Update Dockerfile (#367)

* Update Dockerfile

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update Dockerfile

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update Dockerfile

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/publish.yaml

@@ -29,4 +29,3 @@ jobs:
         run: |
           poetry config pypi-token.pypi $PYPI_TOKEN
           poetry publish --build
-  

Dockerfile

@@ -1,10 +1,17 @@
-ARG MAKE_JOBS="4"
+# Base image
+ARG PYTHON_VERSION="3.11"
+FROM python:${PYTHON_VERSION}
 
-FROM python:3.11
+# Build arguments for dynamic version configuration
+ARG MAKE_JOBS="4"
+ARG CP2K_VERSION="v2024.3"
+ARG PACKMOL_VERSION="20.15.3"
+ARG GROMACS_VERSION="2024.4"
 
 # Set environment variables for non-interactive installs
 ENV DEBIAN_FRONTEND=noninteractive
-ENV PATH="/opt/tools/cp2k/exe/local:/opt/tools/packmol-20.15.3:/opt/tools/gromacs-2024.4/build/bin:$PATH"
+ENV PATH="/opt/tools/cp2k/exe/local:/opt/tools/packmol-${PACKMOL_VERSION}:/opt/tools/gromacs-${GROMACS_VERSION}/build/bin:$PATH"
+
 
 # Update and install essential packages
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
@@ -13,7 +20,7 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \
 
 # Install CP2K
 WORKDIR /opt/tools
-RUN git clone -b v2024.1 --recursive https://github.com/cp2k/cp2k.git cp2k && \
+RUN git clone -b ${CP2K_VERSION} --recursive https://github.com/cp2k/cp2k.git cp2k && \
     cd cp2k/tools/toolchain && ./install_cp2k_toolchain.sh --with-openmpi && \
     cp /opt/tools/cp2k/tools/toolchain/install/arch/* /opt/tools/cp2k/arch/ && \
     cd /opt/tools/cp2k && \
@@ -22,33 +29,33 @@ RUN git clone -b v2024.1 --recursive https://github.com/cp2k/cp2k.git cp2k && \
 
 # Install PACKMOL
 WORKDIR /opt/tools
-RUN wget https://github.com/m3g/packmol/archive/refs/tags/v20.15.3.tar.gz && \
-    tar -xzvf v20.15.3.tar.gz && \
-    cd packmol-20.15.3 && make && \
-    rm /opt/tools/v20.15.3.tar.gz
+RUN wget https://github.com/m3g/packmol/archive/refs/tags/v${PACKMOL_VERSION}.tar.gz && \
+    tar -xzvf v${PACKMOL_VERSION}.tar.gz && \
+    cd packmol-${PACKMOL_VERSION} && make && \
+    rm /opt/tools/v${PACKMOL_VERSION}.tar.gz
 
 # Install GROMACS
 WORKDIR /opt/tools
-RUN wget https://ftp.gromacs.org/gromacs/gromacs-2024.4.tar.gz && \
-    tar xfz gromacs-2024.4.tar.gz && \
-    cd gromacs-2024.4 && \
+RUN wget https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz && \
+    tar xfz gromacs-${GROMACS_VERSION}.tar.gz && \
+    cd gromacs-${GROMACS_VERSION} && \
     mkdir build && cd build && \
     cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON && \
     make -j ${MAKE_JOBS} && make check && make install && \
-    rm /opt/tools/gromacs-2024.4.tar.gz
-
+    rm /opt/tools/gromacs-${GROMACS_VERSION}.tar.gz
 
 # Install additional Python packages
 RUN pip install dvc-s3 jax[cuda12] MDAnalysis pyedr apax
 
-
 # Install IPSuite
 WORKDIR /opt/tools/ipsuite
 COPY ./ ./
 RUN pip install .
 
 # Create a working directory
 RUN mkdir -m 1777 /work
+RUN git config --global --add safe.directory /work
+
 WORKDIR /work
 
 ENTRYPOINT [ "/bin/bash" ]