merge main into dev

.gitignore

@@ -27,3 +27,10 @@ __pycache__/
 
 # cursor
 .cursorrules
+
+# Ignore output directories from Titanic tests
+/tests/test_data/titanic/ray_results/
+/tests/test_data/titanic/test_results/
+
+# Ignore output directories from Dream tests
+/tutorials/dream/dream_train.csv

CHANGELOG.md

@@ -105,7 +105,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - src.stimulus.data -> stimulus.data. ([b04546c](https://github.com/mathysgrapotte/stimulus-py/commit/b04546c2c9bcc1f6218c31d8f7132e57ea1dab91) by mgrapotte).
 - src.stimulus.utils -> stimulus.utils. ([55d1fed](https://github.com/mathysgrapotte/stimulus-py/commit/55d1fed95950adc2782a73a90690783786c9fb85) by mgrapotte).
 
-<!-- insertion marker -->
+
 ## [0.2.4](https://github.com/mathysgrapotte/stimulus-py/releases/tag/0.2.4) - 2025-02-07
 
 <small>[Compare with 0.2.3](https://github.com/mathysgrapotte/stimulus-py/compare/0.2.3...0.2.4)</small>
@@ -114,3 +114,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - test were failing, made format to fix it. ([19dce1f](https://github.com/mathysgrapotte/stimulus-py/commit/19dce1f2f6fc069a24991a843249f7edc876bb43) by mgrapotte).
 
+
+## [0.2.5](https://github.com/mathysgrapotte/stimulus-py/releases/tag/0.3.0) - 2025-02-12
+
+<small>[Compare with 0.2.4](https://github.com/mathysgrapotte/stimulus-py/compare/0.2.4...0.3.0)</small>
+
+### Features
+
+- removed test results from git push. ([3f3f516](https://github.com/mathysgrapotte/stimulus-py/commit/3f3f5161e54dfc2d4db40ff59e5a2e924d30bfe4) by mgrapotte).
+- added dockerfiles. ([c18489f](https://github.com/mathysgrapotte/stimulus-py/commit/c18489f59ba7e0f36c5f90a7ce51248c0bb49a07) by mgrapotte).
+
+### Bug Fixes
+
+- fixed duplicate in ruff config. ([eb9d3bf](https://github.com/mathysgrapotte/stimulus-py/commit/eb9d3bf566c7ab94c02f30b85d5a946b440711b9) by mgrapotte).
+- update ruff config to ignore shadowing python typing. ([55d33be](https://github.com/mathysgrapotte/stimulus-py/commit/55d33be8a6068e3b4649275ec1bf3827c21ffb9a) by mgrapotte).
+- renamed dockerfiles directory as it was causing ci to crash. ([6c19df4](https://github.com/mathysgrapotte/stimulus-py/commit/6c19df4589c2ff6e3a5ded53d561ba50dd4255f0) by mgrapotte).
+- ray init needs to be called in the run command otherwise ray cluster is not found. ([c9526d6](https://github.com/mathysgrapotte/stimulus-py/commit/c9526d60c909ddc8d8dabd751380c5d5e16b8d44) by mgrapotte).
+- ray init needs to be called in the run command, otherwise ray cluster is not found. ([4ebd495](https://github.com/mathysgrapotte/stimulus-py/commit/4ebd495ba348698252598d8e7a3575cead057593) by mgrapotte).
+
+

config/ruff.toml

@@ -63,6 +63,12 @@ ignore = [
     "PLR2004",  # Magic value used in comparison
     "S101",  # Use of assert detected
 ]
+"src/stimulus/typing/**" = [
+    "A005",  # stimulus.typing is not shadowing typing
+]
+"tests/typing/**" = [
+    "A005",  # stimulus.typing is not shadowing typing
+]
 
 # TODO temporary just until all unittests are passed to unittest
 "tests/unittest_*.py" = ["ALL"]

dockerfiles/stimulus-py-0.2.2/Dockerfile

@@ -0,0 +1,38 @@
+# syntax=docker/dockerfile:1.9
+
+FROM python:3.12-slim AS builder
+
+# Install build dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+# Set uv environment variables
+ENV UV_LINK_MODE=copy \
+    UV_COMPILE_BYTECODE=1 \
+    UV_PYTHON_DOWNLOADS=never \
+    UV_SYSTEM_PYTHON=1
+
+# Install stimulus-py
+RUN uv pip install --system --no-build-isolation --compile --no-cache stimulus-py==0.2.2
+
+# Create final image
+FROM python:3.12-slim
+
+RUN apt-get update && apt-get install -y procps && rm -rf /var/lib/apt/lists/*
+
+# Copy installed packages from builder
+COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages
+COPY --from=builder /usr/local/bin/stimulus-* /usr/local/bin
+
+# Create non-root user
+RUN useradd -m -s /bin/bash app
+USER app
+
+# Set working directory
+WORKDIR /app
+
+CMD ["python3"]

dockerfiles/stimulus-py-0.2.4.dev/Dockerfile

@@ -0,0 +1,60 @@
+# syntax=docker/dockerfile:1.9
+
+############################
+# Stage 1: Builder         #
+############################
+FROM python:3.12-slim AS builder
+
+# Install build dependencies
+RUN apt-get update && apt-get install -y build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install uv from the official image
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+# Set uv environment variables for optimized build
+ENV UV_LINK_MODE=copy \
+    UV_COMPILE_BYTECODE=1 \
+    UV_PYTHON_DOWNLOADS=never \
+    UV_SYSTEM_PYTHON=1
+
+# Set working directory for building
+WORKDIR /src
+
+# Copy the entire repository (source code, pyproject.toml, etc.) into the container
+COPY . .
+
+# Install build-system requirements for pdm backend
+RUN uv pip install pdm-backend pdm
+
+# Set fallback version for SCM
+ENV PDM_BUILD_SCM_VERSION=0.2.4.dev
+
+# Build and install stimulus-py from local source using uv pip install
+RUN uv pip install --system --no-build-isolation --compile --no-cache .
+
+############################
+# Stage 2: Final Image     #
+############################
+FROM python:3.12-slim
+
+# Install minimal runtime dependency
+RUN apt-get update && apt-get install -y procps \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy installed packages from builder
+COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages
+
+# Copy stimulus CLI commands (stimulus-*) and the ray command
+COPY --from=builder /usr/local/bin/stimulus-* /usr/local/bin/
+COPY --from=builder /usr/local/bin/ray /usr/local/bin/ray
+
+# Create a non-root user for running the app
+RUN useradd -m -s /bin/bash app
+USER app
+
+# Set working directory
+WORKDIR /app
+
+# Default command
+CMD ["python3"] 

dockerfiles/stimulus-py-0.2.4/Dockerfile

@@ -0,0 +1,39 @@
+# syntax=docker/dockerfile:1.9
+
+FROM python:3.12-slim AS builder
+
+# Install build dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+# Set uv environment variables
+ENV UV_LINK_MODE=copy \
+    UV_COMPILE_BYTECODE=1 \
+    UV_PYTHON_DOWNLOADS=never \
+    UV_SYSTEM_PYTHON=1
+
+# Install stimulus-py (ray will be installed as a dependency)
+RUN uv pip install --system --no-build-isolation --compile --no-cache stimulus-py==0.2.4
+
+# Create final image
+FROM python:3.12-slim
+
+RUN apt-get update && apt-get install -y procps && rm -rf /var/lib/apt/lists/*
+
+# Copy installed packages from builder
+COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages
+COPY --from=builder /usr/local/bin/stimulus-* /usr/local/bin
+COPY --from=builder /usr/local/bin/ray /usr/local/bin/ray
+
+# Create non-root user
+RUN useradd -m -s /bin/bash app
+USER app
+
+# Set working directory
+WORKDIR /app
+
+CMD ["python3"]

src/stimulus/cli/check_model.py

@@ -4,6 +4,7 @@
 import argparse
 import logging
 
+import ray
 import yaml
 from torch.utils.data import DataLoader
 
@@ -189,6 +190,7 @@ def main(
 
 def run() -> None:
     """Run the model checking script."""
+    ray.init(address="auto", ignore_reinit_error=True)
     args = get_args()
     main(
         data_path=args.data,

src/stimulus/cli/tuning.py

@@ -7,6 +7,7 @@
 from pathlib import Path
 from typing import Any
 
+import ray
 import yaml
 
 from stimulus.data import loaders
@@ -225,6 +226,7 @@ def main(
 
 def run() -> None:
     """Run the model checking script."""
+    ray.init(address="auto", ignore_reinit_error=True)
     args = get_args()
     main(
         data_path=args.data,