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Merge branch 'update_blast' of github.com:haddocking/arctic3d into up…
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mgiulini committed Mar 23, 2024
2 parents 7dcad2a + 54fed69 commit 88b90db
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47 changes: 47 additions & 0 deletions .github/workflows/docker-publish.yml
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name: build and publish image

on:
push:
# run only against tags
tags:
- "*"

env:
REGISTRY: ghcr.io
IMAGE_NAME: ${{ github.repository }}

# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
jobs:
build-and-push-image:
runs-on: ubuntu-latest
# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
permissions:
contents: read
packages: write

steps:
- name: Checkout repository
uses: actions/checkout@v4

# Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
- name: Log in to the Container registry
uses: docker/login-action@v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}

# This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@v5
with:
images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}

- name: Build and push
uses: docker/build-push-action@v5
with:
context: .
push: ${{ github.event_name != 'pull_request' }}
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
2 changes: 0 additions & 2 deletions CONTRIBUTING.md
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# Developing ARCTIC-3D

This section is still work in progress

## Installation

We use `poetry` to manage the dependencies and the virtual environment, so it makes things easier if you need to install it first; check the [official documentation](https://python-poetry.org/docs/#installation) for more details.
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6 changes: 6 additions & 0 deletions Dockerfile
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FROM python:3.10
WORKDIR /opt/software
COPY . .
RUN pip install .
WORKDIR /data
ENTRYPOINT [ "arctic3d" ]
15 changes: 15 additions & 0 deletions README.md
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Expand Up @@ -28,6 +28,15 @@ Check [CONTRIBUTING.md](CONTRIBUTING.md) for more information.

### With `conda`

Clone the repository on your computer and navigate to it

```bash
git clone [email protected]:haddocking/arctic3d.git
cd arctic3d
```

Here you can create the arctic3d environment:

```bash
conda create -n arctic3d python=3.10
conda activate arctic3d
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```

Then you can open the file `arctic3d-docs/index.html`, which contains all the necessary documentation.

## Citing us

If you used ARCTIC-3D in your work please cite the following publication:

**Marco Giulini, Rodrigo V. Honorato, Jesús L. Rivera, and Alexandre MJJ Bonvin**: "ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information." Communications Biology 7, no. 1 (2024): 49. (www.nature.com/articles/s42003-023-05718-w)
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