PR to speed up long read mapping #30 #111
Workflow file for this run
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name: CI | |
on: [push,pull_request] | |
jobs: | |
tests: | |
name: "Python ${{ matrix.python-version }}" | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash -el {0} | |
strategy: | |
matrix: | |
os: [macos-latest, ubuntu-latest] | |
python-version: ["3.8", "3.9"] | |
steps: | |
- uses: "actions/checkout@v3" | |
with: | |
fetch-depth: 0 | |
# Setup env | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
activate-environment: plassembler | |
environment-file: build/environment.yaml | |
python-version: ${{ matrix.python-version }} | |
auto-activate-base: false | |
miniforge-variant: Mambaforge | |
channels: conda-forge,bioconda,defaults | |
channel-priority: strict | |
auto-update-conda: true | |
- name: Install project | |
shell: bash -l {0} | |
run: | | |
mamba install python=${{ matrix.python-version }} | |
just install | |
python -m pip install --upgrade pip | |
pip3 install git+https://github.com/rrwick/Unicycler.git | |
unicycler --help | |
- name: Check formatting | |
shell: bash -l {0} | |
run: just check-fmt | |
- name: Test and generate coverage report with pytest | |
shell: bash -l {0} | |
# need to set TERM to linux for some reason,kept getting a nasty error that was breaking unicycler | |
# https://github.com/cypress-io/cypress/issues/15679 | |
run: | | |
export TERM=linux | |
unicycler --version | |
just test-ci | |
- name: Upload coverage reports to Codecov | |
uses: codecov/codecov-action@v3 | |