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alanbchristiealanbchristie
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Merge pull request #50 from xchem/m2ms-2076
Introduce xchem-style release CI (and build)
2 parents 1b6e3e6 + 03cea75 commit 5cfa62f

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‎.github/workflows/build-latest.yml‎

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‎.github/workflows/pip-release.yml‎

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‎.github/workflows/release.yaml‎

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---
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# The standard xchem Python package release process.
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# Run on 'Release' and published to PyPI as a 'trusted' publisher.
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#
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# See https://docs.pypi.org/trusted-publishers/creating-a-project-through-oidc/
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# See https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
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name: Release
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on:
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release:
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types:
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- published
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jobs:
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build:
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name: Build distribution
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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with:
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persist-credentials: false
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.x'
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- name: Install build package
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run: |
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python3 -m pip install --upgrade pip
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python3 -m pip install uv==0.10.6 --user
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- name: Build
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run: uv build
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env:
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FRAG_VERSION: ${{ github.ref_name }}
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- name: Store the distribution
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uses: actions/upload-artifact@v5
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with:
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name: python-package-distribution
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path: dist/
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publish:
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name: Publish to PyPI
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/xchem-hippo
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permissions:
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id-token: write
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steps:
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- name: Download distribution
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uses: actions/download-artifact@v6
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with:
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name: python-package-distribution
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path: dist/
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- name: Publish
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/test.yaml‎

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---
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name: Test
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# Actions that take place after every commit
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# Here every commit is built, tagged as 'latest' and tested.
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#
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# Actions also run on a schedule - the the container is built, tested
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# and pushed (if the relevant secrets are set) based on
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# a defined schedule.
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on:
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push:
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branches:
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- '*'
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tags-ignore:
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- '**'
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schedule:
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# Build every Sunday (0) at 4:45pm
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- cron: '45 16 * * 0'
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jobs:
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source:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version:
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- "3.10"
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- "3.11"
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install requirements
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run: |
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pip install -r build-requirements.txt
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pip install -e .
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pip install rdkit==2023.3.2
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- name: Lint
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run: pre-commit run --all-files
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- name: Test
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run: python -m unittest
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image:
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runs-on: ubuntu-latest
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needs:
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- source
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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- name: Build
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uses: docker/build-push-action@v6
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with:
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context: .
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tags: xchem/frag:latest
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- name: Test
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run: docker run xchem/frag:latest /bin/sh -c "cd /usr/local/frag && python -m unittest"

‎Dockerfile‎

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FROM python:3.11.4-slim-bullseye
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FROM python:3.11.15-slim
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USER root
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RUN apt-get --allow-releaseinfo-change update && \
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apt-get install -y \
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RUN apt-get --allow-releaseinfo-change update \
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&& apt-get install -y \
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git \
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libfontconfig1 \
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libsm6 \
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libxrender1 \
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procps && \
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pip install rdkit==2023.3.2 && \
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git clone https://github.com/rdkit/mmpdb /usr/local/mmpdb && \
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pip install /usr/local/mmpdb
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procps \
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&& pip install rdkit==2023.3.2 \
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&& git clone https://github.com/rdkit/mmpdb /usr/local/mmpdb \
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&& pip install /usr/local/mmpdb
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COPY requirements.txt ./
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RUN pip install -r requirements.txt
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ADD . /usr/local/fragalysis
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RUN pip install /usr/local/fragalysis
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ADD . /usr/local/frag
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RUN pip install /usr/local/frag

‎README.md‎

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# Fragalysis Package
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# Frag
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[![build latest](https://github.com/xchem/fragalysis-package/actions/workflows/build-latest.yml/badge.svg)](https://github.com/xchem/fragalysis-package/actions/workflows/build-latest.yml)
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[![pip release](https://github.com/xchem/fragalysis-package/actions/workflows/pip-release.yml/badge.svg)](https://github.com/xchem/fragalysis-package/actions/workflows/pip-release.yml)
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[![test](https://github.com/xchem/frag/actions/workflows/test.yaml/badge.svg)](https://github.com/xchem/frag/actions/workflows/test.yaml)
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[![release](https://github.com/xchem/frag/actions/workflows/release.yaml/badge.svg)](https://github.com/xchem/frag/actions/workflows/release.yaml)
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[![License](http://img.shields.io/badge/license-Apache%202.0-blue.svg?style=flat)](https://github.com/xchem/fragalysis-package/blob/master/LICENSE.txt)
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[![License](http://img.shields.io/badge/license-Apache%202.0-blue.svg?style=flat)](https://github.com/xchem/frag/blob/master/LICENSE.txt)
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![PyPI](https://img.shields.io/pypi/v/fragalysis-package)
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![PyPI](https://img.shields.io/pypi/v/xchem-frag)
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[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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Basic RDKit based Python tools for analysis of protein-ligand interactions.
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> This was originally the fragalysis GitHub repository, which is now being used for
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another purpose. You can still find the original package on PyPI at
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https://pypi.org/project/fragalysis/ where the latest version posted was v1.1.0.
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All new releases of this package will come from here, with the new name
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`fragalysis-package`.
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another purpose. All new releases of this package will come from here,
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with the new name `xchem-frag`.
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Currently contains: -
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pre-commit run --all-files
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## Publishing (to PyPI)
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If the repository has been provided with a `PYPI_APIKEY` **Secret**
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the GitHub `pip-release` workflow action will automatically publish the package to
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PyPI when you create a new **Release**. The package version will be set using
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the release `tag_name`.
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We rely on out **release** GitHub workflow to publish to PyPI, something that
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is done automatically when the repository main branch is tagged.
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---
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‎frag/tests/test_network.py‎

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:return:
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"""
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try:
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nodes = [x for x in open("frag/tests/data/nodes.txt").readlines()]
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edges = [x.split() for x in open("frag/tests/data/edges.txt").readlines()]
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attrs = [
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Attr(input_str=x)
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for x in open("frag/tests/data/attributes.txt").readlines()
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]
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with open("frag/tests/data/nodes.txt", encoding="utf8") as n_file:
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nodes: list[str] = n_file.readlines()
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attrs: list[Attr] = []
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with open("frag/tests/data/attributes.txt", encoding="utf8") as n_file:
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attrs.extend(Attr(input_str=line) for line in n_file)
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except IOError:
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nodes = [x for x in open("data/nodes.txt").readlines()]
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edges = [x.split() for x in open("data/edges.txt").readlines()]
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attrs = [Attr(input_str=x) for x in open("data/attributes.txt").readlines()]
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with open("data/nodes.txt", encoding="utf8") as n_file:
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nodes: list[str] = n_file.readlines()
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attrs: list[Attr] = []
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with open("data/attributes.txt", encoding="utf8") as a_file:
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attrs.extend(Attr(input_str=line) for line in a_file)
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node_holder = NodeHolder(iso_flag=True)
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node_holder = build_network(attrs, node_holder)
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# Create the nodes and test with output
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# Close enough - and the output looks right...
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self.assertEqual(len(node_holder.get_edges()), 3687)
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@unittest.skip("build_network() causes a segmentation fault")
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def test_generate_nodes_non_iso(self):
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"""
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Test we can generate nodes for the basic data.
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:return:
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"""
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try:
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nodes = [x for x in open("frag/tests/data/nodes.txt").readlines()]
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edges = [x.split() for x in open("frag/tests/data/edges.txt").readlines()]
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attrs = [
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Attr(input_str=x)
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for x in open("frag/tests/data/attributes.txt").readlines()
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]
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with open("frag/tests/data/nodes.txt", encoding="utf8") as n_file:
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nodes: list[str] = n_file.readlines()
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attrs: list[Attr] = []
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with open("frag/tests/data/attributes.txt", encoding="utf8") as n_file:
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attrs.extend(Attr(input_str=line) for line in n_file)
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except IOError:
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nodes = [x for x in open("data/nodes.txt").readlines()]
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edges = [x.split() for x in open("data/edges.txt").readlines()]
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attrs = [Attr(input_str=x) for x in open("data/attributes.txt").readlines()]
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with open("data/nodes.txt", encoding="utf8") as n_file:
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nodes: list[str] = n_file.readlines()
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attrs: list[Attr] = []
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with open("data/attributes.txt", encoding="utf8") as a_file:
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attrs.extend(Attr(input_str=line) for line in a_file)
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node_holder = NodeHolder(iso_flag=False)
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node_holder = build_network(attrs, node_holder)
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# Create the nodes and test with output

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools >= 82.0.0"]
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build-backend = "setuptools.build_meta"

‎requirements.txt‎

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