prevent package caching in Docker images (#288)

* prevent pip caching

* Doing version bumps to prepare for release of images with new caching setup

* Attempt to keep apt caching to a minimum.

---------

Co-authored-by: James Mathews <[email protected]>

build/apiserver/Dockerfile

@@ -1,6 +1,7 @@
 FROM python:3.11-slim
 ENV DEBIAN_FRONTEND=noninteractive
-RUN apt update && apt install -y gcc libpq-dev curl
+RUN apt update && apt install -y gcc libpq-dev curl && apt-get clean
+ARG PIP_NO_CACHE_DIR=1
 RUN python -m pip install psycopg2==2.9.6
 RUN python -m pip install adiscstudies==0.11.0
 RUN python -m pip install numba==0.57.0

build/build_scripts/development.Dockerfile

@@ -1,5 +1,6 @@
 FROM nadeemlab-development/spt-development-prereqs:latest
 ARG WHEEL_FILENAME
+ARG PIP_NO_CACHE_DIR=1
 COPY pyproject.toml .
 COPY spatialprofilingtoolbox spatialprofilingtoolbox
 RUN python -m build

build/build_scripts/development_prereqs.Dockerfile

@@ -1,35 +1,36 @@
 FROM ubuntu:22.04
-RUN apt update && apt-get install -y apt-transport-https
+RUN apt update && apt-get install -y apt-transport-https && apt-get clean
 ARG DEBIAN_FRONTEND=noninteractive
-RUN apt install software-properties-common -y
+RUN apt install software-properties-common -y && apt-get clean
 RUN add-apt-repository ppa:deadsnakes/ppa
 RUN apt update
-RUN apt-get install -y libpq-dev
-RUN apt install openjdk-11-jdk -y
-RUN apt install xxd -y
-RUN apt install file -y
+RUN apt-get install -y libpq-dev && apt-get clean
+RUN apt install openjdk-11-jdk -y && apt-get clean
+RUN apt install xxd -y && apt-get clean
+RUN apt install file -y && apt-get clean
 WORKDIR /usr/src/app
 ENV PATH="/usr/src/app:$PATH"
 RUN apt install curl -y
 RUN curl -s https://get.nextflow.io | bash; if [[ "$(which nextflow)" == "" ]]; then echo "nextflow not really installed."; exit 1; fi;
-RUN apt install python3.11 -y
-RUN apt install python3.11-dev -y
-RUN apt install python3.11-venv -y
-RUN apt install python3.11-distutils
+RUN apt install python3.11 -y && apt-get clean
+RUN apt install python3.11-dev -y && apt-get clean
+RUN apt install python3.11-venv -y && apt-get clean
+RUN apt install python3.11-distutils && apt-get clean
+ARG PIP_NO_CACHE_DIR=1
 RUN ln -s /usr/bin/python3.11 /usr/bin/python
 RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python
-RUN apt install gcc -y
-RUN apt install postgresql-client -y
-RUN apt-get install -y build-essential libssl-dev libffi-dev
+RUN apt install gcc -y && apt-get clean
+RUN apt install postgresql-client -y && apt-get clean
+RUN apt-get install -y build-essential libssl-dev libffi-dev && apt-get clean
 RUN python -m pip install -U pip
 COPY README.md .
 COPY pyproject.toml.unversioned .
 RUN python -m pip install toml
-RUN apt install libgdal-dev -y
+RUN apt install libgdal-dev -y && apt-get clean
 RUN python -c 'import toml; c = toml.load("pyproject.toml.unversioned"); print("\n".join(c["project"]["dependencies"]))' | python -m pip install -r /dev/stdin
 RUN python -c 'import toml; c = toml.load("pyproject.toml.unversioned"); print("\n".join(c["project"]["optional-dependencies"]["all"]))' | python -m pip install -r /dev/stdin
 RUN python -m pip install build
 RUN python -m pip install twine
-RUN apt install -y bc
+RUN apt install -y bc && apt-get clean
 RUN rm pyproject.toml.unversioned
 CMD bash -c "echo 'available for commands'; while [ 0 -le 1 ]; do sleep 3600; echo 'sleep 3600... keep alive the container for availability for ongoing commands.'; done"

build/db/Dockerfile

@@ -1,13 +1,14 @@
 FROM postgres:16.0-bookworm
 WORKDIR /usr/src/app
 ENV DEBIAN_FRONTEND=noninteractive
-RUN apt update && apt upgrade -y
-RUN apt install python3 -y
-RUN apt install python3-dev -y
-RUN apt install python3-venv -y
-RUN apt install python3-pip -y
-RUN apt install -y libpq-dev
-RUN apt install -y libgdal-dev
+ARG PIP_NO_CACHE_DIR=1
+RUN apt update && apt upgrade -y && apt-get clean
+RUN apt install python3 -y && apt-get clean
+RUN apt install python3-dev -y && apt-get clean
+RUN apt install python3-venv -y && apt-get clean
+RUN apt install python3-pip -y && apt-get clean
+RUN apt install -y libpq-dev && apt-get clean
+RUN apt install -y libgdal-dev && apt-get clean
 RUN python3 -m pip install --break-system-packages psycopg2==2.9.6
 RUN python3 -m pip install --break-system-packages adiscstudies==0.11.0
 RUN python3 -m pip install --break-system-packages numba==0.57.0

build/ondemand/Dockerfile

@@ -1,8 +1,9 @@
 FROM python:3.11-slim
 ENV DEBIAN_FRONTEND=noninteractive
-RUN apt update && apt install -y gcc g++ libpq-dev
+ARG PIP_NO_CACHE_DIR=1
+RUN apt update && apt install -y gcc g++ libpq-dev && apt-get clean
 WORKDIR /usr/src/app
-RUN apt install -y libgdal-dev
+RUN apt install -y libgdal-dev && apt-get clean
 RUN python -m pip install psycopg2==2.9.6
 RUN python -m pip install adiscstudies==0.11.0
 RUN python -m pip install numba==0.57.0

spatialprofilingtoolbox/apiserver/__init__.py

@@ -1,2 +1,2 @@
 """API service"""
-__version__ = '0.12.0'
+__version__ = '0.13.0'

spatialprofilingtoolbox/db/__init__.py

@@ -1,2 +1,2 @@
 """Database-related SPT functionality."""
-__version__ = '0.10.0'
+__version__ = '0.13.0'

spatialprofilingtoolbox/ondemand/__init__.py

@@ -1,2 +1,2 @@
 """The fast cell counts service."""
-__version__ = '0.12.0'
+__version__ = '0.13.0'

version.txt

@@ -1 +1 @@
-0.17.5
+0.17.6