CLI reference

Every command below is generated directly from the argparse definition in science_adk/cli.py, so this page cannot describe a flag that does not exist.

science-adk --help

Finding the project

Commands operate on the research project found by searching upward from the current directory. Pass --path DIR to point at one explicitly.

Global options

Option	Description
--version	Print the installed version and exit.
--path DIR	Project directory (default: search upward from the cwd).
-h, --help	Show help for any command or subcommand.

Commands at a glance

Command	What it does
science-adk init
science-adk goal
science-adk experiment
science-adk validate
science-adk run
science-adk score
science-adk audit
science-adk report
science-adk campaign
science-adk learn
science-adk tools
science-adk graph
science-adk status

---

science-adk init

science-adk init [-h] [-q QUESTION] [--example NAME] [--force]
                        [directory]

Argument	Description	Required
directory (optional)
-q, --question	The research question
--example NAME	Start from a bundled example: kepler
--force	Overwrite existing files

Example

science-adk init my-research
science-adk init my-kepler --example kepler

science-adk goal

science-adk goal [-h] [--set-question SET_QUESTION] [--metric METRIC]
                        [--target TARGET] [--json]

Argument	Description	Required
--set-question	Set the research question
--metric	Name of the target metric
--target TARGET	Value the metric must reach
--json

Example

science-adk goal
science-adk goal \
  --set-question "Does a GNN embedding predict aqueous solubility better than Morgan fingerprints?" \
  --metric rmse \
  --target 0.8

science-adk experiment

science-adk experiment [-h] {new,list} ...

science-adk experiment new

science-adk experiment new [-h] [--rationale RATIONALE]
                                  [--parent PARENT]
                                  hypothesis

Argument	Description	Required
hypothesis	The testable claim	yes
--rationale	Why this is worth testing
--parent	Experiment whose findings motivated this one

Example

science-adk experiment new \
  "GNN embeddings outperform Morgan fingerprints on ESOL" \
  --rationale "Learned 3D representations should capture solvation geometry that topological fingerprints discard."

science-adk experiment list

science-adk experiment list [-h] [--json]

Argument	Description	Required
--json

Example

science-adk experiment list --json

science-adk validate

science-adk validate [-h] [--json] [experiment]

Argument	Description	Required
experiment (optional)
--json

Example

science-adk validate

science-adk run

science-adk run [-h] [--only ONLY [ONLY ...]] [--reuse [REUSE]] [-q]
                       [experiment]

Argument	Description	Required
experiment (optional)
--only	Run only these nodes and their dependents
--reuse	Reuse unchanged outputs from a previous run (default: latest)
-q, --quiet

Example

science-adk run
science-adk run --reuse          # re-run only what changed
science-adk run --only analyze evaluate

science-adk score

science-adk score [-h] [--run RUN] [--json] [experiment]

Argument	Description	Required
experiment (optional)
--run	Run id (default: latest)
--json

Example

science-adk score --json

science-adk audit

science-adk audit [-h] [--run RUN] --scientific-value 0..1
                         --method-fidelity 0..1 --implementation-quality 0..1
                         --rationale RATIONALE
                         [experiment]

Argument	Description	Required
experiment (optional)
--run	Run id (default: latest)
--scientific-value 0..1		yes
--method-fidelity 0..1		yes
--implementation-quality 0..1		yes
--rationale	Why these ratings	yes

Example

science-adk audit \
  --scientific-value 0.85 \
  --method-fidelity 0.90 \
  --implementation-quality 0.95 \
  --rationale "GNN embedding reaches RMSE 0.72 on held-out ESOL against 0.95 for Morgan fingerprints."

science-adk report

science-adk report [-h] [--run RUN] [experiment]

Argument	Description	Required
experiment (optional)
--run	Run id (default: latest)

Example

science-adk report

science-adk campaign

science-adk campaign [-h]

Example

science-adk campaign

science-adk learn

science-adk learn [-h] [--evidence EVIDENCE] [--experiment EXPERIMENT]
                         [--run RUN]
                         insight

Argument	Description	Required
insight		yes
--evidence	What supports this
--experiment
--run

Example

science-adk learn "GNN embeddings cut solubility RMSE by 24%." \
  --run latest

science-adk tools

science-adk tools [-h] [--json]

Argument	Description	Required
--json

Example

science-adk tools

science-adk graph

science-adk graph [-h] [experiment]

Argument	Description	Required
experiment (optional)

Example

science-adk graph

science-adk status

science-adk status [-h]

Example

science-adk status