Merge single cell functionality into main branch

.github/workflows/Short_runs.yml

@@ -0,0 +1,31 @@
+name: Short runs
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "master", "sc_*" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  integration-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.8"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        sudo apt-get install -y minimap2 samtools
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Run integration tests
+      run: |
+        pytest tests/console_test.py -v

.github/workflows/Stereo_toy.yml

@@ -0,0 +1,44 @@
+name: Stereo toy data test
+
+on:
+  workflow_dispatch:
+  schedule:
+  - cron: '0 2 * * 0,4'
+
+env:
+  RUN_NAME: Stereo_toy
+  LAUNCHER: ${{github.workspace}}/tests/github/run_pipeline.py
+  CFG_DIR: /abga/work/andreyp/ci_isoquant/data
+  BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/
+  OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/
+
+concurrency:
+  group: ${{github.workflow}}
+  cancel-in-progress: false
+
+jobs:
+  launch-runner:
+    runs-on:
+      labels: [isoquant]
+    name: 'Running IsoQuant and QC'
+
+    steps:
+      - name: 'Cleanup'
+        run: >
+          set -e &&
+          shopt -s dotglob &&
+          rm -rf *
+
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+
+      - name: 'Stereo toy data test'
+        if: always()
+        shell: bash
+        env:
+          STEP_NAME: STEREO.TOY
+        run: |
+          export PATH=$PATH:${{env.BIN_PATH}}
+          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

.gitignore

@@ -104,3 +104,6 @@ venv.bak/
 .mypy_cache/
 
 .idea
+
+# Claude Code documentation (private)
+.claude/

VERSION

@@ -1 +1 @@
-3.10.0
+3.10.0