Merge branch 'main' into fix/dataset-split

.github/workflows/CI.yaml

@@ -3,57 +3,50 @@ name: CI
 on:
   pull_request:
     branches:
-      - master
       - main
   push:
     branches:
-      - master
       - main 
+
   schedule:
     # Nightly tests run on master by default:
     #   Scheduled workflows run on the latest commit on the default or base branch.
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * *"
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   test:
-    name: ${{ matrix.name }}
-    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: Linux, Python 3.8
-            os: ubuntu-latest
-            python-version: "3.8"
-            conda-installer: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-
-          - name: Linux, Python 3.9
-            os: ubuntu-latest
-            python-version: "3.9"
-            conda-installer: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-
-          - name: MacOS, Python 3.9
-            os: macOS-latest
-            python-version: "3.9"
-            conda-installer: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-MacOSX-x86_64.sh
+        os: ['macos', 'ubuntu']
+        python-version:
+          - "3.9"
+          - "3.10"
 
     env:
       OPENMM: ${{ matrix.cfg.openmm }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          installer-url: ${{ matrix.conda-installer }}
-          python-version: ${{ matrix.python-version }}
-          activate-environment: test
-          channel-priority: true
           environment-file: devtools/conda-envs/espaloma.yaml
-          auto-activate-base: false
-          use-mamba: true
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - name: Additional info about the build
         shell: bash
@@ -63,35 +56,27 @@ jobs:
           ulimit -a
 
       - name: Environment Information
-        shell: bash -l {0}
-        run: |
-          conda info --all
-          conda list
-          mamba --version
-
-      - name: Decrypt and check OE 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.OEChemIsLicensed()"
+          micromamba info
+          micromamba list
+          micromamba --version
 
       - name: Install package
-        shell: bash -l {0}
         run: |
-          python -m pip install --no-deps .
+          python -m pip install --no-deps -e .
 
       - name: Run tests
-        shell: bash -l {0}
         run: |
-          pytest -v --cov=espaloma --cov-report=xml --color=yes espaloma/
+          pytest -v -n auto --cov=espaloma --cov-report=xml --color=yes espaloma/
 
       - name: CodeCov
-        uses: codecov/codecov-action@v1
-        if: always()
+        uses: codecov/codecov-action@v3
+        if: ${{ github.repository == 'choderalab/espaloma'
+                && github.event_name == 'pull_request' }} 
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           flags: unittests
           yml: ./.codecov.yml
+          fail_ci_if_error: False
+          verbose: True

.github/workflows/clean_cache.yaml

@@ -0,0 +1,34 @@
+# from https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows#force-deleting-cache-entries
+name: cleanup caches by a branch
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+          
+          REPO=${{ github.repository }}
+          BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
+
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH | cut -f 1 )
+
+          ## Setting this to not fail the workflow while deleting cache keys. 
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
+sphinx:
+   configuration: docs/conf.py
+   fail_on_warning: false
+
+conda:
+  environment: devtools/conda-envs/espaloma.yaml
+
+python:
+  # Install our python package before building the docs
+  install:
+    - method: pip
+      path: .

README.md

@@ -1,18 +1,15 @@
 espaloma: **E**xtensible **S**urrogate **P**otenti**al** **O**ptimized by **M**essage-passing **A**lgorithms 🍹
 ==============================
 [//]: # (Badges)
-[![CI](https://github.com/choderalab/espaloma/actions/workflows/CI.yaml/badge.svg?branch=master)](https://github.com/choderalab/espaloma/actions/workflows/CI.yaml)
-[![Total alerts](https://img.shields.io/lgtm/alerts/g/choderalab/espaloma.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/choderalab/espaloma/alerts/)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/choderalab/espaloma.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/choderalab/espaloma/context:python)
-[![docs stable](https://img.shields.io/badge/docs-stable-5077AB.svg?logo=read%20the%20docs)](https://espaloma.wangyq.net/)
-
+[![CI](https://github.com/choderalab/espaloma/actions/workflows/CI.yaml/badge.svg?branch=main)](https://github.com/choderalab/espaloma/actions/workflows/CI.yaml)
+[![Documentation Status](https://readthedocs.org/projects/espaloma/badge/?version=latest)](https://espaloma.readthedocs.io/en/latest/?badge=latest)
 
 Source code for [Wang Y, Fass J, and Chodera JD "End-to-End Differentiable Construction of Molecular Mechanics Force Fields."](https://arxiv.org/abs/2010.01196)
 
 ![abstract](docs/_static/espaloma_abstract_v2-2.png)
 
 #
-Documentation: https://espaloma.wangyq.net/
+Documentation: https://docs.espaloma.org
 
 # Paper Abstract
 Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry.

devtools/conda-envs/espaloma.yaml

@@ -1,10 +1,8 @@
-name: test
+name: espaloma-test
 channels:
   - conda-forge
   - dglteam
   - openeye
-  - defaults
-  - anaconda
 dependencies:
   # Base dependencies
   - python
@@ -14,7 +12,7 @@ dependencies:
   - numpy
   - matplotlib
   - scipy
-  - openff-toolkit <0.11
+  - openff-toolkit >=0.12
   - openff-forcefields
   - openff-units
   - smirnoff99Frosst
@@ -23,10 +21,12 @@ dependencies:
   - tqdm
   # Pytorch
   - pytorch>=1.8.0
-  - dgl
+  - dgl =0.9.0
   # Testing
   - pytest
   - pytest-cov
+  - pytest-xdist
+  - pytest-randomly
   - codecov
   - nose
   - nose-timer

docs/conf.py

@@ -15,16 +15,10 @@
 # Incase the project was not installed
 import os
 import sys
+import subprocess
 
 sys.path.insert(0, os.path.abspath('..'))
 
-import espaloma
-from espaloma import mm, nn, graphs, data
-
-# download experiments
-import os
-os.system("bash download_experiments.sh")
-
 # -- Project information -----------------------------------------------------
 
 project = 'espaloma'
@@ -37,7 +31,6 @@
 # The full version, including alpha/beta/rc tags
 release = ''
 
-
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -81,7 +74,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

espaloma/data/md.py

@@ -797,7 +797,7 @@ def run(self, g, in_place=True):
         samples = []
         for idx in range(true_n_conformers):
             # put conformer in simulation
-            simulation.context.setPositions(g.mol.conformers[idx])
+            simulation.context.setPositions(g.mol.conformers[idx].to_openmm())
 
             # set velocities
             simulation.context.setVelocitiesToTemperature(self.temperature)
@@ -825,7 +825,7 @@ def run(self, g, in_place=True):
             import random
 
             idx = random.choice(list(range(true_n_conformers)))
-            simulation.context.setPositions(g.mol.conformers[idx])
+            simulation.context.setPositions(g.mol.conformers[idx].to_openmm())
 
             # set velocities
             simulation.context.setVelocitiesToTemperature(self.temperature)