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[DATALAD RUNCMD] Recompute analysis results in dockerized environment
The creation of a containerized environment for the analysis became necessary, because 3+ years after the "final" results have been computed originally, it is getting difficult to recreate a matching computational environment. Even with pinned versions of essential software dependencies, issues of incompatibilities with modern Python versions slowly arise. The container setup used for this recomputation is the result of a detailed exploration on the effect of software versions and deployment methods. A reports is provided at #20 Importantly, the employed setup is NOT capable of yielded exactly identical results. While all statistical scores reported in the paper remain indeed identical, there is a visually small change to one histogram panel in Fig 4. The change is illustrated at #20 (comment) Given the overall state of reproducibility, and the anticipated longevity of the containerized computation, we decided that this small difference with respect to the journal publication is tolerable. This changeset support a DataLad-based re-execution (for verification): ``` datalad rerun <commitsha> ``` After this changeset, a complete manuscript can be compiled, also via DataLad via a: ``` datalad containers-run -n docker-make main.pdf ``` By default this uses the local Python installation via `python` to orchestrate Docker. If python is available via a different name, overide, for example, via: ``` datalad -c datalad.run.subsitutions.python=python3 rerun <commitsha> ``` Closes #20 === Do not change lines below === { "chain": [], "cmd": "{python} -m datalad_container.adapters.docker run container/image sh -c \"mkdir /tmp/dockertmp; HOME=/tmp/dockertmp make -f Docker-Makefile clean results_def.tex && rm -rf /tmp/dockertmp\"", "dsid": "c5a79271-7d24-42aa-a0cf-38d84fd15eaa", "exit": 0, "extra_inputs": [ "container/image" ], "inputs": [ "remodnav/remodnav/tests/data/anderson_etal", "data/studyforrest-data-eyemovementlabels/sub-*/*.tsv", "data/raw_eyegaze/sub-*/ses-movie/func/*_recording-eyegaze_physio.tsv.gz", "data/raw_eyegaze/sub-*/beh/*_recording-eyegaze_physio.tsv.gz" ], "outputs": [ "img", "results_def.tex" ], "pwd": "." } ^^^ Do not change lines above ^^^
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