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One open-source package, reproducible-science, with four command-line tools. Freeze a plan before running it, bind every number in a paper to the run that produced it, and check that quoted passages appear in their sources.

pip install reproducible-science
repro init my_experiment
ToolPyPIWhat it does
preregpreregFreeze a plan before running, record what changed after
resultsresults-cliSeal inputs, record outputs, bind claims to runs, verify the chain
citationscitationsCheck that quoted passages resolve in their sources
reproreproducible-scienceVerify every declared value against a hash-pinned artifact

A number in a manuscript names a claim. The claim names a run. The run names its outputs, hashed when they were recorded. The inputs were hashed before the run started.

prereg freeze                         # lock the plan
results seal PREREG.md analysis.py    # hash inputs
results run output.json --run-id exp_001
results claim "ICC = 0.42" --run-id exp_001 --location "Table 2"
repro verify                          # check the whole chain

Every check is deterministic, and what cannot be established is reported as unestablished rather than assumed.