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Update pypi_publish.yml

Update pypi_publish.yml #246

Workflow file for this run

.github/workflows/CI_build.yml at 36553f0
name: CI Build
on:
push:
pull_request:
types: [opened, reopened]
jobs:
first_check:
name: first code check / python-3.8 / ubuntu-latest
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v1
with:
python-version: 3.8
- name: Python info
run: |
which python
python --version
- name: Build package and create dev environment
run: |
python -m pip install --upgrade pip
pip install -e .[dev]
- name: Show pip list
run: |
pip list
- name: Test with coverage
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
shell: bash -l {0}
run: isort --check-only --diff --conda-env spec2vec-dev .
- name: SonarCloud Scan
if: github.repository == 'iomega/spec2vec'
uses: sonarsource/sonarcloud-github-action@master
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
build_pypi:
name: Pypi and documentation build / python-${{ 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: ['3.7', '3.8', '3.9']
exclude:
# already tested in first_check job
- python-version: 3.8
os: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Python info
run: |
which python
python --version
- name: Install dependencies
run: |
python -m pip install --upgrade pip
- name: Build package
run: |
pip install wheel twine
python setup.py sdist bdist_wheel
- name: Test package
run: |
python -m twine check dist/*
- name: Show pip list
run: |
pip list
- name: Install development dependencies
run: |
pip install -e .[dev]
- name: Test
run: |
pytest
- name: Show environment variables
shell: bash -l {0}
run: |
env | sort
- name: Build documentation
shell: bash -l {0}
run: |
make coverage doctest html
working-directory: readthedocs/
env:
SPHINXOPTS: "-n" # enable nit-picky mode
- name: Check documentation coverage threshold
if: matrix.os == 'ubuntu-latest'
run: |
cat readthedocs/_build/coverage/python.txt
UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l)
UNCOVERED_MEMBERS_ALLOWED=5
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 ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
anaconda_build:
name: Anaconda build / python-3.7 / ubuntu-latest
runs-on: ubuntu-latest
strategy:
fail-fast: false
needs: first_check
steps:
- uses: actions/checkout@v2
with:
fetch-depth: "0"
- name: Create spec2vec-build environment
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: spec2vec-build
auto-update-conda: true
environment-file: conda/environment-build.yml
python-version: 3.8
- name: Show conda config
shell: bash -l {0}
run: |
conda info
conda list
conda config --show-sources
conda config --show
conda env list
- name: Python info
shell: bash -l {0}
run: |
which python
python --version
- name: Show environment variables
shell: bash -l {0}
run: |
env | sort
- name: Build the conda package
shell: bash -l {0}
run: |
export BUILDDIR=$RUNNER_TEMP/spec2vec/_build
[ "$RUNNING_OS" = "Windows" ] && export BUILDDIR=$RUNNER_TEMP\\spec2vec\\_build\\
conda config --set anaconda_upload no
conda build --no-include-recipe \
--channel bioconda --channel conda-forge \
--croot ${BUILDDIR} \
./conda
- name: Upload package artifact from build
uses: actions/upload-artifact@v2
with:
name: conda-package-artifact
path: ${{ runner.temp }}/spec2vec/_build