Merged

.github/workflows/main.yml

@@ -3,7 +3,7 @@ name: CI
 on: [push, pull_request, workflow_dispatch]
 
 env:
-  MIN_COVERAGE_REQUIRED: 50
+  MIN_COVERAGE_REQUIRED: 35
 
 
 jobs:
@@ -28,21 +28,5 @@ 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

README.md

@@ -1,6 +1,7 @@
 ![CI status](https://github.com/bjornwallner/DockQ/actions/workflows/main.yml/badge.svg)
 
-# DockQ: A Quality Measure for Protein-Protein Docking Models
+# DockQ
+## A Quality Measure for Protein-Protein Docking Models
 
 ## Installation
 
@@ -12,7 +13,7 @@ cd DockQ
 pip install .
 ```
 
-## Quick start:
+## Quick start
 
 After installing DockQ with `pip`, the `DockQ` binary will be in your path. Just run DockQ with:
 

run_test.sh

@@ -1,19 +1,42 @@
 #!/bin/bash
 set -euo pipefail
 
+rm -f test .coverage
+
+if command -v coverage &> /dev/null; then
+    binary="coverage run -a -m DockQ.DockQ"
+else
+    binary="DockQ"
+fi
+
 # Test that cython version behaves the same as nocython
-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
+$binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+diff test testdata/1A2K.dockq
+python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+diff test testdata/1A2K.dockq
+$binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
+diff test testdata/1A2K.dockq
+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 -m DockQ.DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short
+$binary examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short > test
+diff test testdata/dimer_dimer.dockq
+
 # Test on structures with slightly different sequences
-coverage run -a -m DockQ.DockQ examples/model.pdb examples/native.pdb --allowed_mismatches 1
+$binary examples/model.pdb examples/native.pdb --allowed_mismatches 1 > test
+diff test testdata/model.dockq
+
 # Test various mapping strategies
-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
+$binary examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping AB*:BA* > test
+diff test testdata/1EXB_AB.BA.dockq
+$binary examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping :ABC > test
+diff test testdata/1EXB_.ABC.dockq
+$binary examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --short --mapping ABCDEFGH:BADCFEHG > test
+diff test testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
+
 # Test that cif parsing behaves same as pdb parsing
-coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE
-coverage run -a -m DockQ.DockQ examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE
+$binary examples/1EXB_r_l_b.model.pdb examples/1EXB_r_l_b.pdb --mapping DH:AE > test
+diff test testdata/1EXB_DH.AE.dockq
+$binary examples/1EXB_r_l_b.model.pdb examples/1EXB.cif.gz --mapping DH:AE > test
+diff test testdata/1EXB_DH.AE_cif.dockq

setup.cfg

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