Merge branch 'main' into feat/add_bond_types

.github/ISSUE_TEMPLATE/BUG_REPORT.md

@@ -21,6 +21,6 @@ Please include a code snippet that can be used to reproduce this bug.
 
 **Software versions**
 
-- Which version of Foyer are you using? (`python -c "import foyer; print(foyer.version)"`)
+- Which version of Foyer are you using? (`python -c "import foyer; print(foyer.__version__)"`)
 - Which version of Python (`python --version`)?
 - Which operating system?

.github/workflows/CI.yaml

@@ -0,0 +1,135 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    - cron:  "0 0 * * *"
+
+jobs:
+  test:
+    if: github.event.pull_request.draft == false
+    name: Foyer Tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, ubuntu-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        exclude:
+          - os: windows-latest
+            python-version: "3.9"
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v3
+        name: Checkout Branch / Pull Request
+
+      - name: Install Mamba (Linux)
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev.yml
+          python-version: ${{ matrix.python-version }}
+        if: runner.os != 'Windows'
+
+      - name: Install Mamba (Windows)
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev-win.yml
+          python-version: ${{ matrix.python-version }}
+        if: runner.os == 'Windows'
+
+      - name: Install Package
+        run: python -m pip install -e .
+
+      - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
+        run: python -m pytest -v -nauto --cov=foyer --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs foyer
+
+      - name: Upload Coverage Report
+        uses: codecov/codecov-action@v2
+        with:
+          name: Foyer-Coverage
+          verbose: true
+          files: ./coverage.xml
+
+  bleeding-edge-test:
+    if: github.event.pull_request.draft == false
+    name: Bleeding Edge mosdef Tests for Foyer
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v3
+        name: Checkout Branch / Pull Request
+
+      - name: Install Mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev.yml
+          python-version: "3.10"
+
+      - name: Clone mBuild and GMSO
+        run: |
+          git clone https://github.com/mosdef-hub/mbuild.git
+          git clone https://github.com/mosdef-hub/gmso.git
+
+      - name: Update Environment with mbuild/gmso Dependencies
+        run: |
+          micromamba update --name foyer-dev --file mbuild/environment.yml
+          micromamba update --name foyer-dev --file gmso/environment.yml
+
+      - name: Install Packages from Source
+        run: |
+          pip install -e mbuild
+          pip install -e gmso
+          pip install -e .
+
+      - name: Run Bleeding Edge Tests
+        run: |
+          python -m pytest -v -nauto --color yes --pyargs foyer
+
+  docker:
+    runs-on: ubuntu-latest
+    needs: test
+    name: Build Docker Image
+    if: ${{ false }}
+
+    steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Get Tagged Version
+        run: |
+          echo "DOCKER_TAGS=mosdef/foyer:${GITHUB_REF_NAME}, mosdef/foyer:stable" >> $GITHUB_ENV        if: github.ref_type == 'tag'
+
+      - name: Get Push Version
+        run: |
+          echo "DOCKER_TAGS=mosdef/foyer:${GITHUB_REF_NAME}, mosdef/foyer:stable" >> $GITHUB_ENV        if: github.ref_type == 'branch'
+
+      - name: Docker Image Info
+        run: |
+          echo Docker Image tags: ${DOCKER_TAGS}
+
+      - name: Build and Push
+        uses: docker/build-push-action@v4
+        with:
+          push: true
+          tags: ${{ env.DOCKER_TAGS }}

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: "20 9 * * 4"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

.pre-commit-config.yaml

@@ -9,25 +9,25 @@ ci:
     submodules: false
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.5.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
       exclude: 'setup.cfg'
 - repo: https://github.com/psf/black
-  rev: 21.9b0
+  rev: 23.9.1
   hooks:
     - id: black
       args: [--line-length=80]
 - repo: https://github.com/pycqa/isort
-  rev: 5.9.3
+  rev: 5.12.0
   hooks:
     - id: isort
       name: isort (python)
       args: [--profile=black, --line-length=80]
 - repo: https://github.com/pycqa/pydocstyle
-  rev: '6.1.1'
+  rev: '6.3.0'
   hooks:
     - id: pydocstyle
       exclude: ^(foyer/tests/|docs/|devtools/|setup.py)

.readthedocs.yml

@@ -1,9 +1,13 @@
 version: 2
 formats:
   - htmlzip
+  - pdf
 conda:
   environment: docs/docs-env.yml
-
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "mambaforge-4.10"
 sphinx:
   builder: html
   configuration: docs/source/conf.py

CITATION.cff

@@ -0,0 +1,118 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: >-
+  Foyer: A package for atom-typing as well as
+  applying and disseminating forcefields
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file and the preferred citation.
+type: software
+authors:
+  - given-names: Christoph
+    family-names: Klein
+    affiliation: "Vanderbilt University"
+  - given-names: "Andrew Z."
+    family-names: Summers
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0001-8477-3059'
+  - given-names: "Matthew W."
+    family-names: Thompson
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0002-1460-3983'
+  - given-names: "Justin B."
+    family-names: Gilmer
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0002-6915-5591'
+  - given-names: "Co D."
+    family-names: Quach
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0002-1255-4161'
+  - given-names: Umesh
+    family-names: Timalsina
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0002-5430-3993'
+  - given-names: Peter
+    family-names: Volgyesi
+    orcid: 'https://orcid.org/0000-0002-7478-4317'
+    affiliation: "Vanderbilt University"
+  - given-names: Janos
+    family-names: Sallai
+    affiliation: "Vanderbilt University"
+  - given-names: "Chris R."
+    family-names: Iacovella
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0003-0557-0427'
+  - given-names: Clare
+    family-names: McCabe
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0002-8552-9135'
+  - given-names: "Peter T."
+    family-names: Cummings
+    affiliation: "Vanderbilt University"
+    orcid: 'https://orcid.org/0000-0002-9766-2216'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.6229092
+    description: Zenodo Doi
+repository-code: 'https://github.com/mosdef-hub/foyer'
+url: 'https://foyer.mosdef.org'
+repository: 'https://github.com/mosdef-hub/foyer'
+repository-artifact: 'https://github.com/mosdef-hub/foyer/releases'
+abstract: >-
+  Foyer is an open-source Python tool for defining
+  and applying force field atom-typing rules in a
+  format that is both human- and machine-readable. It
+  parametrizes chemical topologies, generating,
+  syntactically correct input files for various
+  simulation engines. Foyer provides a framework for
+  force field dissemination, helping to eliminate
+  ambiguity in atom-typing and improving
+  reproducibility.
+keywords:
+  - atom-typing
+  - reproducibility
+  - 'TRUE'
+  - mosdef
+  - python
+license: MIT
+preferred-citation:
+  type: article
+  authors:
+    - given-names: Christoph
+      family-names: Klein
+      affiliation: "Vanderbilt University"
+    - given-names: "Andrew Z."
+      family-names: Summers
+      affiliation: "Vanderbilt University"
+      orcid: 'https://orcid.org/0000-0001-8477-3059'
+    - given-names: "Matthew W."
+      family-names: Thompson
+      affiliation: "Vanderbilt University"
+      orcid: 'https://orcid.org/0000-0002-1460-3983'
+    - given-names: "Justin B."
+      family-names: Gilmer
+      affiliation: "Vanderbilt University"
+      orcid: 'https://orcid.org/0000-0002-6915-5591'
+    - given-names: Clare
+      family-names: McCabe
+      affiliation: "Vanderbilt University"
+      orcid: 'https://orcid.org/0000-0002-8552-9135'
+    - given-names: "Peter T."
+      family-names: Cummings
+      affiliation: "Vanderbilt University"
+      orcid: 'https://orcid.org/0000-0002-9766-2216'
+    - given-names: Janos
+      family-names: Sallai
+      affiliation: "Vanderbilt University"
+    - given-names: "Chris R."
+      family-names: Iacovella
+      affiliation: "Vanderbilt University"
+      orcid: 'https://orcid.org/0000-0003-0557-0427'
+  title: "Formalizing atom-typing and the dissemination of force fields with foyer"
+  journal: "Comput. Mater. Sci."
+  volume: "167"
+  pages: "12"
+  year: "2019"
+  doi: "10.1016/j.commatsci.2019.05.026"