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feature.alignment function refactored #365

feature.alignment function refactored

feature.alignment function refactored #365

Workflow file for this run

# This is a basic workflow to help you get started with Actions
name: R Conda
# Controls when the workflow will run
on:
# Triggers the workflow on push or pull request events but only for the main branch
push:
branches: [ master ]
pull_request:
branches: [ master ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# This workflow contains a single job called "build"
build:
# The type of runner that the job will run on
runs-on: ubuntu-latest
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
defaults:
run:
shell: bash -l {0}
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v4
- name: Create conda environment
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: recetox-aplcms-dev
auto-update-conda: true
environment-file: conda/environment-dev.yaml
auto-activate-base: false
- run: |
conda init bash
conda env list
conda list
- name: Fetch test data
run: |
wget -P tests/testdata/adjusted -i tests/remote-files/adjusted.txt
wget -P tests/testdata/aligned -i tests/remote-files/aligned.txt
wget -P tests/testdata/extracted -i tests/remote-files/extracted.txt
wget -P tests/testdata/input -i tests/remote-files/input.txt
wget -P tests/testdata/recovered -i tests/remote-files/recovered.txt
wget -P tests/testdata/recovered/recovered-extracted -i tests/remote-files/recovered-extracted.txt
wget -P tests/testdata/recovered/recovered-corrected -i tests/remote-files/recovered-corrected.txt
wget -P tests/testdata/filtered -i tests/remote-files/filtered.txt
wget -P tests/testdata/filtered/run_filter -i tests/remote-files/run_filter.txt
wget -P tests/testdata/features -i tests/remote-files/features.txt
wget -P tests/testdata/clusters -i tests/remote-files/clusters.txt
wget -P tests/testdata/hybrid -i tests/remote-files/hybrid.txt
wget -P tests/testdata/template -i tests/remote-files/template.txt
wget -P tests/testdata/unsupervised -i tests/remote-files/unsupervised.txt
- name: Test coverage
run: |
conda activate recetox-aplcms-dev
Rscript -e "covr::codecov(quiet = FALSE)"