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chrisjonesBSU
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‎.github/workflows/build.yml‎

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name: build
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on:
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push:
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branches: [ main ]
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# Run when container or environment is changed
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paths:
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- containers/dockerfile_cpu
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- environment.yml
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# Allows workflow to be manually triggered
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workflow_dispatch:
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defaults:
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run:
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shell: bash -l {0}
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: cmelab/grits
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DOCKERFILE: containers/dockerfile_cpu
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jobs:
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build:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout
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uses: actions/checkout@main
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with:
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fetch-depth: 0
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- name: Get Latest Version
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id: latest-version
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run: |
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LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
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echo $LATEST_TAG
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echo "LATEST_TAG=$LATEST_TAG" >> $GITHUB_OUTPUT
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# slice off the v, ie v0.7.2 -> 0.7.2
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VERSION=${LATEST_TAG:1}
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echo $VERSION
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echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
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- name: Print Latest Version
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run: echo ${{ steps.latest-version.outputs.VERSION }}
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- name: Create fully qualified image registry path
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id: fqirp
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run: |
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FQIRP=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }}
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echo "FQIRP=$FQIRP" >> $GITHUB_OUTPUT
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- name: Print FQIRP
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run: echo ${{ steps.fqirp.outputs.FQIRP }}
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- name: Login to GitHub Container Registry
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uses: docker/login-action@v1
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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tags: |
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type=semver,pattern={{version}},prefix=v
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${{ steps.latest-version.outputs.VERSION }}
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- name: Build Docker Image
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uses: docker/build-push-action@v4
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with:
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context: .
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file: ${{ env.DOCKERFILE }}
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load: true
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push: false
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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VERSION=${{ steps.latest-version.outputs.VERSION }}
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- name: Test image
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run: |
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docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
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- name: Push Docker image
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uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
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with:
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context: .
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file: ${{ env.DOCKERFILE }}
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push: ${{ github.event_name == 'workflow_dispatch' }}
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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VERSION=${{ steps.latest-version.outputs.VERSION }}

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.5.0
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rev: v4.6.0
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hooks:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- repo: https://github.com/psf/black
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rev: 24.1.1
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rev: 24.4.2
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hooks:
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- id: black
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args: [--line-length=80]

‎README.md‎

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# GRiTS : Grits Reduces/Restores Topology with SMILES
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[![Anaconda-Server Badge](https://anaconda.org/conda-forge/grits/badges/version.svg)](https://anaconda.org/conda-forge/grits)
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[![Docker Repository on Quay](https://quay.io/repository/cmelab/grits/status "Docker Repository on Quay")](https://quay.io/repository/cmelab/grits)
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[![pytest](https://github.com/cmelab/grits/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/pytest.yml)
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[![codecov](https://codecov.io/gh/cmelab/grits/branch/main/graph/badge.svg?token=lGG8Zf65HP)](https://codecov.io/gh/cmelab/grits)
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[![Documentation Status](https://readthedocs.org/projects/grits/badge/?version=latest)](https://grits.readthedocs.io/en/latest/?badge=latest)
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[![Docker build](https://github.com/cmelab/grits/actions/workflows/build.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/build.yml)
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![GRiTS workflow](/.github/grits.png)
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@@ -11,29 +12,21 @@ GRiTS is a toolkit for working with coarse-grain systems. It uses [mBuild](https
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### Installation
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#### Using a container
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14-
To use GRiTS in a prebuilt container (using [Singularity](https://singularity.lbl.gov/)), run:
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To use GRiTS in a prebuilt container (using [Apptainer](https://apptainer.org/)), run:
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```bash
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singularity pull docker://quay.io/cmelab/grits:latest
17-
singularity exec grits_latest.sif bash
17+
apptainer pull docker://ghcr.io/cmelab/grits:latest
18+
apptainer run grits_latest.sif python
1819
```
1920

2021
**Or** using [Docker](https://docs.docker.com/), run:
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```bash
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docker pull quay.io/cmelab/grits:latest
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docker pull ghcr.io/cmelab/grits:latest
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docker run -it cmelab/grits:latest
2425
```
2526

26-
#### Custom install
27-
To create a local environment with [conda](https://docs.conda.io/en/latest/miniconda.html), run:
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#### Micromamba install
28+
To create a local environment with [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html), run:
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```bash
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conda env create -f environment.yml
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conda activate grits
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```
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With the `grits` environment active, install the package with pip:
33-
```
34-
pip install .
35-
```
36-
And to test your installation, run:
37-
```
38-
pytest
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micromamba create grits -f environment.yml
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micromamba activate grits
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```

‎containers/dockerfile_cpu‎

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FROM mambaorg/micromamba:0.15.2
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FROM mambaorg/micromamba:1.4.1
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COPY --chown=micromamba:micromamba environment.yml /tmp/env.yml
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ARG VERSION
44

5-
RUN micromamba install -y -n base -f /tmp/env.yml && \
6-
micromamba clean --all --yes
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8-
COPY grits/ /tmp/grits/
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COPY setup.py /tmp/
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RUN ls -la /tmp
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ENV PYTHONUNBUFFERED=1
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14-
RUN python -m pip install /tmp
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COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yml
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16-
RUN pytest -vx
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USER root
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20-
RUN rm -r /tmp/*
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RUN micromamba install -y -n base "grits==$VERSION" -f /tmp/env.yml && \
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micromamba clean --all --yes
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22-
RUN python -c "import grits"
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ARG MAMBA_DOCKERFILE_ACTIVATE=1

‎docs/environment-docs.yml‎

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@@ -7,9 +7,10 @@ dependencies:
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- numpydoc
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- sphinx
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- sphinx_rtd_theme
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- cmeutils
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- ele
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- freud
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- gsd
13-
- mbuild
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- mbuild>=0.17
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- numpy
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- openbabel

‎environment.yml‎

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channels:
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- conda-forge
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dependencies:
5-
- python=3.10
6-
- numpy
5+
- cmeutils >=1.3.0
76
- ele
8-
- freud>=2.13.1
9-
- gsd>=3.0
7+
- freud >=3.0
8+
- gsd >=3.0
109
- jupyterlab
11-
- mbuild
10+
- mbuild >=0.17.1
1211
- ele
13-
- freud
12+
- numpy
1413
- openbabel
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- pip
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- pre-commit
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- py3Dmol
1817
- pytest
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- pytest-cov
20-
- rdkit
21-
- cmeutils >= 1.2.0
19+
- python >=3.10

‎grits/coarsegrain.py‎

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@@ -10,7 +10,7 @@
1010
import freud
1111
import gsd.hoomd
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import numpy as np
13-
from cmeutils.gsd_utils import identify_snapshot_connections
13+
from cmeutils.gsd_utils import get_molecule_cluster, identify_snapshot_connections
1414
from ele import element_from_symbol
1515
from mbuild import Compound, clone
1616
from mbuild.utils.io import run_from_ipython
@@ -24,7 +24,6 @@
2424
get_quaternion,
2525
has_common_member,
2626
has_number,
27-
snap_molecules,
2827
)
2928

3029
__all__ = ["CG_Compound", "CG_System", "Bead"]
@@ -362,7 +361,7 @@ def visualize(
362361
if atom_names:
363362
atomistic.save(
364363
os.path.join(tmp_dir, "atomistic_tmp.mol2"),
365-
show_ports=show_ports,
364+
include_ports=show_ports,
366365
overwrite=True,
367366
)
368367

@@ -397,7 +396,7 @@ def visualize(
397396
simplefilter("ignore")
398397
coarse.save(
399398
os.path.join(tmp_dir, "coarse_tmp.mol2"),
400-
show_ports=show_ports,
399+
include_ports=show_ports,
401400
overwrite=True,
402401
)
403402
with open(os.path.join(tmp_dir, "coarse_tmp.mol2"), "r") as f:
@@ -574,7 +573,7 @@ def _get_compounds(
574573
conversion_dict[i].symbol for i in snap.particles.types
575574
]
576575
# Break apart the snapshot into separate molecules
577-
molecules = snap_molecules(snap)
576+
molecules = get_molecule_cluster(snap=snap)
578577
mol_inds = []
579578
for i in range(max(molecules) + 1):
580579
mol_inds.append(np.where(molecules == i)[0])
@@ -667,7 +666,7 @@ def save_mapping(self, filename):
667666
json.dump(self.mapping, f, cls=NumpyEncoder)
668667
print(f"Mapping saved to {filename}")
669668

670-
def save(self, cg_gsdfile, start=0, stop=None):
669+
def save(self, cg_gsdfile, start=0, stop=None, stride=1):
671670
"""Save the coarse-grain system to a gsd file.
672671
673672
Does not calculate the image of the coarse-grain bead.
@@ -688,6 +687,8 @@ def save(self, cg_gsdfile, start=0, stop=None):
688687
stop : int, default None
689688
Where to stop reading the gsd trajectory the system was created
690689
with. If None, will stop at the last frame.
690+
stride : int, default 1
691+
The step size to use when iterating through start:stop
691692
"""
692693
typeid = []
693694
types = [i.split("...")[0] for i in self.mapping]
@@ -722,7 +723,7 @@ def save(self, cg_gsdfile, start=0, stop=None):
722723
) as old:
723724
# stop being None is fine; slicing [0:None] gives whole array,
724725
# even in edge case where there's only one or two frames
725-
for s in old[start:stop]:
726+
for s in old[start:stop:stride]:
726727
new_snap = gsd.hoomd.Frame()
727728
position = []
728729
mass = []

‎grits/tests/test_coarsegrain.py‎

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@@ -213,6 +213,19 @@ def test_benzene(self, tmp_path):
213213
cg_json = tmp_path / "cg-benzene.json"
214214
system.save_mapping(cg_json)
215215

216+
def test_stride(self, tmp_path):
217+
gsdfile = path.join(asset_dir, "benzene-aa.gsd")
218+
system = CG_System(
219+
gsdfile,
220+
beads={"_B": "c1ccccc1"},
221+
conversion_dict=amber_dict,
222+
mass_scale=12.011,
223+
)
224+
cg_gsd = tmp_path / "cg-benzene.gsd"
225+
system.save(cg_gsdfile=cg_gsd, start=0, stop=-1, stride=2)
226+
with gsd.hoomd.open(cg_gsd) as f:
227+
assert len(f) == 3
228+
216229
def test_anisobenzene(self, tmp_path):
217230
gsdfile = path.join(asset_dir, "benzene-aa.gsd")
218231
system = CG_System(

‎grits/utils.py‎

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8282
return comp
8383

8484

85-
def snap_molecules(snap):
86-
"""Get the molecule indices based on bonding in a gsd.hoomd.Frame."""
87-
system = freud.AABBQuery.from_system(snap)
88-
n_query_points = n_points = snap.particles.N
89-
query_point_indices = snap.bonds.group[:, 0]
90-
point_indices = snap.bonds.group[:, 1]
91-
distances = system.box.compute_distances(
92-
system.points[query_point_indices], system.points[point_indices]
93-
)
94-
nlist = freud.NeighborList.from_arrays(
95-
n_query_points, n_points, query_point_indices, point_indices, distances
96-
)
97-
cluster = freud.cluster.Cluster()
98-
cluster.compute(system=system, neighbors=nlist)
99-
return cluster.cluster_idx
100-
101-
10285
def align(compound, particle, towards_compound, around=None):
10386
"""Spin a compound such that particle points at towards_compound.
10487

‎pyproject.toml‎

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[build-system]
2-
requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
2+
requires = ["setuptools>=61.2", "versioningit"]
33
build-backend = "setuptools.build_meta"
44

5-
[tool.setuptools_scm]
6-
write_to = "grits/__version__.py"
5+
[project]
6+
name = "grits"
7+
description = "A toolkit for working with coarse-grained systems"
8+
readme = "README.md"
9+
authors = [{name = "Jenny Fothergill", email = "[email protected]"}]
10+
license= {text = "GPLv3"}
11+
classifiers=[
12+
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
13+
"Programming Language :: Python",
14+
"Programming Language :: Python :: 3",
15+
]
16+
urls = {Homepage = "https://github.com/cmelab/grits"}
17+
requires-python = ">=3.8"
18+
dynamic = ["version"]
19+
20+
[tool.setuptools]
21+
zip-safe = false
22+
include-package-data = true
23+
license-files = ["LICENSE"]
24+
25+
[tool.setuptools.packages]
26+
find = {namespaces = false}
27+
28+
[tool.setuptools.package-data]
29+
grits = ['"./compounds/*"']
30+
31+
[tool.versioningit]
32+
default-version = "1+unknown"
33+
34+
[tool.versioningit.format]
35+
distance = "{base_version}+{distance}.{vcs}{rev}"
36+
dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
37+
distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
38+
39+
[tool.versioningit.vcs]
40+
method = "git"
41+
match = ["*"]
42+
default-tag = "0.0.0"

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