ci: update gha

.github/workflows/sourcepredict_ci.yml

@@ -0,0 +1,34 @@
+name: sourcepredict_ci
+
+on: [push, pull_request]
+
+
+jobs:
+  pydamage_ci:
+    name: sourcepredict_testing
+    runs-on: 'ubuntu-latest'
+    if: "!contains(github.event.head_commit.message, '[skip_ci]')"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          channel-priority: true
+          environment-file: conda_env.yaml
+          activate-environment: sourcepredict_test
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pip install -e .
+          pip install pytest
+          pytest
+      - name: Check sourcepredict help message
+        shell: bash -l {0}
+        run: |
+          sourcepredict --help
+      - name: Check sourcepredict on test data
+        shell: bash -l {0}
+        run: |
+          sourcepredict -s data/modern_gut_microbiomes_sources.csv -l data/modern_gut_microbiomes_labels.csv data/test/dog_test_sink_sample.cs