Move tests from bash to GitHub Action #7
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| name: Run tests | |
| on: [push, pull_request] | |
| jobs: | |
| test-tools: | |
| runs-on: ubuntu-20.04 | |
| environment: fetch-tools | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| subset: | |
| - test.list | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install requirement | |
| run: python -m pip install -r requirements.txt | |
| - name: Tool extraction | |
| # run: bash bin/extract_all_tools.sh | |
| run: | | |
| python bin/extract_galaxy_tools.py \ | |
| extractools \ | |
| --api $GITHUB_API_KEY \ | |
| --all-tools "results/test_tools.tsv" \ | |
| --all-tools-json "results/test_tools.json" \ | |
| --planemo-repository-list $1 \ | |
| --test | |
| env: | |
| GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }} | |
| - name: Tool filter | |
| run: | | |
| python bin/extract_galaxy_tools.py \ | |
| filtertools \ | |
| --tools "results/all_tools.json" \ | |
| --ts-filtered-tools "results/microgalaxy/tools_filtered_by_ts_categories.tsv" \ | |
| --filtered-tools "results/microgalaxy/tools.tsv" \ | |
| --categories "data/communities/microgalaxy/categories" \ | |
| --status "data/communities/microgalaxy/tool_status.tsv" | |
| - name: Create interactive table | |
| run: | | |
| python bin/create_interactive_table.py \ | |
| --table "results/$community/tools.tsv" \ | |
| --template "data/interactive_table_template.html" \ | |
| --output "results/$community/index.html" | |
| - name: Create wordcloud | |
| run: | | |
| python bin/create_wordcloud.py \ | |
| --table "results/$community/tools.tsv" \ | |
| --wordcloud_mask "data/usage_stats/wordcloud_mask.png" \ | |
| --output "results/$community/tools_wordcloud.png" \ | |
| --stats_column "No. of tool users (2022-2023) (usegalaxy.eu)" | |
| test-tutorials: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install requirement | |
| run: python -m pip install -r requirements.txt | |
| - name: Tutorial extraction | |
| run: | | |
| python bin/extract_gtn_tutorials.py \ | |
| extracttutorials \ | |
| --all_tutorials "results/test_tutorials.json" \ | |
| --tools "results/all_tools.json" \ | |
| --api $PLAUSIBLE_API_KEY \ | |
| --test | |
| env: | |
| PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }} | |
| - name: Tutorial filtering | |
| run: | | |
| python bin/extract_gtn_tutorials.py \ | |
| filtertutorials \ | |
| --all_tutorials "results/test_tutorials.json" \ | |
| --filtered_tutorials "results/microgalaxy/test_tutorials.tsv" \ | |
| --tags "data/communities/microgalaxy/tutorial_tags" |