Add small molecule repex consistency tests

.github/workflows/CI.yaml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.8, 3.9, "3.10"]
-        openmm: ["nightly", "7.7", "beta"]
+        openmm: ["rc", "7.7", "beta"]
         exclude:
           - python-version: "3.10"
             openmm: "7.6"
@@ -48,7 +48,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           environment-file: devtools/conda-envs/test_env.yaml
-          channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge,defaults,omnia-dev,openeye
+          channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge,openeye
           activate-environment: test
           auto-update-conda: true
           auto-activate-base: false
@@ -60,9 +60,9 @@ jobs:
         shell: bash -l {0}
         run: |
           case ${{ matrix.openmm }} in
-            nightly)
-              echo "Using nightly dev build of OpenMM."
-              conda install -y -c omnia-dev openmm --override-channels --force-reinstall
+            rc)
+              echo "Using rc build of OpenMM."
+              conda install -y -c conda-forge/label/openmm_rc openmm==8.0.0rc2 --override-channels --force-reinstall
               echo "Using beta build of openeye toolkit"
               conda install -y -c openeye/label/beta openeye-toolkits --override-channels --force-reinstall;;
             beta)

.github/workflows/self-hosted-gpu-test.yml

@@ -2,12 +2,11 @@ name: self-hosted-gpu-test
 on:
   push:
     branches:
-      - master
       - main
   workflow_dispatch:
   schedule:
-    # nightly tests
-    - cron: "0 0 * * *"
+    # weekly tests
+    - cron: "0 0 * * SUN"
 jobs:
   start-runner:
     name: Start self-hosted EC2 runner
@@ -22,54 +21,61 @@ jobs:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
           aws-region: ${{ secrets.AWS_REGION }}
-      - name: Start EC2 runner
+      - name: Try to start EC2 runner
         id: start-ec2-runner
         uses: machulav/ec2-github-runner@main
         with:
           mode: start
           github-token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
-          ec2-image-id: ami-034abd52dd90b8023
-          ec2-instance-type: p2.xlarge
-          subnet-id: subnet-0e82552b8c708a999
-          security-group-id: sg-0589e74ec03965add
+          ec2-image-id: ami-04d16a12bbc76ff0b
+          ec2-instance-type: g4dn.xlarge
+          subnet-id: subnet-0dee8543e12afe0cd # us-east-1a
+          security-group-id: sg-0f9809618550edb98
           # iam-role-name: self-hosted-runner # optional, requires additional permissions
           aws-resource-tags: > # optional, requires additional permissions
             [
               {"Key": "Name", "Value": "ec2-github-runner"},
               {"Key": "GitHubRepository", "Value": "${{ github.repository }}"}
             ]
+
   do-the-job:
     name: Do the job on the runner
     needs: start-runner # required to start the main job when the runner is ready
     runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner
+    timeout-minutes: 1200 # 20 hrs
     env:
       TEST_MODE: GPU
       OPENMM: ${{ matrix.cfg.openmm }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+      HOME: /home/ec2-user
 
     defaults:
       run:
         shell: bash -l {0}
     steps:
+      - name: setup env
+        run: |
+          echo $HOME
+          export HOME=/home/ec2-user
+          echo $HOME
+
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.9
-          channels: conda-forge,omnia-dev,openeye
+          python-version: "3.10"
           environment-file: devtools/conda-envs/test_env.yaml
-          show-channel-urls: true
-          auto-activate-base: false
+          channels: conda-forge,openeye
           activate-environment: test
-          miniforge-version: latest 
+          auto-update-conda: true
+          auto-activate-base: false
+          show-channel-urls: true
+          channel-priority: true
           miniforge-variant: Mambaforge
-
       - name: Refine test env
-        shell: bash -l {0}
         run: |
-          conda install -y cudatoolkit==11.0.3 openmm>=7.7
+          mamba install -y cudatoolkit==11.7 openmm>=8.0
 
       - name: Additional info about the build
-        shell: bash -l {0}
         run: |
           uname -a
           df -h
@@ -80,26 +86,22 @@ jobs:
           python -m openmm.testInstallation
 
       - name: Install package
-        shell: bash -l {0}
         run: |
           python -m pip install --no-deps -v .
 
       - name: Environment Information
-        shell: bash -l {0}
         run: |
           conda info -a
           conda list
 
       - name: Decrypt OpenEye license
-        shell: bash -l {0}
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
         run: |
           echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
           python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
 
       - name: Test the package
-        shell: bash -l {0}
         run: |
           export TRAVIS=true
           conda list --explicit
@@ -108,10 +110,10 @@ jobs:
       - name: Codecov
         if: ${{ github.repository == 'choderalab/perses'
                 && github.event != 'schedule' }}
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           file: ./coverage.xml
-          fail_ci_if_error: true
+          fail_ci_if_error: false
 
   stop-runner:
     name: Stop self-hosted EC2 runner

devtools/conda-envs/test_env.yaml

@@ -1,9 +1,6 @@
 name: test
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
-  - defaults
-  - omnia-dev
   - openeye
 dependencies:
   - arsenic

perses/app/relative_setup.py

@@ -365,7 +365,7 @@ def __init__(self,
                 spectator_mol = generate_unique_atom_names(spectator_mol)
                 self._spectator_molecules.append(spectator_mol)
                 # add this to a small molecule register
-                molecules.append(Molecule.from_openeye(spectator_mol,allow_undefined_stereo=True))
+                self._molecules.append(Molecule.from_openeye(spectator_mol,allow_undefined_stereo=True))
                 self._spectator_positions.append(extractPositionsFromOEMol(spectator_mol))
                 spectator_topology = forcefield_generators.generateTopologyFromOEMol(spectator_mol)
                 self._spectator_md_topologies.append(md.Topology.from_openmm(spectator_topology))

perses/tests/test_relative.py

@@ -1135,14 +1135,14 @@ def concatenate_files(input_files, output_file):
             base_repo_url = "https://github.com/openforcefield/protein-ligand-benchmark"
             ligand_files = []
             for ligand in ['lig_ejm_42', 'lig_ejm_54']:
-                ligand_url = f"{base_repo_url}/raw/main/data/2020-02-07_tyk2/02_ligands/{ligand}/crd/{ligand}.sdf"
+                ligand_url = f"{base_repo_url}/raw/0.2.1/data/2020-02-07_tyk2/02_ligands/{ligand}/crd/{ligand}.sdf"
                 ligand_file = retrieve_file_url(ligand_url)
                 ligand_files.append(ligand_file)
             concatenate_files(ligand_files, os.path.join(temp_dir, 'ligands.sdf'))
             ligands_filename = os.path.join(temp_dir, 'ligands.sdf')
 
             # Retrieve host PDB
-            pdb_url = f"{base_repo_url}/raw/main/data/2020-02-07_tyk2/01_protein/crd/protein.pdb"
+            pdb_url = f"{base_repo_url}/raw/0.2.1/data/2020-02-07_tyk2/01_protein/crd/protein.pdb"
             host_pdb = retrieve_file_url(pdb_url)
 
             # Generate topology proposal, old/new positions