Test new python versions (#880)

* test new python versions

* need python 3.10 not 3.1

* make matrix easier to understand

* fix yaml

* fix matrix var issue

* hardcode os

* don't need OS in yaml

* fixing yaml syntax

* see if setting these versions will fix the issues

* now lets see which package fixed this

* I think this is it

* not sure if this will work, bash scripting is not my strenght

* install nightly build correctly this time

* make sure to install even if it exits in env

* dropping python 3.10 testing

* lets see if conda will install the dev version

* lets see if this gets us the right openmm nightly

* remove pin to test test fix

* fix tests to check across pcb

* fix silly name error

* mistake in logic for error checking

* force installing from omnia

.github/workflows/CI.yaml

@@ -13,21 +13,17 @@ on:
 
 jobs:
   test:
-    name: Test on ${{ matrix.cfg.os }}, Python ${{ matrix.cfg.python-version }}, OpenMM ${{ matrix.cfg.openmm }}
-    runs-on: ${{ matrix.cfg.os }}
+    name: Test on ubuntu-latest, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}
+    runs-on: ubuntu-latest
+
     strategy:
       fail-fast: false
       matrix:
-        cfg:
-          - { os: ubuntu-latest, python-version: 3.7, openmm: latest }
-          - { os: ubuntu-latest, python-version: 3.8, openmm: latest }
-          - { os: ubuntu-latest, python-version: 3.7, openmm: nightly }
-          - { os: ubuntu-latest, python-version: 3.8, openmm: nightly }
-          - { os: ubuntu-latest, python-version: 3.7, openmm: conda-forge }
-          - { os: ubuntu-latest, python-version: 3.8, openmm: conda-forge }
+        python-version: [3.7, 3.8, 3.9]
+        openmm: ["nightly", "7.5.1.", "7.6.0"]
 
     env:
-      OPENMM: ${{ matrix.cfg.openmm }}
+      OPENMM: ${{ matrix.openmm }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
 
     steps:
@@ -56,16 +52,13 @@ jobs:
       - name: Refine test environment
         shell: bash -l {0}
         run: |
-          case ${{ matrix.cfg.openmm }} in
-            latest)
-              echo "Using latest release OpenMM."
-              mamba install --quiet -c conda-forge openmm;;
-           #rc) # We can uncomment this case when we have this label on conda-forge
-             #echo "Using OpenMM rc" 
-             #mamba install --quiet -c conda-forge/label/openmm_rc openmm;;
+          case ${{ matrix.openmm }} in
             nightly)
-              echo "Using OpenMM nightly dev build."
-              mamba install --quiet -c omnia-dev openmm;;
+              echo "Using nightly dev build of OpenMM."
+              conda install -y -c omnia-dev openmm --override-channels --force-reinstall;;
+            *)
+              echo "installing OpenMM version ${{ matrix.openmm }}"
+              mamba install -y -c conda-forge openmm=${{ matrix.openmm }};;
           esac
 
       - name: Install package

perses/tests/test_coordinate_numba.py

@@ -102,7 +102,10 @@ def test_openmm_dihedral():
         msg += '_internal_to_cartesian generated positions for: {}\n'.format(phi)
         msg += 'OpenMM: {}\n'.format(openmm_phi)
         msg += 'positions: {}'.format(positions)
-        assert np.linalg.norm(openmm_phi - phi) < TORSION_TOLERANCE, msg
+
+        delta = abs(openmm_phi - phi)
+        error = min(delta, 2*np.pi - delta)
+        assert error < TORSION_TOLERANCE, msg
 
         # Check that _cartesian_to_internal agrees
         rtp, detJ = geometry_engine._cartesian_to_internal(xyz_atom1, bond_position, angle_position, torsion_position)

perses/tests/test_geometry_engine.py

@@ -609,7 +609,11 @@ def test_torsion_scan():
     for i, phi in enumerate(phis):
         xyz_ge = xyzs[i]
         r_new, theta_new, phi_new = _get_internal_from_omm(xyz_ge, testsystem.positions[1], testsystem.positions[2], testsystem.positions[3])
-        if np.abs(phi_new - phi) > TOLERANCE:
+
+        delta = abs(phi_new - phi)
+        error = min(delta, 2*np.pi-delta)
+
+        if error > TOLERANCE:
             raise Exception("Torsion scan did not match OpenMM torsion")
         if np.abs(r_new - r) > TOLERANCE or np.abs(theta_new - theta) > TOLERANCE:
             raise Exception("Theta or r was disturbed in torsion scan.")