refactor(python): switch from mamba to conda (#214)

* switch to conda

* remove pre-installed extension from vscode

jupyter/Dockerfile

@@ -9,9 +9,9 @@ RUN /opt/install-jupyterlab.sh && \
     # Install JupyterLab extensions
     pip3 install jupyterlab-git && \
     # If using Conda and Julia is installed, make its kernel available in Jupyter
-    if command -v julia && [ -n "$MAMBA_DIR" ]; then \
+    if command -v julia && [ -n "$CONDA_DIR" ]; then \
         julia -e 'using Pkg; pkg"add IJulia"; pkg"precompile"' && \
-        mv "${HOME}/.local/share/jupyter/kernels/julia"* "${MAMBA_DIR}/share/jupyter/kernels/"; \
+        mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/"; \
     fi && \
     # If R is installed, make its kernel available in Jupyter
     if command -v R; then \
@@ -20,11 +20,11 @@ RUN /opt/install-jupyterlab.sh && \
     # Generate jupyter server config
     jupyter server --generate-config && \
     # Fix permissions
-    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${MAMBA_DIR} && \
+    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${CONDA_DIR} && \
     # Clean
     jupyter lab clean && \
     rm -rf /var/lib/apt/lists/* && \
-    if command -v mamba; then \
+    if command -v conda; then \
         conda clean --all -f -y; \
     fi
 

jupyter/tests.yaml

@@ -40,7 +40,7 @@ commandTests:
   - name: "Does the binary exists?"
     command: "which"
     args: ["jupyter-lab"]
-    expectedOutput: ["/usr/local/bin/jupyter-lab|/opt/mamba/bin/jupyter-lab"]
+    expectedOutput: ["/usr/local/bin/jupyter-lab|/opt/conda/bin/jupyter-lab"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["duckdb"]

python-datascience/Dockerfile

@@ -13,15 +13,15 @@ USER root
 COPY conda-env.yml .
 
 RUN ls -larth /opt/
-RUN mamba env update -n base -f conda-env.yml && \
+RUN conda env update -n base -f conda-env.yml && \
     # Install Python packages not available on conda-forge
     pip3 install opencv-python-headless && \
     # Install Julia
     /opt/install-julia.sh && \
     # Install Quarto latest version
     /opt/install-quarto.sh && \
     # Fix permissions
-    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${MAMBA_DIR} ${JULIA_DIR} && \
+    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${CONDA_DIR} ${JULIA_DIR} && \
     # Clean
     rm conda-env.yml && \ 
     conda clean --all -f -y && \

python-datascience/tests.yaml

@@ -38,16 +38,16 @@ commandTests:
     expectedOutput: ["/usr/local/bin/argo"]
   - name: "Does the binary exists?"
     command: "which"
-    args: ["mamba"]
-    expectedOutput: ["/opt/mamba/bin/mamba"]
+    args: ["conda"]
+    expectedOutput: ["/opt/conda/bin/conda"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["python"]
-    expectedOutput: ["/opt/mamba/bin/python"]
+    expectedOutput: ["/opt/conda/bin/python"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["pip"]
-    expectedOutput: ["/opt/mamba/bin/pip"]
+    expectedOutput: ["/opt/conda/bin/pip"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["julia"]

python-minimal/Dockerfile

@@ -6,31 +6,29 @@ LABEL maintainer="InseeFrLab <[email protected]>"
 ARG PYTHON_VERSION="3.12.4"
 ENV PYTHON_VERSION=${PYTHON_VERSION}
 
-ENV MAMBA_DIR="/opt/mamba"
-ENV PATH="${MAMBA_DIR}/bin:${PATH}"
+ENV CONDA_DIR="/opt/conda"
+ENV PATH="${CONDA_DIR}/bin:${PATH}"
 
 USER root
 
 COPY conda-env.yml .
 
-RUN wget -q "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O miniforge.sh && \
-    # Install mambaforge latest version
-    /bin/bash miniforge.sh -b -p "${MAMBA_DIR}" && \
+RUN /opt/install-conda.sh && \
     # Set specified Python version in base Conda env
-    mamba install python=="${PYTHON_VERSION}" && \
+    conda install python=="${PYTHON_VERSION}" && \
     # Pin Python version to prevent Conda from upgrading it
-    touch ${MAMBA_DIR}/conda-meta/pinned && \
-    echo "python==${PYTHON_VERSION}" >> ${MAMBA_DIR}/conda-meta/pinned && \
+    touch ${CONDA_DIR}/conda-meta/pinned && \
+    echo "python==${PYTHON_VERSION}" >> ${CONDA_DIR}/conda-meta/pinned && \
     # Install essential Python packages
-    mamba env update -n base -f conda-env.yml && \
+    conda env update -n base -f conda-env.yml && \
     # Install duckdb extensions
-    mamba run -n base python /opt/install-duckdb-extensions.py && \
+    conda run -n base python /opt/install-duckdb-extensions.py && \
     # Activate custom Conda env by default in shell
-    echo ". ${MAMBA_DIR}/etc/profile.d/conda.sh && conda activate" >> ${HOME}/.bashrc && \
+    echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate" >> ${HOME}/.bashrc && \
     # Fix permissions
-    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${MAMBA_DIR} && \
+    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${CONDA_DIR} && \
     # Clean
-    rm miniforge.sh conda-env.yml && \ 
+    rm conda-env.yml && \ 
     conda clean --all -f -y && \
     rm -rf /var/lib/apt/lists/*
 

python-minimal/tests.yaml

@@ -38,16 +38,16 @@ commandTests:
     expectedOutput: ["/usr/local/bin/argo"]
   - name: "Does the binary exists?"
     command: "which"
-    args: ["mamba"]
-    expectedOutput: ["/opt/mamba/bin/mamba"]
+    args: ["conda"]
+    expectedOutput: ["/opt/conda/bin/conda"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["python"]
-    expectedOutput: ["/opt/mamba/bin/python"]
+    expectedOutput: ["/opt/conda/bin/python"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["pip"]
-    expectedOutput: ["/opt/mamba/bin/pip"]
+    expectedOutput: ["/opt/conda/bin/pip"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["duckdb"]

python-pytorch/Dockerfile

@@ -13,7 +13,7 @@ RUN if ! [[ -z "${CUDA_VERSION}" ]]; then \
         pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu; \
     fi && \
     # Fix permissions
-    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${MAMBA_DIR} && \
+    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${CONDA_DIR} && \
     # Clean
     conda clean --all -f -y && \
     rm -rf /var/lib/apt/lists/*

python-pytorch/tests.yaml

@@ -38,16 +38,16 @@ commandTests:
     expectedOutput: ["/usr/local/bin/argo"]
   - name: "Does the binary exists?"
     command: "which"
-    args: ["mamba"]
-    expectedOutput: ["/opt/mamba/bin/mamba"]
+    args: ["conda"]
+    expectedOutput: ["/opt/conda/bin/conda"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["python"]
-    expectedOutput: ["/opt/mamba/bin/python"]
+    expectedOutput: ["/opt/conda/bin/python"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["pip"]
-    expectedOutput: ["/opt/mamba/bin/pip"]
+    expectedOutput: ["/opt/conda/bin/pip"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["duckdb"]

python-tensorflow/Dockerfile

@@ -7,7 +7,7 @@ USER root
 
 RUN pip3 install tensorflow && \
     # Fix permissions
-    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${MAMBA_DIR} && \
+    chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${CONDA_DIR} && \
     # Clean
     conda clean --all -f -y && \
     rm -rf /var/lib/apt/lists/*

python-tensorflow/tests.yaml

@@ -38,16 +38,16 @@ commandTests:
     expectedOutput: ["/usr/local/bin/argo"]
   - name: "Does the binary exists?"
     command: "which"
-    args: ["mamba"]
-    expectedOutput: ["/opt/mamba/bin/mamba"]
+    args: ["conda"]
+    expectedOutput: ["/opt/conda/bin/conda"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["python"]
-    expectedOutput: ["/opt/mamba/bin/python"]
+    expectedOutput: ["/opt/conda/bin/python"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["pip"]
-    expectedOutput: ["/opt/mamba/bin/pip"]
+    expectedOutput: ["/opt/conda/bin/pip"]
   - name: "Does the binary exists?"
     command: "which"
     args: ["duckdb"]

scripts/install-conda.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+set -e
+
+# Install Conda via Miniforge
+wget -q "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O miniforge.sh
+chmod +x miniforge.sh
+./miniforge.sh -b -p "${CONDA_DIR}"
+rm miniforge.sh

scripts/install-julia.sh

@@ -25,9 +25,9 @@ tar xzf julia.tar.gz -C "${JULIA_DIR}" --strip-components=1
 rm julia.tar.gz
 
 # Show Julia where conda libraries are
-if command -v mamba ; then \
+if command -v conda ; then \
     mkdir /etc/julia && \
-    echo "push!(Libdl.DL_LOAD_PATH, \"${MAMBA_DIR}/lib\")" >> /etc/julia/juliarc.jl; \
+    echo "push!(Libdl.DL_LOAD_PATH, \"${CONDA_DIR}/lib\")" >> /etc/julia/juliarc.jl; \
 fi
 
 # Update and install basic Julia packages

scripts/install-jupyterlab.sh

@@ -10,8 +10,8 @@ function apt_install() {
     fi
 }
 
-if command -v mamba ; then
-    mamba install -y jupyterlab
+if command -v conda ; then
+    conda install -y jupyterlab
 else
     if [ "`which pip3`" = "" ]; then
         apt_install python3-pip

scripts/onyxia-init.sh

@@ -158,8 +158,8 @@ fi
 
 if [[ "$DARK_MODE" == "true" ]]; then 
     if command -v jupyter-lab; then
-        mkdir ${MAMBA_DIR}/share/jupyter/lab/settings
-        echo "{\"@jupyterlab/apputils-extension:themes\": {\"theme\": \"JupyterLab Dark\"}}" > ${MAMBA_DIR}/share/jupyter/lab/settings/overrides.json;
+        mkdir ${CONDA_DIR}/share/jupyter/lab/settings
+        echo "{\"@jupyterlab/apputils-extension:themes\": {\"theme\": \"JupyterLab Dark\"}}" > ${CONDA_DIR}/share/jupyter/lab/settings/overrides.json;
     fi 
     if command -v code-server; then
         jq '. + {"workbench.colorTheme": "Default Dark Modern"}' ${HOME}/.local/share/code-server/User/settings.json > ${HOME}/tmp.settings.json  && mv ${HOME}/tmp.settings.json ${HOME}/.local/share/code-server/User/settings.json

scripts/onyxia-set-repositories.sh

@@ -18,7 +18,7 @@ if [  "`which conda`" != "" ]; then
         echo "configuration conda (add channels)"
         conda config --add channels $CONDA_REPOSITORY
         conda config --remove channels conda-forge
-        conda config --remove channels conda-forge --file /opt/mamba/.condarc
+        conda config --remove channels conda-forge --file /opt/conda/.condarc
     fi
 
     if [[ -n "$PATH_TO_CA_BUNDLE" ]]; then

vscode/Dockerfile

@@ -21,7 +21,6 @@ RUN code-server --install-extension ms-toolsai.jupyter && \
     code-server --install-extension ms-kubernetes-tools.vscode-kubernetes-tools && \
     code-server --install-extension ms-azuretools.vscode-docker && \
     code-server --install-extension njpwerner.autodocstring && \
-    code-server --install-extension redhat.vscode-yaml && \
     code-server --install-extension mhutchie.git-graph && \
     code-server --install-extension rangav.vscode-thunder-client && \
     code-server --install-extension hediet.vscode-drawio && \