fix the path issue with pytest

.github/workflows/docker-ci.yml

@@ -191,22 +191,6 @@ jobs:
           docker load --input /tmp/pysages.tar
           docker run -t pysages bash -c "cd PySAGES/examples/openmm/cv_ermsd/ermsd_cg && python3 ./unbiased.py && python3 ./check_ermsd.py"
 
-  cv-rmsd-kabsch:
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Download artifact
-        uses: actions/download-artifact@v3
-        with:
-          name: pysages
-          path: /tmp
-      - name: Load and run test
-        run: |
-          docker load --input /tmp/pysages.tar
-          docker run -t pysages bash -c "cd PySAGES/tests && python3 ./test_rmsd.py"
-
   alanine-dipeptide-string:
     runs-on: ubuntu-latest
     needs: build

tests/test_rmsd.py

@@ -4,26 +4,26 @@
 
 from pysages.colvars.orientation import RMSD_Kabsch
 
-base = np.loadtxt("./ci2_1.txt", dtype=str)[:, 6:9].astype(float)
-reference = np.loadtxt("./ci2_2.txt", dtype=str)[:, 6:9].astype(float)
+base = np.loadtxt("tests/ci2_1.txt", dtype=str)[:, 6:9].astype(float)
+reference = np.loadtxt("tests/ci2_2.txt", dtype=str)[:, 6:9].astype(float)
 indices = np.arange(len(base))
 rmsd_kabsch = RMSD_Kabsch(indices, reference)
 rmsd_calculated = rmsd_kabsch.function(base)
 rmsd_expected = 11.7768
 if not np.allclose(rmsd_expected, rmsd_calculated):
     raise ValueError(f"Test Case PDB 1 failed: {rmsd_expected, rmsd_calculated}")
 
-base = np.loadtxt("./ci2_1t.txt", dtype=str)[:, 6:9].astype(float)
-reference = np.loadtxt("./ci2_1.txt", dtype=str)[:, 6:9].astype(float)
+base = np.loadtxt("tests/ci2_1t.txt", dtype=str)[:, 6:9].astype(float)
+reference = np.loadtxt("tests/ci2_1.txt", dtype=str)[:, 6:9].astype(float)
 rmsd_kabsch = RMSD_Kabsch(indices, reference)
 rmsd_calculated = rmsd_kabsch.function(base)
 rmsd_expected = 0.0
 if not np.allclose(rmsd_expected, rmsd_calculated, atol=1e-3):
     raise ValueError(f"Test Case PDB 2 failed: {rmsd_expected, rmsd_calculated}")
 
 
-base = np.loadtxt("./ci2_2.txt", dtype=str)[:, 6:9].astype(float)
-reference = np.loadtxt("./ci2_12.txt", dtype=str)[:, 6:9].astype(float)
+base = np.loadtxt("tests/ci2_2.txt", dtype=str)[:, 6:9].astype(float)
+reference = np.loadtxt("tests/ci2_12.txt", dtype=str)[:, 6:9].astype(float)
 rmsd_kabsch = RMSD_Kabsch(indices, reference)
 rmsd_calculated = rmsd_kabsch.function(base)
 rmsd_expected = 15.422431