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Merge pull request #1031 from openpathsampling/release-1.5.0
OpenPathSampling 1.5
2 parents 8cb8f3f + 82b5284 commit d6d97a2

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‎.coveragerc‎

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openpathsampling/version.py
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exclude_lines =
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pragma: no cover
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pragma: no-cover
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-no-cov-
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def __repr__
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raise NotImplementedError

‎.github/workflows/check-openmm-rc.yml‎

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# Workflow to check for a recent OpenMM release candidate.
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#
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# If a recent RC is found, trigger a second workflow to test against it.
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# See also: test-openmm-rc.yml
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name: "Check for OpenMM RC"
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on:
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schedule:
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- cron: "0 9 * * */2"
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jobs:
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check-rc:
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runs-on: ubuntu-latest
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name: "Check for OpenMM RC"
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steps:
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- uses: actions/checkout@v2
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- uses: dwhswenson/conda-rc-check@main
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id: checkrc
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with:
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channel: conda-forge
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package: openmm
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ndays: 3
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labels: openmm_rc
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- uses: benc-uk/workflow-dispatch@v1
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with:
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workflow: Test OpenMM Release Candidate
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token: ${{ secrets.DISPATCH_TOKEN }}
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if: ${{ steps.checkrc.outputs.hasrc == 'True' }}

‎.github/workflows/deploy_docs.yml‎

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# NOTE: This workflow should obviate the after_success script
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name: "docs"
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on:
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push:
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branches:
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- master
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- docs_deploy
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# TODO: add support for tags/stable
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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docs:
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runs-on: ubuntu-latest
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name: "docs"
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: 3.9
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- name: "Install requirements"
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run: source devtools/conda_install_reqs.sh
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- name: "Install OPS"
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run: |
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python -m pip install --no-deps -e .
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python -c "import openpathsampling"
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- name: "Install doc tools"
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run: |
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python -m pip install numpydoc s3cmd
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conda install -y -c conda-forge --file docs/requirements.txt
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- name: "Versions"
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run: conda list
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- name: "Build docs"
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run: cd docs && python premake.py && make html && cd -
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- name: "Check docs"
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run: |
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ls -lt docs/_build
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ls -ls docs/_build/html
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pwd
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- name: "Deploy docs"
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# TODO: perhaps run docs build on all, but only push on merge
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run: python devtools/ci/push-docs-to-s3.py #--clobber
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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‎.github/workflows/test-openmm-rc.yml‎

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# Workflow to test against release candidate of OpenMM.
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# See also: check-openmm-rc.yml
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name: "Test OpenMM Release Candidate"
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on:
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workflow_dispatch:
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# use this for debugging
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#pull_request:
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#branch: master
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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tests:
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runs-on: ubuntu-latest
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name: "Tests"
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 2
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- uses: actions/setup-python@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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- name: "Install requirements"
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run: |
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CONDA_PY=$(python -c "import sys; print('.'.join(str(s) for s in sys.version_info[:2]))")
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echo "Python version: ${CONDA_PY}"
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source devtools/conda_install_reqs.sh
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- name: "Install OpenMM RC"
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run: |
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conda install -c conda-forge/label/openmm_rc -c conda-forge openmm
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- name: "Install"
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run: |
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python -m pip install --no-deps -e .
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python -c "import openpathsampling"
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- name: "Versions"
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run: conda list
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- name: "Unit Tests"
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env:
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PY_COLORS: "1"
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run: py.test -vv -s --cov --cov-report xml
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- name: "Tests: Experimental"
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if: matrix.MINIMAL == '' && matrix.CONDA_PY != '2.7'
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run: py.test openpathsampling/experimental/ -vv -s
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- name: "Notebook tests"
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run: |
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pushd examples/ && ./ipynbtests.sh || exit 1 && popd

‎.github/workflows/tests.yml‎

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runs-on: ubuntu-latest
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name: "Tests"
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strategy:
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# NOTE: When changing the test matrix:
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# * Update the after_n_builds in codecov.yml to match the number of
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# builds in the matrix
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# * You may need to create another example run for the notebook tests
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# (see examples/ipynbtests.sh; examples/prep_example_data.py). This
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# is because Python internals (usually bytecode, which is saved in
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# CVs) can differ between minor Python versions.
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matrix:
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CONDA_PY:
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#- 3.9
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#- 3.8
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- 3.9
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- 3.8
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- 3.7
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- 2.7
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MINIMAL: [""]
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include:
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- CONDA_PY: 3.7
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MINIMAL: true
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MINIMAL: "minimal"
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 2
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- uses: actions/setup-python@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:

‎README.md‎

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[![Tests](https://github.com/openpathsampling/openpathsampling/workflows/Tests/badge.svg?branch=master)](https://github.com/openpathsampling/openpathsampling/actions?query=workflow%3ATests)
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[![Coverage Status](https://coveralls.io/repos/github/openpathsampling/openpathsampling/badge.svg?branch=master)](https://coveralls.io/github/openpathsampling/openpathsampling?branch=master)
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[![codecov](https://codecov.io/gh/openpathsampling/openpathsampling/branch/master/graph/badge.svg?token=9W18VHasdb)](https://codecov.io/gh/openpathsampling/openpathsampling)
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# OpenPathSampling
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‎codecov.yml‎

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coverage:
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status:
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project:
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default:
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target: auto
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threshold: 0.04%
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codecov:
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notify:
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wait_for_ci: true
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after_n_builds: 5

‎devtools/ci/miniconda_install.sh‎

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export PATH=$HOME/miniconda${pyV}/bin:$PATH
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# this puts the channel priority to (1) conda-forge; (2) omnia (3) defaults
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conda config --add channels http://conda.anaconda.org/omnia
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conda config --add channels http://conda.anaconda.org/conda-forge
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# next two lines are workaround for conda/conda#9337

‎devtools/experimental_reqs.txt‎

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sqlalchemy
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sqlalchemy!=1.4.0
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dill

‎devtools/tested_integrations.txt‎

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jupyter
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openmm
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openmm!=7.5.1
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openmmtools
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py-plumed
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pyemma

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