Merge pull request #4 from RECETOX/add_dockerfile

Updated Dockerfile, build script, added GitHub workflow

.github/workflows/build-docker-image.yml

@@ -0,0 +1,18 @@
+name: Docker Image Build CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Build the Docker image
+      run: docker build . --file Dockerfile --tag recetox/qcxms-docker:main

.github/workflows/push-docker-image.yml

@@ -0,0 +1,26 @@
+name: push Docker image 
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_API_TOKEN }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          tags: recetox/qcxms-docker:${{ github.event.release.tag_name }}

Dockerfile

@@ -1,7 +1,17 @@
 FROM ubuntu:20.04
-RUN sudo apt-get install git
-RUN git clone https://github.com/qcxms/qcxms
-RUN git checkout ...
-COPY build.sh .
-RUN bash build.sh
-...
+
+# Update package lists
+RUN apt-get update -y
+
+# Install wget and xz-utils
+RUN apt-get install -y wget xz-utils python3
+
+# Create directories for extraction
+RUN mkdir /qcxms_bin
+RUN mkdir /plotms_bin
+
+# Download and extract QCxMS and PlotMS
+RUN wget https://github.com/qcxms/QCxMS/releases/download/v.5.2.1/QCxMS.v.5.2.1.tar.xz && tar -xvf QCxMS.v.5.2.1.tar.xz -C /qcxms_bin
+RUN wget https://github.com/qcxms/PlotMS/releases/download/v.6.2.0/PlotMS.v.6.2.0.tar.xz && tar -xvf PlotMS.v.6.2.0.tar.xz -C /plotms_bin
+
+RUN chmod +x /qcxms_bin/getres

build.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+add-apt-repository ppa:ubuntu-toolchain-r/test
+apt-get update
+apt-get install -y gcc-9 gfortran-9
+
+update-alternatives \
+        --install /usr/bin/gcc gcc /usr/bin/gcc-9 100 \
+        --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-9 \
+        --slave /usr/bin/gcov gcov /usr/bin/gcov-9
+
+
+mkdir -p /opt/intel
+chown $USER:$USER /opt/intel
+
+wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+
+apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+
+echo "deb https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list
+
+apt-get update
+apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mkl intel-oneapi-mkl-devel
+
+source /opt/intel/oneapi/setvars.sh
+source /opt/intel/oneapi/compiler/2024.0/env/vars.sh
+
+pip install meson==0.58.0 ninja
+
+set -ex
+export FC=ifort CC=icc
+
+meson setup _build \
+  ${MESON_ARGS:---prefix=$PWD/qcxms_bin --libdir=lib} \
+  --buildtype=release \
+  -Dfortran_link_args=-qopenmp
+
+meson compile -C _build
+
+meson install -C _build --no-rebuild