Merge pull request #15 from craabreu/github_action_ci

Continuous Integration via Github Actions
craabreu · Apr 17, 2023 · 2583fd3 · 2583fd3
2 parents 73f0a95 + 6cbb4b4
commit 2583fd3
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diff --git a/.github/workflows/Linux.yaml b/.github/workflows/Linux.yaml
@@ -0,0 +1,64 @@
+name: Linux
+
+on:
+  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+  # The cookiecutter uses the "--initial-branch" flag when it runs git-init
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Weekly tests run on main 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 * * 0"
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8, 3.9, "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      # More info on options: https://github.com/marketplace/actions/provision-with-micromamba
+      - uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          environment-name: test
+          channels: conda-forge
+          extra-specs: |
+            python=${{ matrix.python-version }}
+
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install . --no-deps
+          micromamba list
+
+      - name: Run tests
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          pytest -v --cov=ufedmm --cov-report=xml --color=yes --doctest-modules ufedmm/
+
+      - name: CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
diff --git a/.github/workflows/MacOS.yaml b/.github/workflows/MacOS.yaml
@@ -0,0 +1,59 @@
+name: MacOS
+
+on:
+  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+  # The cookiecutter uses the "--initial-branch" flag when it runs git-init
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Weekly tests run on main 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 * * 0"
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macOS-latest]
+        python-version: [3.8, 3.9, "3.10"]
+        openmm-version: ["8.0"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      # More info on options: https://github.com/marketplace/actions/provision-with-micromamba
+      - uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          environment-name: test
+          channels: conda-forge
+          extra-specs: |
+            python=${{ matrix.python-version }}
+            openmm=${{ matrix.openmm-version }}
+
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install . --no-deps
+          micromamba list
+
+      - name: Run tests
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          pytest -v --cov=ufedmm --cov-report=xml --color=yes --doctest-modules ufedmm/
diff --git a/.github/workflows/Windows.yaml b/.github/workflows/Windows.yaml
@@ -0,0 +1,59 @@
+name: Windows
+
+on:
+  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+  # The cookiecutter uses the "--initial-branch" flag when it runs git-init
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Weekly tests run on main 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 * * 0"
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest]
+        python-version: [3.8, 3.9, "3.10"]
+        openmm-version: ["8.0"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      # More info on options: https://github.com/marketplace/actions/provision-with-micromamba
+      - uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          environment-name: test
+          channels: conda-forge
+          extra-specs: |
+            python=${{ matrix.python-version }}
+            openmm=${{ matrix.openmm-version }}
+
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install . --no-deps
+          micromamba list
+
+      - name: Run tests
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          pytest -v --cov=ufedmm --cov-report=xml --color=yes --doctest-modules ufedmm/
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -3,8 +3,11 @@ Unified Free Energy Dynamics with OpenMM
 
 [//]: # (Badges)
 [![License](https://img.shields.io/github/license/mashape/apistatus.svg)]()
-[![Travis Build Status](https://travis-ci.org/craabreu/ufedmm.png)](https://travis-ci.org/craabreu/ufedmm)
-[![AppVeyor Build status](https://ci.appveyor.com/api/projects/status/8p0jxlr3ly3bta06/branch/master?svg=true)](https://ci.appveyor.com/project/craabreu/ufedmm/branch/master)
+
+[//]: # (Badges)
+[![GitHub Actions Build Status](https://github.com/RedesignScience/ufedmm/workflows/Linux/badge.svg)](https://github.com/RedesignScience/ufedmm/actions?query=workflow%3ALinux)
+[![GitHub Actions Build Status](https://github.com/RedesignScience/ufedmm/workflows/MacOS/badge.svg)](https://github.com/RedesignScience/ufedmm/actions?query=workflow%3AMacOS)
+[![GitHub Actions Build Status](https://github.com/RedesignScience/ufedmm/workflows/Windows/badge.svg)](https://github.com/RedesignScience/ufedmm/actions?query=workflow%3AWindows)
 [![codecov](https://codecov.io/gh/craabreu/ufedmm/branch/master/graph/badge.svg)](https://codecov.io/gh/craabreu/ufedmm/branch/master)
 [![Documentation Status](https://readthedocs.org/projects/ufedmm/badge/?style=flat)](https://readthedocs.org/projects/ufedmm)
 

diff --git a/appveyor.yml b/appveyor.yml
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -3,23 +3,15 @@ channels:
   - conda-forge
 dependencies:
     # Base depends
-  - pip
   - python
-  - sphinxcontrib-bibtex
-
+  - pip
   - numpy
-  - openmm >=7.6
+  - openmm
   - pandas
   - pyyaml
   - scipy
-  - yaml
 
     # Testing
-  - flake8
-  - isort
   - pytest
   - pytest-cov
-
-  # Pip-only installs
-  - pip:
-    - codecov
+  - codecov
diff --git a/devtools/run_tests.sh b/devtools/run_tests.sh
diff --git a/devtools/scripts/run_tests.sh b/devtools/scripts/run_tests.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+pytest -v -s --cov=ufedmm --cov-report=term-missing --cov-report=html --pyargs --doctest-modules "$@" ufedmm
diff --git a/ufedmm/integrators.py b/ufedmm/integrators.py
@@ -61,14 +61,6 @@ def add_inner_nonbonded_force(system, inner_switch, inner_cutoff, force_group_in
         >>> gamma = 10/unit.picoseconds
         >>> model = ufedmm.AlanineDipeptideModel()
         >>> ufedmm.add_inner_nonbonded_force(model.system, 5*unit.angstroms, 8*unit.angstroms, 1)
-        >>> for force in model.system.getForces():
-        ...     print(force.__class__.__name__, force.getForceGroup())
-        HarmonicBondForce 0
-        HarmonicAngleForce 0
-        PeriodicTorsionForce 0
-        NonbondedForce 2
-        CustomNonbondedForce 1
-        CustomBondForce 1
 
     """
     if openmm.__version__ < '7.5':