Remove Travis and move to GitHub Actions (#31)

* remove travisCI references

* format with Black

* trying initial GHA

* update ci.yml

* use Black default line length in GHA

* revert to Black -l 99

* update gitignore

* fix Black formatting using v21.9b0

* update pylint threshold and test variable names

* fix pylint and add some type hints

* add more type hinting

* update docs

* update env

* Update README.md

* Update README.md

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

.github/workflows/ci.yml

@@ -0,0 +1,125 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "master"
+      - "dev"
+  pull_request:
+    branches:
+      - "master"
+      - "dev"
+  schedule:
+    # Run a cron job once daily
+    - cron: "0 0 * * *"
+
+jobs:
+  test:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Linux, Python 3.7
+            os: ubuntu-latest
+            python-version: "3.7"
+            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 3.7
+            os: macOS-latest
+            python-version: "3.7"
+            conda-installer: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-MacOSX-x86_64.sh
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          installer-url: ${{ matrix.conda-installer }}
+          python-version: ${{ matrix.python-version }}
+          activate-environment: test
+          channel-priority: true
+          environment-file: devtools/conda-envs/env.yaml
+          auto-activate-base: false
+          use-mamba: true
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+      - name: Environment Information
+        shell: bash -l {0}
+        run: |
+          conda info --all
+          conda list
+          mamba --version
+      - name: Install package
+        shell: bash -l {0}
+        run: |
+          python -m pip install --no-deps .
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          pytest -v --cov=openff/arsenic --cov-report=xml --color=yes openff/arsenic/tests/
+      - name: CodeCov
+        uses: codecov/codecov-action@v1
+        if: always()
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          flags: unittests
+          yml: ./.codecov.yml
+
+  lint-format:
+    name: Lint & format checks
+    runs-on: ubuntu-18.04
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
+          python-version: "3.7"
+          activate-environment: test
+          channel-priority: true
+          environment-file: devtools/conda-envs/env.yaml
+          auto-activate-base: false
+          use-mamba: true
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+      - name: Environment Information
+        shell: bash -l {0}
+        run: |
+          conda info --all
+          conda list
+      - name: Install linter / formatter
+        shell: bash -l {0}
+        run: |
+          mamba install pylint black
+      - name: Install package
+        shell: bash -l {0}
+        run: |
+          python -m pip install --no-deps .
+      - name: Run pylint
+        shell: bash -l {0}
+        run: |
+          pylint openff/arsenic/ --fail-under 6
+      - name: Run black check
+        shell: bash -l {0}
+        if: always()
+        run: |
+          black --check -l 99 openff/arsenic/ --exclude openff/arsenic/_version.py

.gitignore

@@ -100,3 +100,7 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# VSCode
+.vscode
+

README.md

@@ -2,7 +2,7 @@ openff-arsenic
 ==============================
 [//]: # (Badges)
 
-[![Travis Build Status](https://travis-ci.com/openforcefield/openff-arsenic.svg?branch=master)](https://travis-ci.com/openforcefield/openff-arsenic)
+
 [![codecov](https://codecov.io/gh/openforcefield/openff-arsenic/branch/master/graph/badge.svg)](https://codecov.io/gh/openforcefield/openff-arsenic/branch/master)
 [![Documentation Status](https://readthedocs.org/projects/openff-arsenic/badge/?version=latest)](https://openff-arsenic.readthedocs.io/en/latest/?badge=latest)
 

devtools/README.md

@@ -11,8 +11,6 @@ conda installation, and other development tools not directly related to the codi
 You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and 
 Windows testing if you only plan to deploy on specific platforms. These are just to help you get started
 
-* `travis-ci`: Linux and OSX based testing through [Travis-CI](https://about.travis-ci.com/) 
-  * `before_install.sh`: Pip/Miniconda pre-package installation script for Travis 
 * `appveyor`: Windows based testing through [AppVeyor](https://www.appveyor.com/) (there are no files directly related to this)
 
 ### Conda Environment:

devtools/conda-envs/test_env.yaml → devtools/conda-envs/env.yaml

@@ -1,22 +1,24 @@
-name: test
+name: arsenic
 channels:
+  - conda-forge
 dependencies:
-    # Base depends
+  # Base depends
   - python
   - pip
-
-    # Testing
-  - pytest
-  - pytest-cov
-  - codecov
+  - black
   - networkx
   - numpy
   - matplotlib
   - seaborn
   - plotly
   - scikit-learn
+  - sphinx
+  - sphinx_rtd_theme
 
-    # Pip-only installs
-#- pip:
-#  - codecov
+  # format
+  - black
 
+  # testing
+  - pytest
+  - pytest-cov
+  - codecov

docs/api.rst

@@ -4,7 +4,7 @@ API Documentation
 .. autosummary::
    :toctree: autosummary
 
-   arsenic.plotting
-   arsenic.plotlying
-   arsenic.stats
-   arsenic.wrangle
+   openff.arsenic.plotting
+   openff.arsenic.plotlying
+   openff.arsenic.stats
+   openff.arsenic.wrangle