Improve dependency mangement with pyproject.toml and uv

Author: maxencefaldor

.gitignore

@@ -1,39 +1,15 @@
-# added elements
-
-.vscode
-last_repertoire
-*logs.csv
-
-# Singularity generated files
-*.simg
-*.sif
-*.swp
-tmp.def
-
-
-# Figures and Videos
+# Generated files
+*.csv
 *.pth
 *.png
 *.svg
 *.pdf
 *.mp4
 *.gif
 
-# IDE configuration file
-.idea/
-
-# Hydra outputs
-hydra_outputs/
-
-
-# Usual python .gitignore
-
-# Mac OS X files
-.DS_Store
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
@@ -79,7 +55,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
+*.py.cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -127,7 +103,37 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 
 # Celery stuff
@@ -139,6 +145,7 @@ celerybeat.pid
 
 # Environments
 .env
+.envrc
 .venv
 env/
 venv/
@@ -170,5 +177,40 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-# HTML files
-*.html
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

dev.Dockerfile

@@ -1,64 +1,32 @@
-FROM mambaorg/micromamba:1.5.1 as conda
+FROM python:3.11-slim as test-image
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 PYTHONDONTWRITEBYTECODE=1 PYTHONUNBUFFERED=1
+WORKDIR /app
 
-# Speed up the build, and avoid unnecessary writes to disk
-ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 PYTHONDONTWRITEBYTECODE=1 PYTHONUNBUFFERED=1 CONDA_DIR=/opt/conda
-ENV PIPENV_VENV_IN_PROJECT=true PIP_NO_CACHE_DIR=false PIP_DISABLE_PIP_VERSION_CHECK=1
-ENV PATH=${CONDA_DIR}/bin:${PATH}
-ENV MAMBA_ROOT_PREFIX="/opt/conda"
+# Minimal OS deps for tests
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git curl \
+    && rm -rf /var/lib/apt/lists/*
 
-COPY requirements.txt /tmp/requirements.txt
-COPY requirements-dev.txt /tmp/requirements-dev.txt
-COPY environment.yaml /tmp/environment.yaml
+# Install uv
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
+ENV PATH="/root/.local/bin:$PATH"
 
-RUN micromamba create -y --file /tmp/environment.yaml \
-    && micromamba clean --all --yes \
-    && find /opt/conda/ -follow -type f -name '*.pyc' -delete
+# Create venv and activate permanently
+RUN uv venv --clear --python 3.13
+ENV VIRTUAL_ENV="/app/.venv"
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
-
-FROM python as test-image
-ENV PATH=/opt/conda/envs/qdaxpy310/bin/:$PATH APP_FOLDER=/app
-ENV PYTHONPATH=$APP_FOLDER:$PYTHONPATH
-
-COPY --from=conda /opt/conda/envs/. /opt/conda/envs/
-COPY requirements-dev.txt ./
-
-RUN pip install -r requirements-dev.txt
+# Install the project with dev extras
+COPY pyproject.toml README.md ./
+COPY qdax ./qdax
+RUN uv pip install jax[cuda] .[dev]
 
 
 FROM nvidia/cuda:11.5.2-cudnn8-devel-ubuntu20.04 as cuda-image
-ENV PATH=/opt/conda/envs/qdaxpy310/bin/:$PATH APP_FOLDER=/app
-ENV PYTHONPATH=$APP_FOLDER:$PYTHONPATH
-
-
-ENV DISTRO ubuntu2004
-ENV CPU_ARCH x86_64
-RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$DISTRO/$CPU_ARCH/3bf863cc.pub
-
-
-COPY --from=conda /opt/conda/envs/. /opt/conda/envs/
-ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.0/targets/x86_64-linux/lib
-
-ENV TZ=Europe/Paris
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
-RUN pip --no-cache-dir install jaxlib==0.4.16+cuda11.cudnn86 \
-    -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html \
-    && rm -rf /tmp/*
-
-WORKDIR $APP_FOLDER
-
-ARG USER_ID=1000
-ARG GROUP_ID=1000
-ENV USER=eng
-ENV GROUP=eng
-RUN groupadd --gid ${GROUP_ID} $GROUP && useradd -g $GROUP --uid ${USER_ID} --shell /usr/sbin/nologin -m $USER  && chown -R $USER:$GROUP $APP_FOLDER
-USER $USER
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 PYTHONDONTWRITEBYTECODE=1 PYTHONUNBUFFERED=1
+WORKDIR /app
 
-
-FROM cuda-image as dev-image
-# The dev-image does not contain the any file, qdax is expected to be mounted
-# afterwards
-
-USER root
+# System packages needed for examples/headless rendering and tooling
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     curl \
@@ -70,8 +38,6 @@ RUN apt-get update && \
     libosmesa6-dev \
     patchelf \
     python3-opengl \
-    python3-dev=3.10* \
-    python3-pip \
     screen \
     sudo \
     tmux \
@@ -82,21 +48,33 @@ RUN apt-get update && \
     xvfb && \
     rm -rf /var/lib/apt/lists/*
 
+# Install uv
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
+ENV PATH="/root/.local/bin:$PATH"
 
-COPY requirements-dev.txt /tmp/requirements-dev.txt
-RUN pip --no-cache-dir install -r /tmp/requirements-dev.txt && rm -rf /tmp/*
-USER $USER
+# Create venv and activate permanently
+RUN uv venv --clear --python 3.13
+ENV VIRTUAL_ENV="/app/.venv"
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
-FROM cuda-image as run-image
-# The run-image (default) is the same as the dev-image with the some files directly
-# copied inside
+# Install the project with dev and examples extras
+COPY pyproject.toml README.md ./
+COPY qdax ./qdax
+RUN uv pip install jax[cuda] .[dev,examples]
 
-COPY qdax qdax
-COPY setup.py ./
-COPY README.md ./
 
-RUN pip install .
+FROM cuda-image as dev-image
+# The dev-image already contains dependencies; repo can be mounted at /app for live dev
 
-WORKDIR /
+ARG USER_ID=1000
+ARG GROUP_ID=1000
+ENV USER=eng
+ENV GROUP=eng
+RUN groupadd --gid ${GROUP_ID} $GROUP && useradd -g $GROUP --uid ${USER_ID} --shell /usr/sbin/nologin -m $USER  && chown -R $USER:$GROUP /app
+USER $USER
 
+
+FROM cuda-image as run-image
+# Default run image
+WORKDIR /
 CMD ["python"]