From 5905ed9e7808c22f0ba26eb11200fa7dd6e121f9 Mon Sep 17 00:00:00 2001
From: richard gowers <richardjgowers@gmail.com>
Date: Fri, 8 Sep 2023 16:18:51 +0100
Subject: [PATCH 1/2] add tests for trajectory transforms

---
 src/tests/test_transformations.py | 66 +++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 src/tests/test_transformations.py

diff --git a/src/tests/test_transformations.py b/src/tests/test_transformations.py
new file mode 100644
index 0000000..9f63a9b
--- /dev/null
+++ b/src/tests/test_transformations.py
@@ -0,0 +1,66 @@
+import MDAnalysis as mda
+from MDAnalysis.analysis import rms
+import numpy as np
+import pytest
+
+from openfe_analysis import FEReader
+from openfe_analysis.transformations import (
+    Minimiser,
+    NoJump,
+    Aligner,
+)
+
+
+@pytest.fixture
+def universe(hybrid_system_pdb, simulation_nc):
+    return mda.Universe(
+        hybrid_system_pdb, simulation_nc,
+        format='openfe rfe',
+        state_id=0,
+    )
+
+
+def test_minimiser(universe):
+    prot = universe.select_atoms('protein and name CA')
+    lig = universe.select_atoms('resname UNK')
+    m = Minimiser(prot, lig)
+    universe.trajectory.add_transformations(m)
+
+    d = mda.lib.distances.calc_bonds(
+        prot.center_of_mass(), lig.center_of_mass()
+    )
+    # in the raw trajectory this is ~71 A as they're in diff images
+    # accounting for pbc should result in ~11.10
+    assert d == pytest.approx(11.10, abs=0.01)
+
+
+def test_nojump(universe):
+    # find frame where protein would teleport across boundary and check it
+    prot = universe.select_atoms('protein and name CA')
+
+    nj = NoJump(prot)
+    universe.trajectory.add_transformations(nj)
+
+    universe.trajectory[169]
+    universe.trajectory[170]
+
+    # without the transformation, the y coordinate would jump up to ~81.86
+    ref = np.array([72.37, -0.27, 66.49])
+    assert prot.center_of_mass() == pytest.approx(ref, abs=0.01)
+
+
+def test_aligner(universe):
+    # checks that rmsd is identical with/without center&super
+    prot = universe.select_atoms('protein and name CA')
+    a = Aligner(prot)
+    universe.trajectory.add_transformations(a)
+
+    p1 = prot.positions
+    universe.trajectory[1]
+
+    raw_rmsd = rms.rmsd(prot.positions, p1, center=False, superposition=False)
+    opt_rmsd = rms.rmsd(prot.positions, p1, center=True, superposition=True)
+
+    # the rmsd should be identical even if the function didn't align
+    # as the transformation should have done this
+    assert raw_rmsd == pytest.approx(opt_rmsd)

From 73f3e9a12367d6cb4fe19077f813a67fc0d878e5 Mon Sep 17 00:00:00 2001
From: richard gowers <richardjgowers@gmail.com>
Date: Fri, 8 Sep 2023 16:21:43 +0100
Subject: [PATCH 2/2] run tests in serial, maybe nc will crash less

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index a8123e9..32f066d 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -53,7 +53,7 @@ jobs:
           python -Ic "import openfe_analysis; print(openfe_analysis.__version__)"
       - name: "Run tests"
         run: |
-          pytest -n auto -v --cov=openfe_analysis --cov-report=xml --durations=10
+          pytest -n 1 -v --cov=openfe_analysis --cov-report=xml --durations=10
       - name: "Save pooch test data cache"
         id: cache-testdata-save
         uses: actions/cache/save@v3