From b86c1f2bac0f1e028e9f13cf4f32609b17c9f4f9 Mon Sep 17 00:00:00 2001 From: Alexander Date: Fri, 27 Mar 2026 16:31:05 -0700 Subject: [PATCH 1/5] initial claude setup --- .claude/rules/uv.md | 11 ++++ CLAUDE.md | 138 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 149 insertions(+) create mode 100644 .claude/rules/uv.md create mode 100644 CLAUDE.md diff --git a/.claude/rules/uv.md b/.claude/rules/uv.md new file mode 100644 index 0000000..9ee33b7 --- /dev/null +++ b/.claude/rules/uv.md @@ -0,0 +1,11 @@ +--- +description: Enforce uv as the package manager for all Python operations +globs: + - "**/*.py" + - "**/pyproject.toml" +--- + +- Always use `uv run` to execute commands — never bare `python`, `pytest`, `ruff`, or other tools. +- Never use `pip install` — use `uv sync` (with `--extra` or `--all-groups` flags) to manage dependencies. +- The `uv.lock` file is the source of truth for resolved dependency versions. +- When adding dependencies, add them to `pyproject.toml` and run `uv sync`. diff --git a/CLAUDE.md b/CLAUDE.md new file mode 100644 index 0000000..fc56ee8 --- /dev/null +++ b/CLAUDE.md @@ -0,0 +1,138 @@ +# LANfactory — Project Context for Claude + +## What is LANfactory? + +Lightweight Python package for training Likelihood Approximation Networks (LANs), Choice Probability Networks (CPNs), and Option Probability Networks (OPNs) using PyTorch or JAX/Flax backends. Trained networks are exported to ONNX format and uploaded to HuggingFace for consumption by HSSM. This package sits in the middle of the HSSM ecosystem: it depends on ssm-simulators for training data and produces the neural network artifacts that HSSM uses at inference time. For ecosystem-wide context, see the HSSMSpine repo. + +## Project Structure + +``` +src/lanfactory/ # Main package + cli/ # Typer CLIs: jaxtrain, torchtrain, transform-onnx, upload-hf, download-hf + config/ # Default network and training configs (LAN, CPN, OPN) + trainers/ # Training implementations (torch_mlp.py, jax_mlp.py) + onnx/ # PyTorch → ONNX export + hf/ # HuggingFace Hub integration (upload, download, model cards) + utils/ # Config save/load, MLflow utilities +tests/ # pytest suite (trainers, CLI, ONNX, HuggingFace, E2E) +docs/ # MkDocs documentation + tutorial notebooks +notebooks/ # Test notebooks +``` + +## Build & Tooling + +- **Build system:** setuptools (pure Python, no compiled extensions) +- **Package manager:** uv (with `uv.lock`) +- **Python:** >3.10, <3.14 (classifiers target 3.11, 3.12, 3.13) +- **Linting:** ruff (line length 120, via pre-commit) +- **Type checking:** mypy +- **No system dependencies** — unlike ssm-simulators, this is pure Python + PyTorch/Flax + +## Common Commands + +```bash +# Install all dependencies (dev + optional) +uv sync --all-groups + +# Run tests +uv run pytest tests/ + +# Lint & format +uv run ruff check src/lanfactory && uv run ruff format --check . + +# Build docs +uv run mkdocs build +uv run mkdocs serve + +# Train a network (PyTorch) +uv run torchtrain --config-path --training-data-folder --networks-path-base + +# Train a network (JAX) +uv run jaxtrain --config-path --training-data-folder --networks-path-base + +# Export PyTorch model to ONNX +uv run transform-onnx --network-config-file config.pickle --state-dict-file model.pt \ + --input-shape 6 --output-onnx-file model.onnx + +# Upload trained models to HuggingFace +uv run upload-hf --model-folder --network-type lan --model-name ddm + +# Download models from HuggingFace +uv run download-hf --network-type lan --model-name ddm --output-folder +``` + +## Key Architecture Patterns + +### Network Types + +| Type | Full Name | Output | Loss | Use Case | +|------|-----------|--------|------|----------| +| LAN | Likelihood Approximation Network | logprob | Huber | Log-likelihood approximation | +| CPN | Choice Probability Network | logits | BCE with logits | Choice probability estimation | +| OPN | Option Probability Network | logits | BCE with logits | Option probability estimation | + +All three use the same MLP architecture (`[100, 100, 1]` default, tanh activations) +but differ in output type and loss function. + +### Training Backends + +- **PyTorch** (`torchtrain` CLI, `trainers/torch_mlp.py`) — primary backend. + Supports CUDA, ONNX export, full training loop with validation. +- **JAX/Flax** (`jaxtrain` CLI, `trainers/jax_mlp.py`) — alternative backend. + Uses optax optimizers. No native ONNX export (train in JAX, convert via PyTorch if needed). + +### ONNX Export Pipeline + +PyTorch model → `torch.onnx.export()` → `.onnx` file. This is the format +HSSM consumes at runtime. Only PyTorch models can be directly exported to ONNX. + +### HuggingFace Integration + +- **Upload:** `lanfactory.hf.upload_model()` — uploads `.onnx`, `.pt`, config pickles, + and auto-generated README to `franklab/HSSM` on HuggingFace. + Requires `model_card.yaml` in the model folder. +- **Download:** `lanfactory.hf.download_model()` — downloads by network type + model name. +- **Default repo:** `franklab/HSSM` +- **Optional dependency:** `huggingface-hub>=0.20.0` (install via `uv sync --extra hf`) + +### Config System + +Training configs are YAML files parsed by the CLI. Key fields: +- `NETWORK_TYPE`: `lan`, `cpn`, or `opn` +- `layer_sizes`, `activations`: network architecture +- `n_epochs`, `learning_rate`, `loss`, `optimizer`: training hyperparams +- `cpu_batch_size`, `gpu_batch_size`: device-specific batch sizes + +Default configs available in `lanfactory.config.network_configs`. + +### MLflow Integration + +Optional experiment tracking via MLflow. CLI flags: `--run-name`, `--experiment-name`, +`--tracking-uri`, `--artifact-location`. Supports resuming runs via `--run-id`. + +## CLI Entry Points + +| Command | Module | Purpose | +|---------|--------|---------| +| `torchtrain` | `lanfactory.cli.torch_train` | Train PyTorch networks from YAML config | +| `jaxtrain` | `lanfactory.cli.jax_train` | Train JAX networks from YAML config | +| `transform-onnx` | `lanfactory.onnx.transform_onnx` | Convert PyTorch model → ONNX | +| `upload-hf` | `lanfactory.cli.upload_hf` | Upload trained models to HuggingFace | +| `download-hf` | `lanfactory.cli.download_hf` | Download models from HuggingFace | + +## CI Workflows + +| Workflow | Purpose | +|----------|---------| +| `run_tests.yml` | Tests on Python 3.11/3.12/3.13 + ruff lint/format + codecov | +| `build_wheels.yml` | Build sdist, upload to TestPyPI → PyPI on release publish | + +## Known Issues + +- `__init__.py` version (`0.5.3`) is out of sync with `pyproject.toml` (`0.6.1`) + +## Compaction + +When compacting, preserve: file list of modified files, the three network types +(LAN/CPN/OPN) and their differences, CLI entry points, ONNX export flow, +HuggingFace upload/download interface, and all test commands. From 255e95bff0267c1f7533f2071e68cf857daca502 Mon Sep 17 00:00:00 2001 From: Alexander Date: Sun, 29 Mar 2026 16:06:57 -0700 Subject: [PATCH 2/5] align pre-commit hooks across projects --- .claude/settings.json | 15 +++++++++++++++ .pre-commit-config.yaml | 15 ++++++++++----- pyproject.toml | 7 +++---- src/lanfactory/hf/upload.py | 10 ++++------ src/lanfactory/trainers/torch_mlp.py | 5 +++-- 5 files changed, 35 insertions(+), 17 deletions(-) create mode 100644 .claude/settings.json diff --git a/.claude/settings.json b/.claude/settings.json new file mode 100644 index 0000000..b2df465 --- /dev/null +++ b/.claude/settings.json @@ -0,0 +1,15 @@ +{ + "hooks": { + "PostToolUse": [ + { + "matcher": "Edit|Write", + "hooks": [ + { + "type": "command", + "command": "FILE=$(jq -r '.tool_input.file_path'); if [[ \"$FILE\" == *.py ]]; then cd \"$CLAUDE_PROJECT_DIR\" && uv run ruff format \"$FILE\" --quiet 2>/dev/null; fi" + } + ] + } + ] + } +} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index af7b8af..cca8382 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,19 +1,24 @@ repos: - # Ruff linting and formatting - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.4 + rev: v0.14.13 hooks: - id: ruff - args: [--fix] + args: [--fix, --exit-non-zero-on-fix] - id: ruff-format - # Pre-commit hooks - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer - id: check-yaml - args: [--unsafe] # this helps with some MkDocs YAML files + exclude: ^mkdocs\.yml$ - id: check-added-large-files - id: check-merge-conflict + + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.19.1 + hooks: + - id: mypy + args: [--no-strict-optional, --ignore-missing-imports] + additional_dependencies: [types-PyYAML] diff --git a/pyproject.toml b/pyproject.toml index 478a787..a460283 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -72,6 +72,7 @@ dev = [ "pytest-xdist>=3.6.1", "pytest>=8.3.1", "ruff>=0.14.4", + "types-PyYAML", "mlflow>=3.6.0", ] @@ -94,11 +95,11 @@ addopts = [ ] [tool.ruff] -# Specify the directories to check +line-length = 88 src = ["src/lanfactory", "tests"] exclude = [ "notebooks/*", - "docs/*", # Exclude the entire docs folder + "docs/*", "docs/basic_tutorial/basic_tutorial.ipynb", ] @@ -131,8 +132,6 @@ exclude_lines = [ "logger.error", ] -# Add any additional configuration options for ruff -line-length = 120 [project.scripts] diff --git a/src/lanfactory/hf/upload.py b/src/lanfactory/hf/upload.py index f85f891..c223ef2 100644 --- a/src/lanfactory/hf/upload.py +++ b/src/lanfactory/hf/upload.py @@ -233,19 +233,17 @@ def _collect_files( list[Path] List of file paths to upload. """ - files = set() + matched: set[Path] = set() # Collect files matching include patterns for pattern in include_patterns: - files.update(folder.glob(pattern)) + matched.update(folder.glob(pattern)) # Remove files matching exclude patterns if exclude_patterns: for pattern in exclude_patterns: excluded = set(folder.glob(pattern)) - files -= excluded + matched -= excluded # Filter to only regular files (not directories) - files = [f for f in files if f.is_file()] - - return sorted(files) + return sorted(f for f in matched if f.is_file()) diff --git a/src/lanfactory/trainers/torch_mlp.py b/src/lanfactory/trainers/torch_mlp.py index 35bdc30..d439bb7 100755 --- a/src/lanfactory/trainers/torch_mlp.py +++ b/src/lanfactory/trainers/torch_mlp.py @@ -337,8 +337,9 @@ def TorchMLPFactory( """ if isinstance(network_config, str): with open(network_config, "rb") as f: - network_config = pickle.load(f) + network_config = pickle.load(f) # noqa: S301 + assert isinstance(network_config, dict) return TorchMLP( network_config=network_config, input_shape=input_dim, @@ -506,7 +507,7 @@ def __init__( elif isinstance(train_config, dict): print("train_config is passed as dictionary: \n") print(train_config) - self.train_config: dict = train_config + self.train_config = train_config self.model: TorchMLP = model.to(self.dev) self.allow_abs_path_folder_generation: bool = allow_abs_path_folder_generation From bb1da0511bd7fec02d29b48f1b95afa4affafa1c Mon Sep 17 00:00:00 2001 From: Alexander Date: Mon, 30 Mar 2026 15:38:34 -0700 Subject: [PATCH 3/5] Track uv.lock and address PR #77 Copilot review comments - Remove uv.lock from .gitignore and commit lockfile - Raise check-added-large-files limit to 1000 KB - Fix uv sync comment: dev + optional -> all dependency groups - Fix MLflow CLI flags to use correct --mlflow- prefix - Scope no pip install rule to development only Co-Authored-By: Claude Opus 4.6 (1M context) --- .claude/rules/uv.md | 2 +- .gitignore | 1 - .pre-commit-config.yaml | 1 + CLAUDE.md | 6 +- uv.lock | 4537 +++++++++++++++++++++++++++++++++++++++ 5 files changed, 4542 insertions(+), 5 deletions(-) create mode 100644 uv.lock diff --git a/.claude/rules/uv.md b/.claude/rules/uv.md index 9ee33b7..16db5b2 100644 --- a/.claude/rules/uv.md +++ b/.claude/rules/uv.md @@ -6,6 +6,6 @@ globs: --- - Always use `uv run` to execute commands — never bare `python`, `pytest`, `ruff`, or other tools. -- Never use `pip install` — use `uv sync` (with `--extra` or `--all-groups` flags) to manage dependencies. +- When working in this repo (local development, CI, or scripts), do not use `pip install`; use `uv sync` (with `--extra` or `--all-groups` flags) to manage dependencies. End-user installation docs may still reference `pip`. - The `uv.lock` file is the source of truth for resolved dependency versions. - When adding dependencies, add them to `pyproject.toml` and run `uv sync`. diff --git a/.gitignore b/.gitignore index c8fef8b..d429c47 100755 --- a/.gitignore +++ b/.gitignore @@ -44,7 +44,6 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST -uv.lock # PyInstaller # Usually these files are written by a python script from a template diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cca8382..8ef5a64 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,6 +14,7 @@ repos: - id: check-yaml exclude: ^mkdocs\.yml$ - id: check-added-large-files + args: ['--maxkb=1000'] - id: check-merge-conflict - repo: https://github.com/pre-commit/mirrors-mypy diff --git a/CLAUDE.md b/CLAUDE.md index fc56ee8..d8b6545 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -31,7 +31,7 @@ notebooks/ # Test notebooks ## Common Commands ```bash -# Install all dependencies (dev + optional) +# Install all dependency groups (e.g. dev) uv sync --all-groups # Run tests @@ -107,8 +107,8 @@ Default configs available in `lanfactory.config.network_configs`. ### MLflow Integration -Optional experiment tracking via MLflow. CLI flags: `--run-name`, `--experiment-name`, -`--tracking-uri`, `--artifact-location`. Supports resuming runs via `--run-id`. +Optional experiment tracking via MLflow. CLI flags: `--mlflow-run-name`, `--mlflow-experiment-name`, +`--mlflow-tracking-uri`, `--mlflow-artifact-location`. 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+sdist = { url = "https://files.pythonhosted.org/packages/e3/02/0f2892c661036d50ede074e376733dca2ae7c6eb617489437771209d4180/zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166", size = 25547 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e", size = 10276 }, +] From b45838418130f6c74a8e444b64ac4c83feb9cd35 Mon Sep 17 00:00:00 2001 From: Alexander Date: Mon, 30 Mar 2026 15:45:29 -0700 Subject: [PATCH 4/5] Raise check-added-large-files limit to ~99.9 MB Match GitHub's own 100 MB hard limit rather than imposing an artificial lower threshold. Notebooks and lock files should not be blocked. Co-Authored-By: Claude Opus 4.6 (1M context) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8ef5a64..94eb114 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,7 +14,7 @@ repos: - id: check-yaml exclude: ^mkdocs\.yml$ - id: check-added-large-files - args: ['--maxkb=1000'] + args: ['--maxkb=99900'] - id: check-merge-conflict - repo: https://github.com/pre-commit/mirrors-mypy From dd261014baecf365760a6df6a9f5aed968d9128c Mon Sep 17 00:00:00 2001 From: Alexander Date: Mon, 30 Mar 2026 16:14:41 -0700 Subject: [PATCH 5/5] Fix documented ruff line length: 120 -> 88 to match pyproject.toml Co-Authored-By: Claude Opus 4.6 (1M context) --- CLAUDE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CLAUDE.md b/CLAUDE.md index d8b6545..d9a4aab 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -24,7 +24,7 @@ notebooks/ # Test notebooks - **Build system:** setuptools (pure Python, no compiled extensions) - **Package manager:** uv (with `uv.lock`) - **Python:** >3.10, <3.14 (classifiers target 3.11, 3.12, 3.13) -- **Linting:** ruff (line length 120, via pre-commit) +- **Linting:** ruff (line length 88, via pre-commit) - **Type checking:** mypy - **No system dependencies** — unlike ssm-simulators, this is pure Python + PyTorch/Flax