code coverage test

bjornwallner · Mar 22, 2024 · 2e298d3 · 2e298d3
1 parent 0718689
commit 2e298d3
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Showing 2 changed files with 21 additions and 11 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -2,6 +2,10 @@ name: CI
 
 on: [push, pull_request, workflow_dispatch]
 
+env:
+  MIN_COVERAGE_REQUIRED: 50
+
+
 jobs:
   test:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
@@ -16,7 +20,11 @@ jobs:
       - name: Test pipeline output
         run: |
           python -m pip install .
+          python -m pip install coverage
           bash ./run_test.sh
+      - name: Coverage
+        run: |
+          test $(coverage report | grep TOTAL | awk '{ print $4 }' | tr -d "%") -ge $MIN_COVERAGE_REQUIRED
 
   test_oldbio:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
@@ -31,5 +39,6 @@ jobs:
       - name: Test pipeline output
         run: |
           python -m pip install biopython==1.79
+          python -m pip install coverage
           python -m pip install .
           bash ./run_test.sh
diff --git a/run_test.sh b/run_test.sh
@@ -2,18 +2,19 @@
 set -euo pipefail
 
 # Test that cython version behaves the same as nocython
-DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
-python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
-DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
-python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
+coverage run -a -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
+coverage run -a src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
+coverage run -a -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
+coverage run -a src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
 # Multiple interfaces
-DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short
+coverage run -a -m DockQ.DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short
 # Test on structures with slightly different sequences
-DockQ examples/model.pdb examples/native.pdb --allowed_mismatches 1
+coverage run -a -m DockQ.DockQ examples/model.pdb examples/native.pdb --allowed_mismatches 1
 # Test various mapping strategies
-DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping AB*:BA*
-DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping :ABC
-DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping ABCDEFGH:BADCFEHG
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping AB*:BA*
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping :ABC
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping ABCDEFGH:BADCFEHG
 # Test that cif parsing behaves same as pdb parsing
-DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE
-DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE
+coverage report