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Add docker container recipe and makefile for reproducing the analysis #23

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mih merged 1 commit from docker into master 2023-10-11 16:55:58 +00:00
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23
Docker-Makefile Normal file
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# use `chronic` to make output look neater, if available
CHRONIC=$(shell which chronic || echo '' )
PYTHON=python3
all: main.pdf
main.pdf: main.tex results_def.tex references.bib
$(MAKE) main.pdf
# the stats-script outputs all scores and figures
results_def.tex: code/mk_figuresnstats.py
@echo "# Ensure REMODNAV installation"
@$(CHRONIC) $(PYTHON) -m pip install --break-system-packages -e remodnav
@rm -f $@
@REMODNAV_RESULTS=$@ $(PYTHON) code/mk_figuresnstats.py -s -f -r -m
clean:
$(MAKE) clean
rm -rf .cache .config .local .texlive*
.PHONY: clean

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container/Dockerfile Normal file
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FROM debian:bookworm-slim
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update -qq -y --allow-releaseinfo-change && \
# basic tooling we need for building/installing
apt-get install -q --no-install-recommends -y make && \
# for compiling custom python package installs
apt-get install -q --no-install-recommends -y build-essential python3-dev && \
# any python package we do NOT need to compile
apt-get install -q --no-install-recommends -y python3-virtualenv python3-wheel python3-scipy python3-sklearn python3-statsmodels python3-pyparsing python3-pil python3-pip && \
# now python packages that we need specific versions of
# we need the following packages pinned
# - matplotlib for a particular SVG file content (structure)
# - pandas as the last per v2 release for an API incompatibility that with 2x
# - seaborn for minor changes in figure composition in later versions
# - and numpy...the version does not matter, but it has to be different from
# the Debian-provided one, such that pip will compile it
# full and long story at
# https://github.com/psychoinformatics-de/paper-remodnav/issues/20
python3 -m pip install --break-system-packages numpy==1.24.3 pandas==1.5.3 seaborn==0.10.1 matplotlib==3.4.3 && \
# now the pieces we need to build the PDF
apt-get install -q --no-install-recommends -y inkscape latexmk texlive-latex-extra && \
# trim the image size
rm -rf /root/.local /root/.cache /var/lib/apt/lists/deb.debian.org* ; \
apt-get purge -y build-essential ; \
apt-get autoremove -y ; \
apt-get clean