Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

chore: use conda setup action #548

Merged
merged 6 commits into from
Nov 13, 2024
Merged

chore: use conda setup action #548

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
35530d1
chore: use conda setup action
tedil Nov 13, 2024
aafcd97
checkout first, then install conda
tedil Nov 13, 2024
a5d2216
remove outdated checks
tedil Nov 13, 2024
18f15bd
auto activate base env
tedil Nov 13, 2024
4059a34
don't auto-activate base
tedil Nov 13, 2024
bd599d5
configure bash as default shell for runner
tedil Nov 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 15 additions & 20 deletions .github/workflows/ci.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,13 @@ on:
branches_ignore: []

jobs:
default-shell:
name: Default shell
runs-on: ubuntu-latest
defaults:
run:
shell: bash -el {0}

cancel-previous:
runs-on: ubuntu-latest
if: github.ref != 'refs/heads/main'
Expand Down Expand Up @@ -77,31 +84,19 @@ jobs:
- "3.12"
needs: linting
steps:
- name: Install Python via conda
uses: s-weigand/setup-conda@v1
with:
python-version: ${{ matrix.python-version }}
conda-channels: defaults,bioconda,conda-forge
- name: Checkout repository
uses: actions/checkout@v4
with:
lfs: true
fetch-depth: 2
- name: Install mamba
run: conda install -y mamba>=1.0.0
- name: Prepare environment.yml file
run: >
cp environment.yml /tmp/environment.yml && sed -i -e
's/- python=.*/- python=${{ matrix.python-version }}/'
/tmp/environment.yml
- name: Update environment using mamba
run: mamba env update --name root --file /tmp/environment.yml
- name: Fail early on htslib etc. problems
run: |
set -euo pipefail
bgzip -c /dev/null >/dev/null
samtools version
bcftools version
- name: Setup conda
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
environment-file: environment.yml
channels: conda-forge,bioconda,nodefaults
channel-priority: strict
- name: Install some more dependencies via pip
# Workaround - see https://github.com/pytest-dev/pytest/issues/10420#issuecomment-1290697849
run: pip install ".[test]"; pip install --ignore-installed py
Expand Down
Loading