Move tests from bash to GitHub Action

galaxyproject · Jun 25, 2024 · 7c400f6 · 7c400f6
1 parent d7d63ec
commit 7c400f6
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Showing 3 changed files with 56 additions and 59 deletions.
diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml
@@ -2,29 +2,73 @@ name: Run tests
 on: [push, pull_request]
 
 jobs:
-  test:
+  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: ${{ matrix.python-version }}
+          python-version: '3.11'
       - name: Install requirement
         run: python -m pip install -r requirements.txt
-      - name: Test tool extraction
+      - name: Tool extraction
         # run: bash bin/extract_all_tools.sh
         run: | 
-          bash ./bin/extract_all_tools_test.sh "${{ matrix.subset }}"
+          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 "test.list" \
+            --test
         env: 
           GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }}
-      - name: Test tutorial extraction and filtering
+      - name: Tool filter
         run: | 
-          bash ./bin/extract_filter_tutorials_test.sh
+          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/microgalaxy/tools.tsv" \
+            --template "data/interactive_table_template.html" \
+            --output "results/microgalaxy/index.html"
+      - name: Create wordcloud
+        run: | 
+          python bin/create_wordcloud.py \
+            --table  "results/microgalaxy/tools.tsv" \
+            --wordcloud_mask "data/usage_stats/wordcloud_mask.png" \
+            --output "results/microgalaxy/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: '3.11'
+      - 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 }}
+          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"
diff --git a/bin/extract_all_tools_test.sh b/bin/extract_all_tools_test.sh
diff --git a/bin/extract_filter_tutorials_test.sh b/bin/extract_filter_tutorials_test.sh