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name: CI | ||
on: | ||
pull_request: | ||
branches: ["main"] | ||
push: | ||
branches: ["main"] | ||
|
||
jobs: | ||
test: | ||
environment: dev | ||
runs-on: ubuntu-latest | ||
outputs: | ||
latest-dev-tag: ${{ steps.fetch_latest_tags.outputs.latest-dev-tag }} | ||
latest-stable-tag: ${{ steps.fetch_latest_tags.outputs.latest-stable-tag }} | ||
steps: | ||
- uses: actions/checkout@v4 | ||
|
||
- name: Checkout utilities | ||
uses: actions/checkout@v4 | ||
with: | ||
repository: bokulich-lab/utilities | ||
token: ${{ secrets.BOTULICH_TOKEN }} | ||
path: utilities | ||
|
||
- name: Install dependencies | ||
run: python -m pip install requests | ||
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||
- name: Fetch latest tags | ||
id: fetch-tags | ||
run: | | ||
latest_tags=$(python utilities/ci/get-tags.py) | ||
echo "$latest_tags" > tags.txt | ||
echo "latest-dev-tag=$(grep 'latest-dev-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT | ||
echo "latest-stable-tag=$(grep 'latest-stable-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT | ||
- name: Create conda yaml | ||
run: | | ||
bash utilities/ci/get-dependencies.sh ${{ vars.DISTRO }} ${{ steps.fetch-tags.outputs.latest-dev-tag }} | ||
cat environment.yml | ||
- name: Setup miniconda | ||
uses: conda-incubator/setup-miniconda@v3 | ||
with: | ||
python-version: 3.8 | ||
mamba-version: "*" | ||
channels: conda-forge,defaults | ||
channel-priority: true | ||
activate-environment: conda-env | ||
condarc-file: utilities/ci/condarc | ||
# use-only-tar-bz2: true | ||
|
||
- name: Get date | ||
id: get-date | ||
run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | ||
shell: bash | ||
|
||
- name: Cache Conda env | ||
uses: actions/cache@v3 | ||
with: | ||
path: /usr/share/miniconda/envs | ||
key: | ||
conda-${{ runner.os }}--${{ runner.arch }}--${{ | ||
steps.get-date.outputs.today }}-${{ | ||
hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER | ||
}} | ||
env: | ||
# Increase this value to reset cache if environment.yml has not changed | ||
CACHE_NUMBER: 0 | ||
id: cache | ||
|
||
- name: Update environment | ||
run: | ||
mamba env update -n conda-env -f environment.yml | ||
if: steps.cache.outputs.cache-hit != 'true' | ||
|
||
- name: Install plugin | ||
run: pip install . | ||
|
||
- name: Install dev dependencies | ||
run: pip install pytest coverage | ||
|
||
- name: Run tests | ||
run: make test-cov | ||
|
||
- uses: codecov/codecov-action@v4 | ||
name: Upload coverage report | ||
with: | ||
files: ./coverage.xml | ||
fail_ci_if_error: true | ||
env: | ||
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | ||
# name: CI | ||
# on: | ||
# pull_request: | ||
# branches: ["main"] | ||
# push: | ||
# branches: ["main"] | ||
# | ||
# jobs: | ||
# test: | ||
# environment: dev | ||
# runs-on: ubuntu-latest | ||
# outputs: | ||
# latest-dev-tag: ${{ steps.fetch_latest_tags.outputs.latest-dev-tag }} | ||
# latest-stable-tag: ${{ steps.fetch_latest_tags.outputs.latest-stable-tag }} | ||
# steps: | ||
# - uses: actions/checkout@v4 | ||
# | ||
# - name: Checkout utilities | ||
# uses: actions/checkout@v4 | ||
# with: | ||
# repository: bokulich-lab/utilities | ||
# token: ${{ secrets.BOTULICH_TOKEN }} | ||
# path: utilities | ||
# | ||
# - name: Install dependencies | ||
# run: python -m pip install requests | ||
# | ||
# - name: Fetch latest tags | ||
# id: fetch-tags | ||
# run: | | ||
# latest_tags=$(python utilities/ci/get-tags.py) | ||
# echo "$latest_tags" > tags.txt | ||
# echo "latest-dev-tag=$(grep 'latest-dev-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT | ||
# echo "latest-stable-tag=$(grep 'latest-stable-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT | ||
# | ||
# - name: Create conda yaml | ||
# run: | | ||
# bash utilities/ci/get-dependencies.sh ${{ vars.DISTRO }} ${{ steps.fetch-tags.outputs.latest-dev-tag }} | ||
# cat environment.yml | ||
# | ||
# - name: Setup miniconda | ||
# uses: conda-incubator/setup-miniconda@v3 | ||
# with: | ||
# python-version: 3.8 | ||
# mamba-version: "*" | ||
# channels: conda-forge,defaults | ||
# channel-priority: true | ||
# activate-environment: conda-env | ||
# condarc-file: utilities/ci/condarc | ||
# # use-only-tar-bz2: true | ||
# | ||
# - name: Get date | ||
# id: get-date | ||
# run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | ||
# shell: bash | ||
# | ||
# - name: Cache Conda env | ||
# uses: actions/cache@v3 | ||
# with: | ||
# path: /usr/share/miniconda/envs | ||
# key: | ||
# conda-${{ runner.os }}--${{ runner.arch }}--${{ | ||
# steps.get-date.outputs.today }}-${{ | ||
# hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER | ||
# }} | ||
# env: | ||
# # Increase this value to reset cache if environment.yml has not changed | ||
# CACHE_NUMBER: 0 | ||
# id: cache | ||
# | ||
# - name: Update environment | ||
# run: | ||
# mamba env update -n conda-env -f environment.yml | ||
# if: steps.cache.outputs.cache-hit != 'true' | ||
# | ||
# - name: Install plugin | ||
# run: pip install . | ||
# | ||
# - name: Install dev dependencies | ||
# run: pip install pytest coverage | ||
# | ||
# - name: Run tests | ||
# run: make test-cov | ||
# | ||
# - uses: codecov/codecov-action@v4 | ||
# name: Upload coverage report | ||
# with: | ||
# files: ./coverage.xml | ||
# fail_ci_if_error: true | ||
# env: | ||
# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |