Update supporting files (#712)

Add Ruff cache to the .gitignore file list.
Introduce a .dockerignore file list to prevent copying of non-essential files when building Docker containers.
Add an empty installers folder in repo for developers to store offline installers in when building Docker containers.
Add logic to murfey-server Dockerfile to check for an IMOD installation file before attempting to download it.

Author: tieneupin

.dockerignore

@@ -0,0 +1,12 @@
+# Ignore everything by default
+**
+
+# Whitelist only the files and folders needed for building
+!Dockerfiles/
+!installers/
+!src/
+!pyproject.toml
+!setup.py
+!LICENSE
+!MANIFEST.in
+!README.md

.gitignore

@@ -106,3 +106,6 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# ruff
+.ruff_cache/

Dockerfiles/murfey-server

@@ -17,6 +17,10 @@ RUN apt-get update && \
 
 # Build Murfey and IMOD in a branch image
 FROM base as build
+
+# Set up build argumentss for this stage
+ARG IMOD_INSTALLER=imod_5.1.9_RHEL8-64_CUDA12.0.sh
+
 COPY ./ /python-murfey/
 RUN apt-get update && \
     apt-get upgrade -y && \
@@ -35,10 +39,13 @@ RUN apt-get update && \
         psycopg2-binary \
         && \
     /venv/bin/python -m pip install /python-murfey[server] && \
-    curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.9_RHEL8-64_CUDA12.0.sh > imod_5.1.9_RHEL8-64_CUDA12.0.sh && \
-    chmod +x imod_5.1.9_RHEL8-64_CUDA12.0.sh && \
+    if [ ! -f /python-murfey/installers/${IMOD_INSTALLER} ]; then \
+        echo "IMOD installer not found; downloading..."; \
+        curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/${IMOD_INSTALLER} > /python-murfey/installers/${IMOD_INSTALLER}; \
+    fi && \
+    chmod +x /python-murfey/installers/${IMOD_INSTALLER} && \
     mkdir imod && \
-    ./imod_5.1.9_RHEL8-64_CUDA12.0.sh -dir imod -skip -y
+    /python-murfey/installers/${IMOD_INSTALLER} -dir imod -skip -y
 
 
 # Transfer completed builds to base image

installers/README.md

@@ -0,0 +1,2 @@
+This is placeholder folder in which installation files for the Docker containers can be placed.
+The Dockerfiles will first check to see if the desired file is located here before attempting to download it.