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add missing checkout action #33

add missing checkout action

add missing checkout action #33

name: check compatibility ilastik
concurrency: ilastik
on:
push:
branches:
- main
paths:
- .github/workflows/check_compatibility_ilastik.yaml
- scripts/check_compatibility_ilastik.py
workflow_dispatch:
schedule:
- cron: 0 1 * * * # update compatibility once a day
jobs:
setup:
runs-on: ubuntu-latest
outputs:
version_matrix: ${{ steps.cvm.outputs.version_matrix }}
steps:
- name: download version list
run: wget https://files.ilastik.org/ilastik-versions-bmz.json
- name: create version matrix
id: cvm
shell: python
run: |
import json
import os
with open("ilastik-versions-bmz.json") as f:
vs = json.load(f)
version_matrix = dict(include=[dict(v=v, env_url=f"https://files.ilastik.org/ilastik-{v}-Linux.yml") for v in vs])
with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
print(f"version_matrix={version_matrix}", file=fh)
generate-reports:
runs-on: ubuntu-latest
needs: setup
environment: 'production'
strategy:
fail-fast: false
matrix: ${{ fromJson(needs.setup.outputs.version_matrix) }}
steps:
- uses: actions/checkout@v4
- run: wget https://${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/all_versions_draft.json
- run: wget https://${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/all_versions.json
- name: Download ilastik env
run: wget --output-document env.yaml ${{ matrix.env_url }}
- name: ignore unrelated packages
run: sed -i '/multi-hypotheses-tracking-with-gurobi/d; /gurobi-symlink/d' env.yaml
- name: Setup ilastik env
uses: mamba-org/setup-micromamba@v1
with:
environment-file: env.yaml
cache-downloads: true
cache-environment: true
- name: test drafts with ilastik ${{ matrix.v }}
shell: bash -l {0}
run: python scripts/check_compatibility_ilastik.py ${{ matrix.v }} all_versions_draft.json generated-reports
- name: test published versions with ilastik ${{ matrix.v }}
shell: bash -l {0}
run: python scripts/check_compatibility_ilastik.py ${{ matrix.v }} all_versions.json generated-reports
- uses: actions/upload-artifact@v4
with:
name: generated-reports
path: generated-reports
upload-reports:
needs: generate-reports
environment: 'production'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: "3.12"
cache: "pip" # caching pip dependencies
- run: pip install .
- uses: actions/download-artifact@v4
with:
name: generated-reports
path: generated-reports
- run: python scripts/upload_reports.py generated-reports