FIX use python 3.9 in Docker

Dockerfile

@@ -26,22 +26,21 @@ RUN meshlab --version
 ENV SKLEARN_NO_OPENMP="1"
 COPY [".", \
       "/headcase-pipeline"]
-ENV CONDA_DIR="/opt/miniconda-latest" \
-    PATH="/opt/miniconda-latest/bin:$PATH"
+ENV CONDA_DIR="/opt/miniconda-py39_24.1.2-0" \
+    PATH="/opt/miniconda-py39_24.1.2-0/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            bzip2 \
            ca-certificates \
            curl \
     && rm -rf /var/lib/apt/lists/* \
     # Install dependencies.
-    && export PATH="/opt/miniconda-latest/bin:$PATH" \
+    && export PATH="/opt/miniconda-py39_24.1.2-0/bin:$PATH" \
     && echo "Downloading Miniconda installer ..." \
     && conda_installer="/tmp/miniconda.sh" \
-    && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    && bash "$conda_installer" -b -p /opt/miniconda-latest \
+    && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-py39_24.1.2-0-Linux-x86_64.sh \
+    && bash "$conda_installer" -b -p /opt/miniconda-py39_24.1.2-0 \
     && rm -f "$conda_installer" \
-    && conda update -yq -nbase conda \
     # Prefer packages in conda-forge
     && conda config --system --prepend channels conda-forge \
     # Packages in lower-priority channels not considered if a package with the same
@@ -174,14 +173,14 @@ RUN printf '{ \
     { \
       "name": "env", \
       "kwds": { \
-        "CONDA_DIR": "/opt/miniconda-latest", \
-        "PATH": "/opt/miniconda-latest/bin:$PATH" \
+        "CONDA_DIR": "/opt/miniconda-py39_24.1.2-0", \
+        "PATH": "/opt/miniconda-py39_24.1.2-0/bin:$PATH" \
       } \
     }, \
     { \
       "name": "run", \
       "kwds": { \
-        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bzip2 \\\\\\n    ca-certificates \\\\\\n    curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y  --name base \\\\\\n    \\"python=3.9\\" \\\\\\n    \\"gxx_linux-64\\"\\nbash -c \\"source activate base\\n  python -m pip install --no-cache-dir  \\\\\\n      \\"-r\\" \\\\\\n      \\"/headcase-pipeline/requirements.txt\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
+        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bzip2 \\\\\\n    ca-certificates \\\\\\n    curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py39_24.1.2-0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py39_24.1.2-0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py39_24.1.2-0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y  --name base \\\\\\n    \\"python=3.9\\" \\\\\\n    \\"gxx_linux-64\\"\\nbash -c \\"source activate base\\n  python -m pip install --no-cache-dir  \\\\\\n      \\"-r\\" \\\\\\n      \\"/headcase-pipeline/requirements.txt\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
       } \
     }, \
     { \

generate_dockerfile.sh

@@ -17,7 +17,7 @@ docker run --rm repronim/neurodocker:latest generate docker \
 	--env SKLEARN_NO_OPENMP=1 \
 	--copy . "/headcase-pipeline" \
 	--miniconda \
-	version=latest \
+	version="py39_24.1.2-0" \
 	conda_install="python=3.9 gxx_linux-64" \
 	pip_install="-r /headcase-pipeline/requirements.txt" \
 	--run "useradd -m -s /bin/bash -G users headcase" \