Move more tests from the original repository.

The original ontology-development-kit repository has two other types of
configuration tests:

* a handful of tests that do not use a configuration file at all;
* a test based on an Go-inspired example configuration.

We move those tests to the present repository, as they are all tests of
the seeding system and workflows.

Author: gouttegd

examples/chr/project.yaml

@@ -0,0 +1,11 @@
+id: chr
+title: monochrom
+github_org: monarch-initiative
+repo: monochrom
+contact: mbrush
+edit_format: ttl
+import_group:
+  ids:
+    - ro
+    - so
+  

examples/go-mini/go-edit.obo

@@ -0,0 +1,20 @@
+id: go
+title: "Gene Ontology (mini example)"
+github_org: geneontology
+repo: go
+#report_fail_on: ERROR
+report_fail_on: None
+export_formats:
+  - owl
+  - obo
+  - json
+import_group:
+  products:
+    - id: ro
+subset_group:
+  products:
+    - id: goslim_metagenomics
+    - id: goslim_virus
+
+
+  

examples/go-mini/project.yaml

@@ -0,0 +1,37 @@
+id: go
+title: Gene Ontology
+github_org: geneontology
+repo: envo
+report_fail_on: ERROR
+export_formats:
+  - owl
+  - obo
+  - json
+import_group:
+  products:
+    - id: go-bridge
+      subdir: extensions
+      native: True
+    - id: go-gcis
+      subdir: extensions
+      native: True
+    - id: x-disjoint
+      native: True
+    - id: go-taxon-groupings
+      native: True
+    - id: caro
+    - id: chebi
+    - id: cl
+    - id: fao
+    - id: oba
+    - id: pato
+    - id: pr
+    - id: ro
+    - id: so
+    - id: uberon
+subset_group:
+  ids:
+    - goslim_agr
+
+
+  

examples/go/project.yaml

@@ -0,0 +1,3 @@
+## illustrates the bare minimum config:
+## ontology ID
+id: minimal

examples/minimal/project.yaml

@@ -0,0 +1,9 @@
+id: triffo
+title: Triffid Behavior ontology
+github_org: cmungall
+repo: triffo
+import_group:
+  products:
+    - id: ro
+    - id: bfo
+    - id: pato

examples/triffo/project.yaml

@@ -0,0 +1,10 @@
+id: upa
+title: Unipathway
+github_org: geneontology
+repo: unipathway
+contact: amorgat
+edit_format: obo
+import_group:
+  ids:
+    - ro
+  

examples/unipathway/project.yaml

@@ -42,6 +42,8 @@ build-backend = "uv_build"
 module-name = "incatools.odk"
 source-include = [
     "NEWS",
+    "examples/**",
+    "tests/**",
 ]
 
 [dependency-groups]

pyproject.toml

@@ -8,6 +8,10 @@ rm -rf testenv status.txt
 GITNAME=$(git config --get user.name)
 GITEMAIL=$(git config --get user.email)
 
+run_odk_seed() {
+    uv --project .. run odk seed --gitname "$GITNAME" --gitemail "$GITEMAIL" "$@"
+}
+
 # Create native ODK environment for testing
 mkdir testenv
 uv --project .. run odk install testenv
@@ -16,8 +20,18 @@ uv --project .. run odk install testenv
 # Seed and build all the test configurations
 for t in configs/*.yaml ; do
     echo -n "$t... " >> status.txt
-    uv --project .. run odk seed --gitname "$GITNAME" --gitemail "$GITEMAIL" -c -C $t
+    run_odk_seed -c -C $t
     echo DONE >> status.txt
 done
 
+# Additional tests without an explicit config file
+run_odk_seed -c -t my-ontology1 my-ont
+run_odk_seed -c -d pato -d ro -t my-ontology2 my-ont
+run_odk_seed -c -d pato -d cl -d ro -t my-ontology3 my-ont
+
+# Additional "GO mini" test
+run_odk_seed -c -D target/go-mini \
+             -C ../examples/go-mini/project.yaml \
+             -s ../examples/go-mini/go-edit.obo
+
 rm -rf target testenv status.txt