fixing Docker and tests

Author: Barthelemy-Drabczuk

.dockerignore

@@ -0,0 +1,23 @@
+# Pixi-managed conda environment — rebuilt by `pixi install` inside Docker (20 GB)
+.pixi/
+
+# Python cache
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+.pytest_cache/
+.hypothesis/
+
+# Git internals (not needed in the image)
+.git/
+
+# Editor / CI artefacts
+.vscode/
+*.env
+.env
+settings.json
+*.prof
+
+# GitHub Actions (Dockerfile is specified with -f, not needed in context)
+.github/

.github/Dockerfile.base

@@ -20,10 +20,9 @@ RUN curl -fsSL https://pixi.sh/install.sh | bash
 
 WORKDIR ${HOME}/app
 
-# Clone pipeline & utils
-RUN git clone --depth 1 https://github.com/neurospin/champollion_pipeline.git && \
-    cd champollion_pipeline && \
-    git submodule update --init --recursive
+# Copy pipeline from build context (reflects local changes; submodules in external/)
+COPY --chown=user:user . champollion_pipeline/
+# Clone champollion_utils (separate external repository)
 RUN git clone --depth 1 -b master https://github.com/neurospin/champollion_utils.git
 
 # Pipeline environment (pixi + BrainVISA)

.gitignore

@@ -4,4 +4,21 @@ settings.json
 __pycache__*
 .pytest_cache
 *.prof
-.env
+.env
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+
+# Python compiled files
+*.pyc
+__pycache__/
+*.pyo
+*.pyd
+.Python
+
+# MCP configuration
+.mcp.json
+
+
+# Fuzzy testing whit Hypothesis
+.hypothesis

pixi.lock

@@ -25,6 +25,7 @@ transformers = ">=4.36.0"
 datasets = ">=2.16.0"
 ruff = ">=0.9.0"
 pip-audit = ">=2.7.0"
+hypothesis = ">=6.0"
 
 [tasks]
 # Initialize submodules