move includes to setup.cfg

.github/workflows/main.yml

@@ -28,22 +28,4 @@ jobs:
           bash run_test.sh
       - name: Coverage
         run: |
-          coverage report
           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
-  #  runs-on: ubuntu-latest
-  #  timeout-minutes: 10
-  #  defaults:
-  #    run:
-  #      shell: bash -l {0}
-#
-#    steps:
-#      - uses: actions/checkout@v3
-#      - 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

run_test.sh

@@ -1,39 +1,37 @@
 #!/bin/bash
 set -euo pipefail
 
-
-src=$(find $(dirname $(which DockQ))/../ -name "DockQ.py"  -exec dirname {} \;)
-echo $src
+rm -f .coverage
 # Test that cython version behaves the same as nocython
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+coverage run -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
 diff test testdata/1A2K.dockq
-coverage run -a --source=$src $src/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
 diff test testdata/1A2K.dockq
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
+coverage run -a -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
 diff test testdata/1A2K.dockq
-coverage run -a --source=$src $src/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
+python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
 diff test testdata/1A2K.dockq
 
 # Multiple interfaces
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short > test
+coverage run -a -m DockQ.DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short > test
 diff test testdata/dimer_dimer.dockq
 
 # Test on structures with slightly different sequences
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/model.pdb examples/native.pdb --allowed_mismatches 1 > test
+coverage run -a -m DockQ.DockQ examples/model.pdb examples/native.pdb --allowed_mismatches 1 > test
 diff test testdata/model.dockq
 
 # Test various mapping strategies
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping AB*:BA* > test
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping AB*:BA* > test
 diff test testdata/1EXB_AB.BA.dockq
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping :ABC > test
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping :ABC > test
 diff test testdata/1EXB_.ABC.dockq
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping ABCDEFGH:BADCFEHG > test
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping ABCDEFGH:BADCFEHG > test
 diff test testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
 
 # Test that cif parsing behaves same as pdb parsing
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE > test
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE > test
 diff test testdata/1EXB_DH.AE.dockq
-coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE > test
+coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE > test
 diff test testdata/1EXB_DH.AE_cif.dockq
 
 coverage report

setup.cfg

@@ -21,3 +21,7 @@ where=src
 console_scripts =
     DockQ = DockQ.__main__:main
 
+[coverage:run]
+include =
+    */DockQ/*
+