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.github/workflows/autorelease-default-env.sh

@@ -0,0 +1,5 @@
+INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.6"
+if [ -f autorelease-env.sh ]; then
+    source autorelease-env.sh
+fi
+

.github/workflows/autorelease-deploy.yml

@@ -0,0 +1,33 @@
+name: Autorelease
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy_pypi:
+    runs-on: ubuntu-latest
+    name: "Deploy to PyPI"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: |
+          python -m pip install twine wheel
+        name: "Install release tools"
+      - run: |
+          python setup.py sdist bdist_wheel
+          twine check dist/*
+        name: "Build and check package"
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.pypi_password }}
+        name: "Deploy to pypi"
+

.github/workflows/autorelease-gh-rel.yml

@@ -0,0 +1,29 @@
+name: Autorelease
+on:
+  push:
+    branches:
+      - stable
+
+jobs:
+  release-gh:
+    runs-on: ubuntu-latest
+    name: "Cut release"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.7"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: |
+          VERSION=`python setup.py --version`
+          PROJECT=`python setup.py --name`
+          echo $PROJECT $VERSION
+          autorelease-release --project $PROJECT --version $VERSION --token $AUTORELEASE_TOKEN
+        env:
+          AUTORELEASE_TOKEN: ${{ secrets.AUTORELEASE_TOKEN }}

.github/workflows/autorelease-prep.yml

@@ -0,0 +1,60 @@
+name: "Autorelease"
+on:
+  pull_request:
+    branches:
+      - stable
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  deploy_testpypi:
+    runs-on: ubuntu-latest
+    name: "Deployment test"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: |
+          python -m pip install twine wheel
+        name: "Install release tools"
+      - run: |
+          bump-dev-version
+          python setup.py --version
+        name: "Bump testpypi dev version"
+      - run: |
+          python setup.py sdist bdist_wheel
+          twine check dist/*
+        name: "Build and check package"
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.testpypi_password }}
+          repository_url: https://test.pypi.org/legacy/
+        name: "Deploy to testpypi"
+  test_testpypi:
+    runs-on: ubuntu-latest
+    name: "Test deployed"
+    needs: deploy_testpypi
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: test-testpypi
+

.github/workflows/unit-tests.yml

@@ -0,0 +1,65 @@
+name: "Unit tests"
+on:
+  pull_request:
+    branches:
+      - master
+      - stable
+  push:
+    branches:
+      - master
+    tags:
+      - "v*"
+  schedule:
+    - cron: "20 5 * * *"
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  test_suite:
+    runs-on: ubuntu-latest
+    name: "Unit Tests"
+    strategy:
+      matrix:
+        CONDA_PY:
+          - 3.9
+          - 3.8
+          - 3.7
+          - 3.6
+        MDTRAJ: ["mdtraj-release"]
+        include:
+          - CONDA_PY: 3.9
+            MDTRAJ: "mdtraj-dev"
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-python: true
+          python-version: ${{ matrix.CONDA_PY }}
+      - name: "Install"
+        env:
+          MDTRAJ: ${{ matrix.MDTRAJ }}
+        run: |
+          source ci/pip-install/install_requirements.sh
+          pip install -e .
+          pip install -U -r ci/pip-install/testing_requirements.txt
+          if [ "$MDTRAJ" = "mdtraj-dev" ]; then
+            pip install --upgrade --force-reinstall -r ci/pip-install/mdtraj_dev.txt
+            pip install -r optional_installs.txt
+          fi
+      - name: "Versions"
+        run: pip list
+      - name: "Autorelease check"
+        run: python autorelease_check.py
+      - name: "Tests"
+        env:
+          PY_COLORS: "1"
+        run: |
+          python -c "import contact_map"
+          py.test -vv --cov=contact_map --cov-report xml
+      - name: "Report coverage"
+        if: ${{ github.event }} != "schedule"
+        run: bash <(curl -s https://codecov.io/bash)

README.md

@@ -1,13 +1,13 @@
 [![Documentation Status](https://readthedocs.org/projects/contact-map/badge/?version=latest)](http://contact-map.readthedocs.io/en/latest/?badge=latest)
-[![Build Status](https://travis-ci.com/dwhswenson/contact_map.svg?branch=master)](https://travis-ci.com/dwhswenson/contact_map)
+![Unit tests](https://github.com/dwhswenson/contact_map/workflows/Unit%20tests/badge.svg)
 [![Windows Build status](https://ci.appveyor.com/api/projects/status/em3fo96sjrg2vmcc/branch/master?svg=true)](https://ci.appveyor.com/project/dwhswenson/contact-map/branch/master)
-[![Coverage Status](https://coveralls.io/repos/github/dwhswenson/contact_map/badge.svg?branch=master)](https://coveralls.io/github/dwhswenson/contact_map?branch=master)
+[![codecov](https://codecov.io/gh/dwhswenson/contact_map/branch/master/graph/badge.svg?token=4so8QmiC5W)](https://codecov.io/gh/dwhswenson/contact_map)
 [![PyPI](https://img.shields.io/pypi/v/contact-map.svg)](https://pypi.python.org/pypi/contact-map/)
 [![conda-forge](https://img.shields.io/conda/v/conda-forge/contact_map.svg)](https://github.com/conda-forge/contact_map-feedstock)
 
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dwhswenson/contact_map/master)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/f7f3cf53698e4655ac8895f13fa5dea6)](https://www.codacy.com/app/dwhswenson/contact_map?utm_source=github.com&utm_medium=referral&utm_content=dwhswenson/contact_map&utm_campaign=Badge_Grade)
 [![Maintainability](https://api.codeclimate.com/v1/badges/84768756d594176d8da6/maintainability)](https://codeclimate.com/github/dwhswenson/contact_map/maintainability)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dwhswenson/contact_map/master)
 # Contact Map Explorer
 
 This package provides tools for analyzing and exploring contacts

autorelease_check.py

@@ -25,5 +25,5 @@
     )
     checker.release_branches = RELEASE_BRANCHES + [RELEASE_TAG]
 
-    tests = checker.select_tests_from_sysargs()
+    tests = checker.select_tests()
     n_fails = checker.run_as_test(tests)