Refactorisation

- remove the second sequana tab from the UI. the input_directory and
  input_pattern are back into the config file to have a behaviour
   similar to generic pipeline
- removed function to save log in case of error. was not used
- update about/help sections
- added version, removed sequana imports

.github/workflows/main.yml

@@ -15,18 +15,27 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
+      matrix:
+        python: ['3.8', '3.9']
+        qt-api: ['pyside6']
+      fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python '3.9'
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v3
       with:
-        python-version: '3.9'
+        python-version: ${{ matrix.python }}
     - name: Setup ubuntu
       run: |
-        sudo apt install xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0
+        sudo apt update -y --fix-missing
+        sudo apt install -y build-essential
+        sudo apt install -y xvfb libxkbcommon-x11-0 x11-xserver-utils
+        sudo apt install libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 libxcb-xkb-dev libxcb-cursor0 libxcb-shape0
+
         sudo apt install graphviz
-        sudo apt install libgl1 libgl1-mesa-glx libegl1
+        sudo apt install libgl1 libgl1-mesa-glx libegl1 libgles2-mesa-dev libgl1-mesa-dev
+
     - name: Install dependencies
       run: |
         pip install .[testing]
@@ -37,13 +46,21 @@ jobs:
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude sequanix/ui/
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude '*/ui/'
+
+
     - name: Test with pytest
+      env:
+        QT_DEBUG_PLUGINS: 1
+        DISPLAY: ":99.0"
+        QT_API: ${{ matrix.qt-api }}
+        T_QPA_PLATFORM: offscreen
       run: |
-        sudo Xvfb :1 -screen 0 1024x768x24 </dev/null &
-        export DISPLAY=":1"
-        export QT_DEBUG_PLUGINS=1
-        pytest --cov-report term-missing --cov=sequanix
+        Xvfb :99 -screen 0 1024x768x24 > dev>null 2>&1 &
+        # gives xvfb some time to start
+        #sh -e /etc/init.d/xvfb start
+        sleep 3
+        pytest -s --cov-report term-missing --cov=sequanix -v 
 
     - name: coveralls
       run: |

requirements.txt

@@ -1,9 +1,8 @@
 colorlog
 PySide6
 PySide6-Essentials
-PyQtWebEngine==5.15.4
-PyOpenGL==3.1.5
-PyOpenGL_accelerate==3.1.5
+PyOpenGL==3.1.6
+PyOpenGL_accelerate==3.1.6
 qtconsole>=5.4.1
 snakemake>=6.0.0
 sequana_pipetools

sequanix/__init__.py

@@ -1 +1,10 @@
+
+import pkg_resources
+
+try:
+    version = pkg_resources.require("sequanix")[0].version
+except:
+    version = ">=0.2"
+
+
 from .sequanix import SequanixGUI, main