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update to peotry as a buildsystem and update dependencies #129

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update to peotry as a buildsystem and update dependencies

update to peotry as a buildsystem and update dependencies #129

Workflow file for this run

.github/workflows/CI_build.yml at 5c38853
name: CI Build
on:
push:
pull_request:
types: [opened, reopened]
workflow_dispatch:
inputs:
tag:
description: Tag for manually running CI Build workflow
required: False
default: ''
jobs:
first_check:
name: first code check / python-3.10 / ubuntu-latest
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.10
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Python info
run: |
which python
python --version
- name: Build package and create dev environment
run: |
python -m pip install --upgrade pip poetry
poetry install
- name: Show pip list
run: |
pip list
- name: Test with coverage
run: |
poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
- name: Correct coverage paths
run: sed -i "s+$PWD/++g" coverage.xml
- name: Check style against standards using prospector
shell: bash -l {0}
run: prospector -o grouped -o pylint:pylint-report.txt
- name: Check whether import statements are used consistently
run: isort . --check-only --diff
build_pypi:
name: Test pypi build
runs-on: ubuntu-latest
needs: first_check
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.10
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Python info
run: |
which python
python --version
- name: Install dependencies
run: |
python -m pip install --upgrade pip poetry
- name: Build package
run: |
poetry build
- name: Test package
run: |
poetry install --only dev
python -m twine check dist/*
- name: Show pip list
run: |
pip list
- name: Install development dependencies
run: |
poetry install
- name: Show pip list again
run: |
pip list
- name: Run tests
run: |
poetry run pytest
- name: Show environment variables
shell: bash -l {0}
run: |
env | sort
test_dev:
name: test dev environment / python-${{ matrix.python-version }} / ${{ matrix.os }}
runs-on: ${{ matrix.os }}
needs: first_check
strategy:
fail-fast: false
matrix:
os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
python-version: ['3.10', '3.11', '3.12', '3.13']
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Python info
run: |
which python
python --version
- name: Install dependencies (includinv dev + chemistry)
run: |
python -m pip install --upgrade pip poetry
poetry install
- name: Show pip list
run: |
pip list
- name: Run tests
run: |
poetry run pytest
test_with_conda:
name: Anaconda build and test documentation
runs-on: ubuntu-latest
needs: first_check
steps:
- uses: actions/checkout@v4
with:
fetch-depth: "0"
- name: Create conda environment
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
python-version: '3.10'
- name: Show conda config
shell: bash -l {0}
run: |
conda info
conda list
conda config --show-sources
conda config --show
conda env list
- name: Python info
shell: bash -l {0}
run: |
which python
python --version
- name: Show environment variables
shell: bash -l {0}
run: |
env | sort
- name: Install conda dependencies
shell: bash -l {0}
run: |
conda install -c conda-forge poetry
- name: Install with development dependencies
shell: bash -l {0}
run: |
python -m pip install --upgrade pip
poetry install --with dev,docs
- name: Build documentation
shell: bash -l {0}
run: |
make coverage doctest html
working-directory: readthedocs/
env:
SPHINXOPTS: "-n" # enable nit-picky mode
- name: Check documentation coverage threshold
run: |
cat readthedocs/_build/coverage/python.txt
UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l)
UNCOVERED_MEMBERS_ALLOWED=10
if (( $UNCOVERED_MEMBERS > $UNCOVERED_MEMBERS_ALLOWED )) ; then echo "There are currently ${UNCOVERED_MEMBERS} uncovered members in the documentation, which is more than the ${UNCOVERED_MEMBERS_ALLOWED} allowed." && exit 1;fi
echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
- name: Test with coverage
shell: bash -l {0}
run: |
poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
- name: Correct coverage paths
run: sed -i "s+$PWD/++g" coverage.xml
- name: Store PR metadata in json file
env:
PR_NUMBER: ${{ github.event.pull_request.number }}
HEAD_REF: ${{ github.event.pull_request.head.ref }}
BASE_REF: ${{ github.event.pull_request.base.ref }}
run: |
jq -n --arg pr_number "$PR_NUMBER"\
--arg head_ref "$HEAD_REF"\
--arg base_ref "$BASE_REF"\
'{"pr_number": $pr_number, "head_ref": $head_ref, "base_ref": $base_ref}' > pr_metadata.json
- uses: actions/upload-artifact@v4
with:
name: sonarcloud-data-conda
path: |
coverage.xml
xunit-result.xml
pr_metadata.json