Merge 9065477 into b972628

.github/workflows/main.yml

@@ -6,36 +6,65 @@ on:
       - main
   pull_request:
     branches-ignore: []
+  schedule:
+    - cron: '0 0 13 * *'
+
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
+      matrix:
+        python: ['3.8', '3.9', '3.10']
+        qt-api: ['pyside6']
+      fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v3
       with:
-        python-version: 3.7
+        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
+        # cursor0 and shape0 required as well. Others were provided on pytest-qt and qt page
+        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 libgles2-mesa-dev libgl1-mesa-dev
+
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt -r requirements_dev.txt
-        python setup.py install
+        pip install .[testing]
+        pip install sequana_fastqc
     - name: Lint with flake8
       run: |
         pip install flake8
         # 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: |
+        Xvfb :99 -screen 0 1024x768x24 > dev>null 2>&1 &
+        # gives xvfb some time to start
+        sleep 3
+        pytest -s --cov-report term-missing --cov=sequanix -v 
+
+    - name: coveralls
       run: |
-        sudo Xvfb :1 -screen 0 1024x768x24 </dev/null &
-        export DISPLAY=":1"
-        pytest
+        pip install coveralls
+        coveralls --service=github
+      env:
+          GITHUB_TOKEN: ${{ github.token }}

MANIFEST.in

@@ -1,5 +1,7 @@
 recursive-exclude * __pycache__
 recursive-exclude * *pyc
+recursive-exclude test *
+recursive-exclude doc *
 include requirements*txt
 include CONTRIBUTING.rst
 include LICENSE

README.rst

@@ -5,20 +5,20 @@ Sequanix is a graphical user interface (GUI) that can be used to run Snakemake w
 
 .. image:: https://github.com/sequana/sequanix/actions/workflows/main.yml/badge.svg?branch=main
     :target: https://github.com/sequana/sequanix/actions/workflows/main.yml
-    
+
 .. image:: https://coveralls.io/repos/github/sequana/sequanix/badge.svg?branch=main
     :target: https://coveralls.io/github/sequana/sequanix?branch=main
 
-.. image:: http://readthedocs.org/projects/sequana/badge/?version=master
-    :target: http://sequana.readthedocs.org/en/latest/?badge=master
+.. image:: http://readthedocs.org/projects/sequana/badge/?version=main
+    :target: https://sequana.readthedocs.io/en/main/sequanix.html
     :alt: Documentation Status
 
 .. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
    :target: http://joss.theoj.org/papers/10.21105/joss.00352
    :alt: JOSS (journal of open source software) DOI
 
 
-:Python version: 3.6, 3.7.3 (below for now)
+:Python version: 3.8, 3.9, 3.10
 :Documentation: `On readthedocs <http://sequana.readthedocs.org/>`_
 :Issues: `On github <https://github.com/sequana/sequana/issues>`_
 :How to cite: Citations are important for us to carry on developments.
@@ -29,8 +29,7 @@ Sequanix is a graphical user interface (GUI) that can be used to run Snakemake w
     Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034
     Also available on bioRxiv (DOI: https://doi.org/10.1101/162701)
 
-**Sequanix** is a derivative of the **Sequana** projects that is dedicated to the analyse of NGS data (sequencing data). We provide a set of NGS pipelines  including quality control, variant calling, coverage, taxonomy, transcriptomics. Please see the Sequana `documentation <http://sequana.readthedocs.org>`_ for an
-up-to-date status and further information.
+**Sequanix** is a derivative of the **Sequana** project that is dedicated to the analyse of NGS data (sequencing data). We provide a set of NGS pipelines  including quality control, variant calling, coverage, taxonomy, transcriptomics. Please see the Sequana `documentation <http://sequana.readthedocs.org>`_ for an up-to-date status and further information.
 
 
 
@@ -44,3 +43,40 @@ Installation
 ############
 
 Please see the installation notes and installation steps on the https://sequana.readthedocs.io link.
+
+
+In brief::
+
+    pip install sequanix
+
+For developers, use::
+
+
+    git clone git@github.com:sequana/sequanix.git
+    pip install -e .[testing]
+
+
+Design choice
+#############
+
+Uses PySide6 from v0.2.0. See e.g., https://www.pythonguis.com/faq/pyqt6-vs-pyside6/ from information
+on the switch to PySide6. In brief, the Qt project has recently adopted PySide as the official Qt for Python release which should ensure its viability going forward. When we migrate PyQt5 to PyQt6, we therefore decided to use PySide instead of PyQt.
+
+Changelog
+~~~~~~~~~
+
+========= ==========================================================================
+Version   Description
+========= ==========================================================================
+0.2.0     * add logo
+          * remove pin on python3.7
+          * switch from PyQt5 to PySide6
+          * remove automatic creation of readtag in config. we let the pipelines
+            handle it
+0.1.0     * revamp Sequanix independently of Sequana
+========= ==========================================================================
+
+
+
+
+

requirements.txt

@@ -1,11 +1,9 @@
 colorlog
-PyQt5==5.15.4
-PyQt5-sip<13,>=12.8
-PyQt5-Qt5==5.15.2
-PyQtWebEngine==5.15.4
-PyOpenGL==3.1.5
-PyOpenGL_accelerate==3.1.5
-qtconsole==5.1.1
+PySide6
+PySide6-Essentials
+PyOpenGL==3.1.6
+PyOpenGL_accelerate==3.1.6
+qtconsole>=5.4.1
 snakemake>=6.0.0
 sequana_pipetools
 ipython

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