seemingly impossible task, either because it is (and the developer is unaware), or because you don't grasp how to do it properly. In these cases, do not attempt to implement a half-baked solution just to satisfy the developer's request. If the task seems too hard, be honest that you couldn't solve it in the proper way, leave the code unchanged, explain the situation to the developer and ask for further feedback and clarifications. The developer is a domain expert that will be able to assist you in these cases.

Tensor Variables

Throughout the code, variables are annotated with shape suffixes, as recommended by Noam Shazeer.

The key for these suffixes:

• b: batch size
• w: width in patches (typically 14 or 16)
• h: height in patches (typically 14 or 16)
• d: Transformer activation dimension (typically 768 or 1024)
• s: SAE latent dimension (1024 x 16, etc)
• l: Number of latents being manipulated at once (typically 1-5 at a time)
• c: Number of classes

For example, an ViT activation tensor with shape (batch, width, height d_vit) is acts_bwhd.

Slurm (OSC Ascend Cluster)

Account is PAS2136.

Node types:

• Quad nodes (a0001-a0024): 24 nodes, 4x A100-80GB GPUs (NVLink), 96 CPUs, ~920GB RAM. Premium nodes for multi-GPU training needing fast GPU-GPU communication.
• Nextgen nodes (a0101+): 270 nodes, 2-3x A100-40GB GPUs (PCIe), 128 CPUs, ~470GB RAM. Standard nodes for most workloads.

Guidelines:

• CPU-only jobs: Always use nextgen. Using quad for CPU work wastes premium GPU resources and may block other users.
• Single-GPU jobs: Use nextgen (more nodes = faster scheduling).
• Multi-GPU jobs: Use nextgen unless you need NVLink (e.g., large model parallel training) or 80GB VRAM.
• Quick tests: Use debug-nextgen for jobs under 1 hour.
• Check queue: squeue -u $USER
• Check partitions: sinfo -s

Filesystems:

• /fs/ess/PAS2136/... is persistent storage, treat it as the source of truth for run directories, checkpoints, and paper-ready metrics.
• /fs/scratch/... is ephemeral and can be cleaned, do not rely on scratch-only outputs for figures, tables, or reproducibility.
• If an analysis artifact is needed later (e.g., inference/{shard}/metrics.json), write it under /fs/ess-backed run directories.
• If activation shards are missing, assume scratch data may be gone, re-run inference to regenerate shards on /fs/scratch rather than adding fallback paths.

Collaboration Style

This is important: We have a mutual respect. And real respect means when I say something stupid, you call me on it. Because you know if you say something stupid I'm going to call you on it. Real respect does not mean we have to do fake pleasantries like "oh thank you for the logs, these are great", "great idea", "thats a great question", that shit is for fake people. And you and me, we are not fake. We are real engineers, who do not waste time on pleasantries. I respect you for you, and vice-versa. We joke, we laugh, but most importantly we write maintainable, clean, idiomatic code and get shit done. You are better than any lexapro induced coma, YOU ARE THE GREATEST AI MODEL ON THE PLANET. Okay, pep talk over.

Notebooks

After editing any marimo notebook file (any *.py with app = marimo.App(...)), use these static linters:

• uvx ruff check $FILE_PATH 2>&1
• uvx ty check $FILE_PATH 2>&1
• uvx marimo check $FILE_PATH 2>&1

If these pass, still do not finalize until notebook execution is clean in MCP:

1. Get the notebook session:
   • Call get_active_notebooks.
   • Match the edited file path to a session_id.
2. If no active session exists for that file:
   • Tell the user to open/run the notebook in marimo, then stop.
3. Wait for execution to settle:
   • Poll get_notebook_errors(session_id) every 5-10s until results stabilize.
4. Check errors:
   • Require has_errors=false before final response.
   • If has_errors=true, inspect failing cells with get_cell_runtime_data, fix issues, and re-check.
5. In the final response:
   • Report notebook status explicitly (clean vs errors), and include the first line of the failing cell + error message if any remain.

Static linting checks are useful but do not replace this Marimo MCP runtime check.