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

Merged

mih merged 1 commit from docker into master

2023-10-11 16:55:58 +00:00

mih commented

2023-10-11 15:17:03 +00:00

(Migrated from github.com)

Recently the original virtualenv-baseed approach started to fall apart, because mutual incompatibilities between the dependencies (some pinned at old versions) increased.

This changeset provides a container recipe to generate a modern (or most modern, given todays possibilities) environment to still reproduce the analysis.

The container image can be built with

docker build -t remodnav:latest container

And the manuscript can be generated with

docker run -v $PWD:/tmp -w /tmp --rm --interactive --tty \
  -u $(id -u):$(id -g) -e HOME=/tmp \
  remodnav:latest \
   make -f Docker-Makefile main.pdf

This does not reproduce everything exactly. There is a small (I'd say insignificant) change in one panel of a Fig 4. The full backstory and analysis of the cause is in
https://github.com/psychoinformatics-de/paper-remodnav/issues/20. However, besides that all reported statistical scores and performance measures reported in the paper remain identical.

Not that execution inside the container requires all inputs to be provisioned before. Here is the specification

remodnav/remodnav/tests/data/anderson_etal
remodnav/remodnav/tests/data/studyforrest
data/studyforrest-data-eyemovementlabels/*/*.tsv
data/raw_eyegaze/sub-*/ses-movie/func/*_recording-eyegaze_physio.tsv.gz
data/raw_eyegaze/sub-*/beh/*_recording-eyegaze_physio.tsv.gz

This will again be automated in a future changeset, based on a container-run provenance record.

Recently the original virtualenv-baseed approach started to fall apart, because mutual incompatibilities between the dependencies (some pinned at old versions) increased. This changeset provides a container recipe to generate a modern (or most modern, given todays possibilities) environment to still reproduce the analysis. The container image can be built with ``` docker build -t remodnav:latest container ``` And the manuscript can be generated with ``` docker run -v $PWD:/tmp -w /tmp --rm --interactive --tty \ -u $(id -u):$(id -g) -e HOME=/tmp \ remodnav:latest \ make -f Docker-Makefile main.pdf ``` This does not reproduce everything exactly. There is a small (I'd say insignificant) change in one panel of a Fig 4. The full backstory and analysis of the cause is in https://github.com/psychoinformatics-de/paper-remodnav/issues/20. However, besides that **all** reported statistical scores and performance measures reported in the paper remain identical. Not that execution inside the container requires all inputs to be provisioned before. Here is the specification ``` remodnav/remodnav/tests/data/anderson_etal remodnav/remodnav/tests/data/studyforrest data/studyforrest-data-eyemovementlabels/*/*.tsv data/raw_eyegaze/sub-*/ses-movie/func/*_recording-eyegaze_physio.tsv.gz data/raw_eyegaze/sub-*/beh/*_recording-eyegaze_physio.tsv.gz ``` This will again be automated in a future changeset, based on a container-run provenance record.