From 05cf34032f44c61b1ef204ad65bb1ac9a783222c Mon Sep 17 00:00:00 2001
From: Florez Ospina Juan Felipe <juan.florez-ospina@psi.ch>
Date: Wed, 12 Mar 2025 16:15:49 +0100
Subject: [PATCH] WIP: Add dockerignore and Dockerfile. I have built the Docker
 image and seems to be working fine but haven't tested all aspects of the
 applicaton

---
 .dockerignore |  8 ++++++++
 Dockerfile    | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)
 create mode 100644 .dockerignore
 create mode 100644 Dockerfile

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..5e8b390
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,8 @@
+data/
+figures/
+pipelines/params/
+envs/
+logs/
+*.pyc
+__pycache__/
+*.h5
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..0e9e2a1
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,35 @@
+# Get additional info about the Dockerfile at https://docs.docker.com/reference/dockerfile/ 
+
+FROM continuumio/miniconda3:latest
+
+# Define the name of the environment
+ARG ENV_NAME=apog_penv
+ENV ENV_NAME=apog_penv
+
+# Set the working directory
+WORKDIR /acsmdc
+
+# Use mamba if available for faster installation
+RUN conda install -y -n base -c conda-forge mamba && \
+    mamba create -y -n $ENV_NAME -c conda-forge -c defaults python=3.11 \
+    jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip && \
+    conda clean --all -y && rm -rf /root/.cache/pip
+
+# Activate the environment and install additional pip packages
+RUN conda run -n $ENV_NAME pip install pybis==1.35 igor2 ipykernel sphinx dash dash-bootstrap-components
+
+# Set the default environment when the container starts
+ENV CONDA_DEFAULT_ENV=$ENV_NAME
+ENV PATH=/opt/conda/envs/$ENV_NAME/bin:$PATH
+
+# Create necessary directories for VOLUME
+RUN mkdir -p /acsmdc/data /acsmdc/figures /acsmdc/pipelines/params
+
+# Copy project files, excluding certain directories (handled via .dockerignore)
+COPY . /
+
+# Define volumes for excluded directories
+VOLUME ["/acsmdc/data", "/acsmdc/figures", "/acsmdc/pipelines/params"]
+
+# Default command: Run Conda shell so Python and Conda are accessible
+CMD ["/bin/bash"]