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Incorporate charge handling #124

Incorporate charge handling

Incorporate charge handling #124

Workflow file for this run

name: Continuous Integration / Deployment
on: [pull_request, push]
jobs:
Format:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Apply formatting
uses: github/super-linter@v4
env:
VALIDATE_ALL_CODEBASE: false
VALIDATE_PYTHON_PYLINT: true
VALIDATE_PYTHON_FLAKE8: true
VALIDATE_PYTHON_ISORT: true
DEFAULT_BRANCH: main
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
IGNORE_GITIGNORED_FILES: true
Test_Linux:
needs:
- Format
runs-on: ubuntu-latest
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Setup environment
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-variant: Mambaforge
miniforge-version: 4.9.2-4
use-mamba: true
environment-file: envs/linux.yml
use-only-tar-bz2: true
auto-activate-base: false
activate-environment: isicle
- name: Install ISiCLE
run: pip install --no-deps .
# - name: Test environment
# run: |
# pytest
Test_Mac:
needs:
- Format
runs-on: macos-latest
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Setup environment
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-variant: Mambaforge
miniforge-version: 4.9.2-4
use-mamba: true
environment-file: envs/osx.yml
use-only-tar-bz2: true
auto-activate-base: false
activate-environment: isicle
- name: Install ISiCLE
run: pip install --no-deps .
# - name: Test environment
# run: |
# pytest
Deploy:
needs:
- Test_Linux
- Test_Mac
runs-on: ubuntu-latest
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Setup environment
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-variant: Mambaforge
miniforge-version: 4.9.2-4
use-mamba: true
python-version: 3.9
channels: conda-forge,bioconda
use-only-tar-bz2: true
auto-activate-base: true
- name: Install dependencies
run: |
mamba install boa anaconda-client conda-verify
- name: Build conda package
run: |
mkdir build/
conda mambabuild conda-recipe/ --output-folder build/
conda index build/
- name: Convert to osx-64
run: conda convert -p osx-64 build/linux-64/*.tar.bz2 -o build/
- name: Upload packages
env:
ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
run: |
anaconda upload build/linux-64/*.tar.bz2
anaconda upload build/osx-64/*.tar.bz2