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Fix issue with gecco convert when given a relative path #301

Fix issue with gecco convert when given a relative path

Fix issue with gecco convert when given a relative path #301

Workflow file for this run

name: Package
on:
- push
- pull_request
jobs:
sdist:
runs-on: ubuntu-latest
name: Build source distribution
steps:
- name: Checkout code
uses: actions/checkout@v2
with:
submodules: true
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: List project dependencies
run: python setup.py list_requirements
- name: Install project dependencies
run: python -m pip install -r requirements.txt
- name: Build wheel distribution
run: python setup.py sdist
- name: Store built archive
uses: actions/upload-artifact@v2
with:
name: dist
path: dist/*
wheel:
runs-on: ubuntu-latest
name: Build wheel distribution
steps:
- name: Checkout code
uses: actions/checkout@v2
with:
submodules: true
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: List project dependencies
run: python setup.py list_requirements
- name: Install project dependencies
run: python -m pip install -r requirements.txt
- name: Build wheel distribution
run: python setup.py bdist_wheel
- name: Store built wheel
uses: actions/upload-artifact@v2
with:
name: dist
path: dist/*
upload:
environment: PyPI
runs-on: ubuntu-latest
name: Upload to PyPI
if: startsWith(github.ref, 'refs/tags/v')
permissions:
id-token: write
needs:
- sdist
- wheel
steps:
- name: Checkout code
uses: actions/checkout@v1
- name: Set up Python 3.9
uses: actions/setup-python@v1
with:
python-version: 3.9
- name: Download built distributions
uses: actions/download-artifact@v2
with:
name: dist
path: dist
- name: Publish distributions to PyPI
if: startsWith(github.ref, 'refs/tags/v')
uses: pypa/gh-action-pypi-publish@release/v1
changelog:
runs-on: ubuntu-latest
if: startsWith(github.ref, 'refs/tags/v')
name: Update GitHub release notes
needs: upload
steps:
- name: Checkout code
uses: actions/checkout@v1
- name: Release a Changelog
uses: rasmus-saks/[email protected]
with:
github-token: '${{ secrets.GITHUB_TOKEN }}'
attach:
runs-on: ubuntu-latest
name: Attach artifacts to GitHub release
if: startsWith(github.ref, 'refs/tags/v')
needs: changelog
steps:
- name: Checkout code
uses: actions/checkout@v2
with:
submodules: true
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: List project dependencies
run: python setup.py list_requirements
- name: Install project dependencies
run: python -m pip install -r requirements.txt
- name: Build new HMM artifacts
run: python setup.py build_data -f -r
- name: Compress Pfam HMM
run: gzip -c build/lib/gecco/hmmer/Pfam.h3m > Pfam.h3m.gz
- name: Upload HMM
uses: softprops/action-gh-release@v1
if: startsWith(github.ref, 'refs/tags/')
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
files: Pfam.h3m.gz