Build and Deploy workflow (pyranges/pyranges0)
The Build and Deploy workflow from pyranges/pyranges0, explained and optimized by Latchkey.
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What it does
This is the Build and Deploy workflow from the pyranges/pyranges0 repository, a real project running GitHub Actions. It is shown here with attribution under its MIT license.
Below, Latchkey shows a faster, safer version produced by its optimization engine.
The workflow
name: Build and Deploy
on: [workflow_dispatch]
jobs:
build-and-deploy:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2.3.1
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
echo $CONDA/bin >> $GITHUB_PATH
- name: Install pyranges
run: |
pip install cython
pip install sorted_nearest
python setup.py install
pip install bamread
pip install fisher
- name: Install dependencies
run: |
conda config --set always_yes yes --set changeps1 no
conda config --add channels bioconda
conda config --add channels r
conda install mamba -n base -c conda-forge
mamba install -c r r
mamba install -c conda-forge r-reticulate
# mamba install -c conda-forge r-bookdown
mamba install -y conda-forge::ncurses
mamba install -c conda-forge matplotlib
mamba install -c conda-forge pandoc
mamba install -c bioconda pybigwig
echo 'install.packages("bookdown")' > install.R
Rscript install.R
- name: Build book
run: |
cd book
Rscript compile.R
- name: Deploy
uses: JamesIves/github-pages-deploy-action@4.1.9
with:
branch: gh-pages # The branch the action should deploy to.
folder: book/build # The folder the action should deploy.
The same workflow, on Latchkey
Removes redundant runs and caps runaway jobs. Added and changed lines are highlighted.
name: Build and Deploy on: [workflow_dispatch] jobs: build-and-deploy: timeout-minutes: 30 runs-on: latchkey-small steps: - name: Checkout uses: actions/checkout@v2.3.1 - name: Add conda to system path run: | # $CONDA is an environment variable pointing to the root of the miniconda directory echo $CONDA/bin >> $GITHUB_PATH - name: Install pyranges run: | pip install cython pip install sorted_nearest python setup.py install pip install bamread pip install fisher - name: Install dependencies run: | conda config --set always_yes yes --set changeps1 no conda config --add channels bioconda conda config --add channels r conda install mamba -n base -c conda-forge mamba install -c r r mamba install -c conda-forge r-reticulate # mamba install -c conda-forge r-bookdown mamba install -y conda-forge::ncurses mamba install -c conda-forge matplotlib mamba install -c conda-forge pandoc mamba install -c bioconda pybigwig echo 'install.packages("bookdown")' > install.R Rscript install.R - name: Build book run: | cd book Rscript compile.R - name: Deploy uses: JamesIves/github-pages-deploy-action@4.1.9 with: branch: gh-pages # The branch the action should deploy to. folder: book/build # The folder the action should deploy.
What changed
- Run on Latchkey managed runners with one line (
runs-on), which apply the fixes below automatically and self-heal transient failures. This example useslatchkey-small; pick the runner size that fits the job. - Add a job timeout so a hung step cannot burn hours of runner time.
1 third-party action is referenced by a movable tag. Pin it to the commit SHA (Latchkey resolves and applies this automatically) so a repointed tag cannot change what runs.
What Latchkey heals here
This workflow has steps that commonly fail on transient issues (network, registries, flaky browsers). On Latchkey managed runners they are detected, retried, and self-healed instead of failing your build:
- Dependency installs
This workflow runs 1 job per trigger. On Latchkey the same minutes cost up to 58% less than GitHub-hosted, with zero queue time.