speed up and improve CI and update readme

.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
@@ -63,27 +56,27 @@ jobs:
  ulimit -a
 
  - name: Environment Information
- shell: bash -l {0}
  run: |
- conda info --all
- conda list
- mamba --version
+ 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 }}

README.md

@@ -1,11 +1,8 @@
 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)