Ensure quality checking is run by `make test`

[matentzn]

Too many quality checks are not being run by GitHub actions.. See https://github.com/obophenotype/uberon/issues/1968

Need to re-instate.

[matentzn]

Right now very few checks are being run compared to the original Uberon QC pipeline (which can run because of resource limitations). We need to identify a minimum number of critical tests to be run.

• [X] We just re-introduced cycle checking on basic, for example

These make goals are being run for now:

• `odkversion'.
• `sparql_test'.
• `reports/uberon-edit.obo-obo-report.tsv'. (no fail setting!)
• `tmp/GO.xrf_abbs'.
• `reports/uberon-edit.obo-gocheck'.
• `reports/uberon-edit.obo-iconv'.
• `bridge/uberon-bridge-to-bfo.owl'.
• `tmp/unreasoned.owl'.
• `tmp/materialized.owl'.
• `ext.owl'.
• `basic.owl'.
• `reports/basic-allcycles'.

[github-actions[bot]]

This issue has not seen any activity in the past 6 months; it will be closed automatically in one year from now if no action is taken.

[matentzn]

Needs to be done by the next master of Uberon pipeline.. Still important.

[github-actions[bot]]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[uberon]

This is important let’s keep open

On Sun, Feb 12, 2023 at 3:20 AM github-actions[bot] < @.***> wrote:

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/1970#issuecomment-1426924249, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGZRCGHX6QUWYDJPRXRRWTWXBCHBANCNFSM5AZTC7PQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[github-actions[bot]]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[gouttegd]

FYI, since the overhaul of the custom Makefile (#3028), it’s very easy to see and change the list of tests that are being run by each command.

All test suites are defined near the top of the custom Makefile, in the “TESTS/QC” section:

# ----------------------------------------
# TESTS/QC
# ----------------------------------------
# This section defines the composition of the test suites (i.e., which
# checks are performed). The checks themselves are defined elsewhere in
# this Makefile (mostly in the REPORTS section further below).

# This target is invoked as part of the automated CI workflow.
# To include a specific check/report in the CI workflow, add it
# to the pre-requisites here.
test: $(REPORTDIR)/uberon-basic-allcycles \
	$(REPORTDIR)/bfo-check.txt \
	$(REPORTDIR)/taxon-constraint-check.txt \
	$(REPORTDIR)/uberon-edit-xp-check \
	obocheck \
	test_obo_serialisation \
	test_obsolete \
	test_owlaxioms

# The other targets are manually triggered.
# 'checks' is a subset of 'uberon-qc'.
checks: $(REPORTDIR)/bfo-check.txt \
	$(REPORTDIR)/uberon-edit-obscheck.txt \
	$(REPORTDIR)/uberon-edit-xp-check \
	$(REPORTDIR)/uberon-obscheck.txt \
	$(REPORTDIR)/uberon-orphans \
	$(REPORTDIR)/uberon.obo-OWL-check

uberon-qc: checks \
	quick-bridge-checks \
	bridge-checks \
	extra-full-bridge-checks \
	$(REPORTDIR)/uberon-basic-allcycles \
	$(REPORTDIR)/basic-orphans \
	$(REPORTDIR)/composite-metazoan-dv.txt \
	$(REPORTDIR)/taxon-constraint-check.txt \
	$(REPORTDIR)/uberon-dv.txt \
	$(REPORTDIR)/uberon-orphans \
	$(REPORTDIR)/stages
	cat $(REPORTDIR)/uberon-orphans \
		$(REPORTDIR)/uberon-edit-obscheck.txt \
		$(REPORTDIR)/uberon-edit-xp-check \
		$(REPORTDIR)/uberon-orphans \
		$(REPORTDIR)/uberon-dv.txt \
		$(REPORTDIR)/composite-metazoan-dv.txt

quick-qc: $(REPORTDIR)/uberon-edit-obscheck.txt
	cat $(REPORTDIR)/uberon-edit-obscheck.txt

As explained in the comments, the test target is the one invoked by the Github Action-based CI. If more tests should always be run automatically as part of the GA-based CI, one simply needs to add them to that target.