Merge branch 'main' into add/performance_tests

.github/workflows/CI.yaml

@@ -0,0 +1,128 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    - cron:  "0 0 * * *"
+
+jobs:
+  test:
+    if: github.event.pull_request.draft == false
+    name: GMSO Tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        pydantic-version: ["2"]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v3
+        name: Checkout Branch / Pull Request
+
+      - name: Install Mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev.yml
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pydantic=${{ matrix.pydantic-version }}
+
+      - name: Install Package
+        run: python -m pip install -e .
+
+      - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
+        run: python -m pytest -v --cov=gmso --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs gmso
+
+      - name: Upload Coverage Report
+        uses: codecov/codecov-action@v2
+        with:
+          name: GMSO-Coverage
+          verbose: true
+
+  bleeding-edge-test:
+    if: github.event.pull_request.draft == false
+    name: Bleeding Edge mosdef Tests for GMSO
+    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: python="3.10"
+
+      - name: Clone mBuild and Foyer and forcefield-utilities
+        run: |
+          git clone https://github.com/mosdef-hub/mbuild.git
+          git clone https://github.com/mosdef-hub/foyer.git
+          git clone https://github.com/mosdef-hub/forcefield-utilities.git
+
+      - name: Update Environment with mbuild/foyer/ffutils Dependencies
+        run: |
+          micromamba update --name gmso-dev --file mbuild/environment.yml
+          micromamba update --name gmso-dev --file foyer/environment.yml
+          micromamba update --name gmso-dev --file forcefield-utilities/environment-dev.yml
+
+      - name: Install Packages from Source
+        run: |
+          pip install -e mbuild
+          pip install -e foyer
+          pip install -e forcefield-utilities
+          pip install -e .
+
+      - name: Run Bleeding Edge Tests
+        run: |
+          python -m pytest -v --color yes --pyargs gmso
+
+  docker:
+    runs-on: ubuntu-latest
+    needs: test
+    name: Build Docker Image
+    if: ${{ false }}
+
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Get Tagged Version
+        run: |
+          echo "DOCKER_TAGS=mosdef-gmso-${CI_COMMIT_REF_SLUG}, mosdef-gmso-stable" >> $GITHUB_ENV
+        if: github.ref_type == 'tag'
+
+      - name: Get Push Version
+        run: |
+          echo "DOCKER_TAGS=mosdef-gmso-${CI_COMMIT_REF_SLUG}, mosdef-gmso-latest" >> $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@v2
+        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: "41 4 * * 6"
+
+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 }}"

.gitignore

@@ -1,5 +1,7 @@
 *.py[cod]
 *.ipynb_checkpoints
+.pymon
+test-output.xml
 
 # C extensions
 *.so

.pre-commit-config.yaml

@@ -9,24 +9,26 @@ ci:
     submodules: false
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.4.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
+      exclude: 'setup.cfg|gmso/tests/files/.*'
 - repo: https://github.com/psf/black
-  rev: 21.8b0
+  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]
+      exclude: "gmso/tests/files/.*"
 - repo: https://github.com/pycqa/pydocstyle
-  rev: '6.1.1'
+  rev: '6.3.0'
   hooks:
     - id: pydocstyle
       exclude: ^(gmso/abc|gmso/core|gmso/tests/|docs/|devtools/|setup.py)

.readthedocs.yml

@@ -1,10 +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/conf.py

Dockerfile

@@ -1,11 +1,9 @@
-ARG PY_VERSION=3.7
-FROM continuumio/miniconda3:4.8.2-alpine AS builder
-ARG PY_VERSION
+FROM mambaorg/micromamba:1.4.3
 
 EXPOSE 8888
 
 LABEL maintainer.name="mosdef-hub"\
-      maintainer.url="https://mosdef.org"
+  maintainer.url="https://mosdef.org"
 
 ENV PATH /opt/conda/bin:$PATH
 
@@ -15,30 +13,17 @@ ADD . /gmso
 
 WORKDIR /gmso
 
-RUN conda update conda -yq && \
-	conda config --set always_yes yes --set changeps1 no && \
-	. /opt/conda/etc/profile.d/conda.sh && \
-	sed -i -E "s/python.*$/python="$PY_VERSION"/" environment-dev.yml && \
-  conda install -c conda-forge mamba && \
-	mamba env create nomkl -f environment-dev.yml && \
-	conda activate gmso-dev && \
-	mamba install -c conda-forge nomkl jupyter && \
-        python setup.py install && \
-	echo "source activate gmso-dev" >> \
-	/home/anaconda/.profile && \
-	conda clean -afy && \
-	mkdir /home/anaconda/data && \
-	chown -R anaconda:anaconda /gmso && \
-	chown -R anaconda:anaconda /opt && \
-	chown -R anaconda:anaconda /home/anaconda
-
-WORKDIR /home/anaconda
-
-COPY devtools/docker-entrypoint.sh /entrypoint.sh
-
-RUN chmod a+x /entrypoint.sh
-
-USER anaconda
+RUN apt-get update && apt-get install -y git
+
+RUN micromamba create --file environment-dev.yml && \
+  micromamba clean -afy
+ARG MAMBA_DOCKERFILE_ACTIVATE=1  # (otherwise python will not be found)
+
+RUN  micromamba install -c conda-forge nomkl jupyter python="3.10" && \
+  python setup.py install && \
+  echo "source activate gmso-dev" >> /home/.bashrc && \
+  mkdir -p /home/data
+
 
 ENTRYPOINT ["/entrypoint.sh"]
 CMD ["jupyter"]

README.md

@@ -1,7 +1,7 @@
 ## GMSO: General Molecular Simulation Object
 ![](https://anaconda.org/conda-forge/gmso/badges/license.svg)
 [![](https://anaconda.org/conda-forge/gmso/badges/version.svg)](https://anaconda.org/conda-forge/gmso)
-[![Build Status](https://dev.azure.com/mosdef/mosdef/_apis/build/status/mosdef-hub.gmso?branchName=master)](https://dev.azure.com/mosdef/mosdef/_build/latest?definitionId=9&branchName=master)
+[![CI](https://github.com/mosdef-hub/gmso/actions/workflows/CI.yaml/badge.svg)](https://github.com/mosdef-hub/gmso/actions/workflows/CI.yaml)
 [![codecov](https://codecov.io/gh/mosdef-hub/gmso/branch/master/graph/badge.svg?token=rqPGwmXDzu)](undefined)
 
 `GMSO`is a flexible storage of chemical topology for molecular simulation.
@@ -14,23 +14,26 @@ To learn more, get started, or contribute, check out our [Documentation](https:/
   <img src="docs/images/mosdef_graphic_gmso.png?raw=true" alt="GMSO within the MoSDeF Ecosystem" width="500" height="500"/>
 </p>
 
-This is an example using `mBuild` and `Foyer` to build a `GMSO` topology through [`ParmEd`](https://parmed.github.io/ParmEd/html/index.html) and write out to [`LAMMPS`](https://docs.lammps.org/).
+This is an example using `mBuild` and `Foyer` to build a `GMSO` topology and write out to [`LAMMPS`](https://docs.lammps.org/).
 ```python
 import foyer
+import forcefield_utilities as ffutils
 from mbuild.lib.molecules import Ethane
-from gmso.external.convert_parmed import from_parmed
+from gmso.external.convert_mbuild import from_mbuild
+from gmso.parameterization import apply
 from gmso.formats.lammpsdata import write_lammpsdata
 # Start with a mBuild compound
 mb_ethane = Ethane()
-oplsaa = foyer.Forcefield(name='oplsaa')
+oplsaa = ffutils.FoyerFFs().load('oplsaa').to_gmso_ff()
 # atomtype the system with foyer, and convert the resulting structure to a topology
-typed_ethane = from_parmed(oplsaa.apply(mb_ethane))
-typed_ethane.name = 'ethane'
+gmso_ethane = from_mbuild(mb_ethane)
+apply(top=gmso_ethane,
+      forcefields=oplsaa,
+      identify_connections=True)
 # Write out lammps datafile
-write_lammpsdata(typed_ethane, filename='ethane.lammps', atom_style='full')
+write_lammpsdata(gmso_ethane, filename='ethane.lammps', atom_style='full')
 ```
 
-
 Introduction
 ------------
 
@@ -107,19 +110,36 @@ For full, detailed instructions, refer to the [documentation for installation](h
 conda install -c conda-forge gmso
 ```
 
-### `pip` installation quickstart
-_Note: `GMSO` is not on `pypi` currently, but its dependencies are._
+### Installing from source
 
-```bash
-git clone  https://github.com/mosdef-hub/gmso.git
+Dependencies of GMSO are listed in the files ``environment.yml`` (lightweight environment specification containing minimal dependencies) and ``environment-dev.yml`` (comprehensive environment specification including optional and testing packages for developers).
+The ``gmso`` or ``gmso-dev`` conda environments can be created with
+
+
+```.. code-block:: bash
+git clone https://github.com/mosdef-hub/gmso.git
 cd gmso
-pip install -r requirements.txt
-pip install -e .
+# for gmso conda environment
+conda env create -f environment.yml
+conda activate gmso
+
+# for gmso-dev
+conda env create -f environment-dev.yml
+conda activate gmso-dev
+
+# install a non-editable version of gmso
+pip install .
 ```
 
-`pip` quickstart will install `GMSO` in [`editable` mode](https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs), which means that as you edit the source code of `GMSO` those edits will be reflected in your installation.
+### Install an editable version from source
 
+Once all dependencies have been installed and the ``conda`` environment has been created, the ``GMSO`` itself can be installed.
 
+``` code-block:: bash
+cd gmso
+conda activate gmso-dev # or gmso depending on your installation
+pip install -e .
+```
 Documentation
 -------------