Add test_godag_ecs() per #292 (#293)

* Add test_godag_ecs() per #292

* upgrade versions in build.yml

* Add test_get_godag.py in test list

.github/workflows/build.yml

@@ -8,14 +8,14 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.7", "3.10"]
+        os: [ubuntu-latest, macos-13]
+        python-version: ["3.8", "3.10"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

makefile

@@ -330,7 +330,6 @@ dnld_anno_uniprot:
 #    tests/test_nbt3102.py \
 #    tests/test_optional_fields.py \
 #    tests/test_dnlds.py \
-#    tests/test_get_godag.py \
 #    tests/test_gpad_dnld.py \
 #
 #    tests/test_plot_get_parents.py \
@@ -347,50 +346,51 @@ dnld_anno_uniprot:
 #    tests/test_quickgo_xml.py \
 
 NOSETESTS := \
-    tests/test_study_zero.py \
-    tests/test_annotations_gaf.py::test_gaf_read_fb \
-	tests/test_parents_ancestors.py \
-    tests/test_rpt_gene2go_evidencecodes.py \
-    tests/test_sorter_sections.py \
-    tests/test_sorter_desc2nts.py \
-    tests/test_compare_gos.py \
-    tests/test_wr_sections_txt.py \
-    tests/test_altid_gosubdag.py \
-    tests/test_dcnt_r01.py \
-    tests/test_grprobj.py \
-    tests/test_grpr_get_sections_2d.py \
-    tests/test_sorter.py \
-    tests/test_gosubdag_relationships.py \
-    tests/test_go_depth1.py \
-    tests/test_i92_relationship_parentchild.py \
-    tests/test_i96_goea_ncbi.py \
-    tests/test_gosearch_emptydict.py \
-    tests/test_david_nts.py \
-    tests/test_get_parents.py \
-    tests/test_get_children.py \
-    tests/test_optional_attributes.py \
-    tests/test_genes_cell_cycle.py \
-    tests/test_semantic_similarity.py \
-    tests/test_goea_errors.py \
-    tests/test_ncbi_entrez_annotations.py \
-    tests/test_wr_tbl_subset.py \
-    tests/test_goea_local.py \
-    tests/test_write_hier.py \
+	tests/test_altid_godag.py \
+	tests/test_altid_gosubdag.py \
+	tests/test_annotations_gaf.py::test_gaf_read_fb \
 	tests/test_cli_write_hierarchy.py \
-    tests/test_go_print.py \
-    tests/test_read_gaf_allow_nd.py \
-    tests/test_write_summary_cnts.py \
-    tests/test_pvalcalc.py \
-    tests/test_altid_godag.py \
-    tests/test_combine_nt_lists.py \
-    tests/test_get_paths.py \
-    tests/test_get_unique_fields.py \
-    tests/test_go_draw.py \
-    tests/test_goea_statsmodels.py \
-    tests/test_goea_rpt_bonferroni.py \
-    tests/test_wr_py_goea_results.py \
-    tests/test_mapslim.py \
-	tests/test_multiple_testing.py
+	tests/test_combine_nt_lists.py \
+	tests/test_compare_gos.py \
+	tests/test_david_nts.py \
+	tests/test_dcnt_r01.py \
+	tests/test_genes_cell_cycle.py \
+	tests/test_get_children.py \
+	tests/test_get_godag.py \
+	tests/test_get_parents.py \
+	tests/test_get_paths.py \
+	tests/test_get_unique_fields.py \
+	tests/test_go_depth1.py \
+	tests/test_go_draw.py \
+	tests/test_go_print.py \
+	tests/test_goea_errors.py \
+	tests/test_goea_local.py \
+	tests/test_goea_rpt_bonferroni.py \
+	tests/test_goea_statsmodels.py \
+	tests/test_gosearch_emptydict.py \
+	tests/test_gosubdag_relationships.py \
+	tests/test_grpr_get_sections_2d.py \
+	tests/test_grprobj.py \
+	tests/test_i92_relationship_parentchild.py \
+	tests/test_i96_goea_ncbi.py \
+	tests/test_mapslim.py \
+	tests/test_multiple_testing.py \
+	tests/test_ncbi_entrez_annotations.py \
+	tests/test_optional_attributes.py \
+	tests/test_parents_ancestors.py \
+	tests/test_pvalcalc.py \
+	tests/test_read_gaf_allow_nd.py \
+	tests/test_rpt_gene2go_evidencecodes.py \
+	tests/test_semantic_similarity.py \
+	tests/test_sorter_desc2nts.py \
+	tests/test_sorter_sections.py \
+	tests/test_sorter.py \
+	tests/test_study_zero.py \
+	tests/test_wr_py_goea_results.py \
+	tests/test_wr_sections_txt.py \
+	tests/test_wr_tbl_subset.py \
+	tests/test_write_hier.py \
+	tests/test_write_summary_cnts.py
 
 # Run all tests. If you are submitting a pull request, all tests must pass.
 update:

tests/test_get_godag.py

@@ -5,14 +5,29 @@
 import sys
 from goatools.base import get_godag
 
+
 def test_godag(prt=sys.stdout):
-    """Test downloading GO DAG."""
+    """
+    Test downloading GO DAG.
+    """
     cwd = os.getcwd()
-    for fin_obo in ['go-basic.obo', 'goslim_generic.obo']:
+    for fin_obo in ["go-basic.obo", "goslim_generic.obo"]:
         fin_full = os.path.join(cwd, fin_obo)
         os.system("rm -f {OBO}".format(OBO=fin_obo))
-        godag = get_godag(fin_full, prt, loading_bar=None) # Get GODag object
+        godag = get_godag(fin_full, prt, loading_bar=None)  # Get GODag object
         assert godag, "GO-DAG({OBO}) NOT PROPERLY LOADED".format(OBO=fin_obo)
 
-if __name__ == '__main__':
+
+def test_godag_ecs():
+    """
+    Test downloading GO DAG and extract ECs.
+    """
+    godag = get_godag("go-basic.obo", optional_attrs="xref")
+    go = godag["GO:0000010"]
+    ecs = [x for x in go.xref if x.startswith("EC:")]
+    assert "EC:2.5.1.30" in ecs
+
+
+if __name__ == "__main__":
     test_godag()
+    test_godag_ecs()