add ci

.github/workflows/test.yaml

@@ -0,0 +1,41 @@
+name: run-test
+
+on:
+  push:
+    branches: [dev, master]
+  pull_request:
+    branches: [dev, master]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Python # Set Python version
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+        # Install pip and pytest
+      - name: Install dependencies
+        run: |
+          pip install .
+      - name: Install xpore-package
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-dependency
+      - name: Test with pytest
+        run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: pytest-results-${{ matrix.python-version }}
+          path: junit/test-results-${{ matrix.python-version }}.xml
+        # Use always() to always run this step to publish test results when there are test failures
+        if: ${{ always() }}

xpore/test/data/config.yml

@@ -0,0 +1,15 @@
+notes: Pairwise comparison without replicates with default parameter setting.
+
+data:
+    KO:
+        rep1: data/data/HEK293T-METTL3-KO-rep1/dataprep
+    WT:
+        rep1: data/data/HEK293T-WT-rep1/dataprep    
+
+out: ./out
+
+method:
+    prefiltering:
+        method: t-test
+        threshold: 0.1
+

xpore/test/data/data/HEK293T-METTL3-KO-rep1/dataprep/data.index

@@ -0,0 +1,3 @@
+idx,start,end
+ENSG00000114125,0,743597
+ENSG00000159111,743597,1675247

xpore/test/data/data/HEK293T-METTL3-KO-rep1/dataprep/data.readcount

@@ -0,0 +1,3 @@
+idx,n_reads
+ENSG00000114125,178
+ENSG00000159111,125

xpore/test/data/data/HEK293T-METTL3-KO-rep1/dataprep/eventalign.index

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xpore/test/data/data/HEK293T-WT-rep1/dataprep/data.index

@@ -0,0 +1,4 @@
+idx,start,end
+ENSG00000114125,0,385701
+ENSG00000159111,385701,929888
+ENSG00000095380,929888,952343

xpore/test/data/data/HEK293T-WT-rep1/dataprep/data.readcount

@@ -0,0 +1,4 @@
+idx,n_reads
+ENSG00000114125,91
+ENSG00000159111,71
+ENSG00000095380,1