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Reproducible Research #145

Reproducible Research

Reproducible Research #145

Workflow file for this run

name: Reproducible Research
on:
push:
branches:
- master
pull_request:
branches:
- master
schedule:
- cron: 42 8 */21 * *
jobs:
tcpdbench-ubuntu:
name: Check TCPDBench (direct)
runs-on: ubuntu-latest
steps:
- name: Install dependencies
run: sudo apt-get update && sudo apt-get install build-essential latexmk texlive-latex-extra
shell: bash
- name: Install Python 3.8
uses: actions/setup-python@v2
with:
python-version: '3.8'
- name: Install R
uses: r-lib/actions/setup-r@v2-branch
with:
r-version: 'release'
- name: Install R dependencies
run: |
install.packages(c('argparse', 'exactRankTests'))
shell: Rscript {0}
- name: Checkout code
uses: actions/checkout@v2
with:
submodules: true
- name: Install Python dependencies
run: pip install -r ./analysis/requirements.txt
shell: bash
- name: Clone TCPD
run: git clone https://github.com/alan-turing-institute/TCPD ../TCPD
shell: bash
- name: Build TCPD
run: cd ../TCPD && make export
shell: bash
- name: Copy datasets
run: mkdir -p ./datasets && cp ../TCPD/export/*.json ./datasets/ && pwd && ls -1 .
shell: bash
- name: Skip annotation simulation p-values
run: touch ./analysis/output/tables/annotation_simulation_pvalues.tex
shell: bash
- name: Make results
run: make results
shell: bash
- name: Check results
run: git checkout ./analysis/output/cd_diagrams/*.pdf && git checkout ./analysis/output/figures/anno_hist/histogram*.pdf && git diff --exit-code
shell: bash
tcpdbench-docker:
name: Check TCPDBench (docker)
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2
- name: TCPDBench docker check
run: ./.github/scripts/test_docker.sh
shell: bash