Skip to content

Commit

Permalink
Fix Testing Action
Browse files Browse the repository at this point in the history
Fixes the GitHub Action that automatically tests the module. Also fixes a "bug" in the testing suite introduced by errors in EFO
  • Loading branch information
paynejason committed Mar 11, 2024
1 parent ddf0af8 commit 6c4ff68
Show file tree
Hide file tree
Showing 2 changed files with 4 additions and 3 deletions.
3 changes: 2 additions & 1 deletion .github/workflows/python-app.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,14 +23,15 @@ jobs:
uses: actions/setup-python@v3
with:
python-version: "3.10"
cache: 'pip'
- name: show python path
run: |
python -c "import sys; print('\n'.join(sys.path))"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements.txt
pip install flake8 pytest
pip install flake8 pytest wheel
- name: Check package location
run: |
pip show pandas
Expand Down
4 changes: 2 additions & 2 deletions test/simple_tests.py
Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,8 @@ def test_mapping_to_cached_ontology_using_syntactic_mapper(self):
def test_mapping_using_ontology_acronym(self):
# Test mapping a list of terms by specifying the target ontology acronym, which gets resolved by bioregistry
print(
"Test mapping a list of terms by specifying the ontology acronym, which gets resolved by bioregistry")
df2 = text2term.map_terms(["contains", "asthma"], "MONDO")
"Test mapping a list of terms to EFO by specifying the ontology acronym, which gets resolved by bioregistry")
df2 = text2term.map_terms(["contains", "asthma"], "MONDO", term_type=OntologyTermType.CLASS)
print(f"{df2}\n")
assert df2.size > 0

Expand Down

0 comments on commit 6c4ff68

Please sign in to comment.