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Module Packaging: Manual Test Checklist

Purpose

This checklist verifies the change that made aop_wiki_cli an installable module (issue #5). Before that change the tool ran only from a clone with the working directory set to the repo root; now it installs from a Git URL, exposes an aop-wiki-cli command, and resolves every input, output, cache and log path against a configurable data directory.

Run it after any change that touches the package layout, the entry point, or src/aop_wiki_cli/paths.py. Steps 1 and 2 run from the clone; steps 3 through 5 confirm the installed tool works from anywhere.

The unit tests (uv run pytest) do not cover any of this — they exercise search functions, not packaging — so this checklist is the only thing standing between a layout change and a broken install.

1. From the clone (the development path still works)

cd ~/Developer/aop_wiki_cli
uv sync
uv run pytest
uv run aop-wiki-cli --help          # should list all 8 commands
uv run python -m aop_wiki_cli --help

Expected: the test suite passes, and both invocations print the same command list.

2. No bare relative paths remain

grep -rn --include="*.py" -E "'(outputs|inputs|logs|xml_inputs)/|\"(outputs|inputs|logs|xml_inputs)/" src/

Expected: no output. Any hit is a path that would resolve against the caller's working directory instead of the data directory, which is exactly what the packaging change removed.

3. Install it as a tool

uvx --from against the local checkout is the same code path as the Git URL, so it can be checked before pushing.

uvx --from "$PWD" aop-wiki-cli --help     # no install, like uvx --from git+...
uv tool install --force "$PWD"            # puts aop-wiki-cli on PATH
aop-wiki-cli --help

Once the branch is on main, the published form is:

uvx --from git+https://github.com/gingin77/aop_wiki_cli aop-wiki-cli --help
uv tool install git+https://github.com/gingin77/aop_wiki_cli

Note: if aop-wiki-cli is not found after the install, run uv tool update-shell and open a new shell.

4. Run every command from a directory that is not the repo

This is the real test: the commands must find their own configs, workbook and curated inputs without a clone anywhere in sight, and must write only under the data directory.

mkdir -p /tmp/aop-test && cd /tmp/aop-test

# Optional: reuse the XML you already have instead of a 49MB download.
# The filename is keyed to today's date.
mkdir -p xml_inputs
cp ~/Developer/aop_wiki_cli/xml_inputs/aop-wiki-xml-2026-08-06 \
   xml_inputs/aop-wiki-xml-$(date +%Y-%m-%d)

aop-wiki-cli collect-event-integration-rankings
aop-wiki-cli collect-ker-analytics
aop-wiki-cli find-kers-for-events --ke-ids 1346 --limit 5
aop-wiki-cli search-kers-for-concordance-text
aop-wiki-cli harmonize-ker-evidence
aop-wiki-cli search-with-config methods_nams
aop-wiki-cli search-with-config lung_and_immune_aops   # exercises the entities_and_fields path
aop-wiki-cli collect-harmonized-seizure-aops           # uses the shipped workbook + curated files

echo '{"a": {"input_term": "x", "matched_term": "y", "match_score": 0.95}}' > m.json
aop-wiki-cli manually-review-matches m.json --threshold 0.5

find . -type d -maxdepth 2   # outputs/, xml_inputs/, logs/ all under /tmp/aop-test

Expected: all eight commands complete, and nothing is written outside /tmp/aop-test.

Note: collect-harmonized-seizure-aops runs without prompting because the curated files ship in the wheel. Add --skip-curated to confirm the two interactive review stages still work.

5. Data-directory precedence

The data directory is chosen in this order: --data-dir, then $AOP_WIKI_CLI_DATA_DIR, then the current directory.

cd /tmp/aop-test
aop-wiki-cli --data-dir /tmp/aop-alt collect-event-integration-rankings
ls /tmp/aop-alt                      # outputs/, logs/, xml_inputs/ land here instead

AOP_WIKI_CLI_DATA_DIR=/tmp/aop-env aop-wiki-cli collect-ker-analytics
ls /tmp/aop-env

Expected: each run writes under the directory it was given, not under /tmp/aop-test.

Cleanup

uv tool uninstall aop-wiki-cli
rm -rf /tmp/aop-test /tmp/aop-alt /tmp/aop-env

Broader coverage

bash test_cli_integration.sh from the clone drives the same commands through the console script and honors AOP_WIKI_CLI_DATA_DIR. It is slower than this checklist because it forces a couple of cache refreshes, but it also checks the shape of the search output JSON.