github to docker build

.github/workflows/build.yml

@@ -0,0 +1,30 @@
+name: Build Docker Container
+
+on:
+  push:
+    branches:
+      - main
+      - master 
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          push: true
+          tags: simoneponcioni/hfe_development:latest

02_CODE/Dockerfile.ubuntu24.04

@@ -2,34 +2,42 @@ FROM ubuntu:24.04
 
 ENV DEBIAN_FRONTEND noninteractive
 
-# Set GitHub username and personal access token
-ARG GITHUB_USERNAME
-ARG GITHUB_TOKEN
-ARG USER_UID=1000
-ARG USER_GID=1000
-
 # RUN apt-get update && apt-get install -y wget git apt-utils git cmake gcc g++ gfortran python3 python3-numpy python3-scipy python3-pip swig clang-tidy emacs-nox valgrind texlive texlive-latex-recommended texlive-latex-extra texinfo libreoffice fonts-cmu libpetsc-complex-dev libslepc-complex3.19-dev python3-dev libopenblas-dev libfltk1.3-dev libfreetype6-dev libgl1-mesa-dev libxi-dev libxmu-dev mesa-common-dev tcl-dev tk-dev libhdf5-dev libcgns-dev libxft-dev libxinerama-dev libxcursor-dev libxfixes-dev libocct-foundation-dev libocct-data-exchange-dev libocct-ocaf-dev libopenmpi-dev libboost-dev cargo clang gcovr ftp libgl1-mesa-dri && apt-get clean
-RUN apt-get update && apt-get install -y wget git apt-utils git cmake gcc g++ gfortran python3-pip swig clang-tidy emacs-nox valgrind fonts-cmu libpetsc-complex-dev libslepc-complex3.19-dev libopenblas-dev libfltk1.3-dev libfreetype6-dev libgl1-mesa-dev libxi-dev libxmu-dev mesa-common-dev tcl-dev tk-dev libhdf5-dev libcgns-dev libxft-dev libxinerama-dev libxcursor-dev libxfixes-dev libocct-foundation-dev libocct-data-exchange-dev libocct-ocaf-dev libopenmpi-dev libboost-dev cargo clang gcovr ftp libgl1-mesa-dri && apt-get clean
+RUN apt-get update && apt-get install -y \
+apt-utils cargo clang clang-tidy cmake \
+emacs-nox fonts-cmu ftp gcc gcovr \
+git g++ gfortran libboost-dev libcgns-dev \
+libfltk1.3-dev libfreetype6-dev libgl1-mesa-dev libgl1-mesa-dri libhdf5-dev \
+libocct-data-exchange-dev libocct-foundation-dev libocct-ocaf-dev libopenblas-dev libopenmpi-dev \
+libpetsc-complex-dev libxfixes-dev libxcursor-dev libxft-dev libxi-dev \
+libxinerama-dev libxmu-dev libslepc-complex3.19-dev mesa-common-dev python3-pip \
+swig tcl-dev tk-dev valgrind wget \
+&& apt-get clean
 
 # Install miniconda
 RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
-    bash ~/miniconda.sh -b -p /opt/miniconda && \
-    rm ~/miniconda.sh
+bash ~/miniconda.sh -b -p /opt/miniconda && rm ~/miniconda.sh
 ENV PATH="/opt/miniconda/bin:$PATH"
 
 # Create a conda environment
 RUN conda create -n hfe-essentials python=3.12
 SHELL ["conda", "run", "-n", "hfe-essentials", "/bin/bash", "-c"]
 # Copy hfe requirements.txt and install requirements
 COPY ./requirements.txt .
-RUN pip install -r requirements.txt
+RUN pip install --no-cache-dir -r requirements.txt
 RUN pip install -U scikit-image
 RUN pip install imutils
 
-# Install the meshing package
-RUN git clone https://${GITHUB_USERNAME}:${GITHUB_TOKEN}@github.com/artorg-unibe-ch/spline_mesher.git ./pyhexspline/spline_mesher
-WORKDIR ./pyhexspline/spline_mesher
-RUN pip install -e .
+# Set GitHub username and personal access token
+ARG GITHUB_USERNAME
+ARG GITHUB_TOKEN
+ARG USER_UID=1000
+ARG USER_GID=1000
+
+# Install the meshing package # TODO: reactivate when github action is cloning from public repo
+# RUN git clone https://${GITHUB_USERNAME}:${GITHUB_TOKEN}@github.com/artorg-unibe-ch/spline_mesher.git ./pyhexspline/spline_mesher
+# WORKDIR ./pyhexspline/spline_mesher
+# RUN pip install -e .
 
 # Change ownership of the conda environment to the hfe user
 RUN useradd -ms /bin/bash hfe
@@ -43,6 +51,7 @@ ENV PATH="/opt/cargo/bin:${PATH}"
 
 # conda init, source .bashrc, conda activate
 RUN conda init bash
+RUN echo "conda activate hfe-essentials" >> ~/.bashrc
 RUN echo "source ~/.bashrc" >> ~/.bash_profile
-RUN echo "conda activate hfe-essentials" >> ~/.bash_profile
-CMD ["/bin/bash", "-c", "source ~/.bashrc && conda activate hfe-essentials && exec /bin/bash"]
+
+# https://pythonspeed.com/articles/activate-conda-dockerfile/

README.md

@@ -33,5 +33,9 @@ This will start a Docker container with the built image and open an interactive
 Once you're inside the Docker container, you can run the project. The exact command depends on how your project is structured, but it will generally look something like this:
 
 ```sh
+conda init
+source .bashrc
+conda activate hfe-essentials
+cd 02_CODE
 python src/pipeline_runner.py
 ```