Update ci.yml: Simulating display and updating test

Author: niklases

.github/workflows/ci.yml

@@ -16,7 +16,8 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
     env:
-      QT_QPA_PLATFORM: offscreen
+     QT_QPA_PLATFORM: offscreen
+     DISPLAY: ':99.0'
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -41,10 +42,15 @@ jobs:
     - name: Export Pythonpath and run tests using pip-installation
       run: |
         export PYTHONPATH=""
-        sudo apt update && sudo apt install -y libegl1
+        sudo apt update
+        sudo apt install -y libegl1 xvfb \
+         libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
+         libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0
+        Xvfb :99 -screen 0 1920x1080x24 -ac &
+        sleep 3
         pip install .[gui]
         echo $(which pypef)
-        python -m pytest ./tests/ -v -m "not main_script_specific"
+        python -m pytest ./tests/ -v -m "not main_script_specific" --capture=tee-sys --log-cli-level=INFO
 
   windows:
     name: windows
@@ -82,5 +88,5 @@ jobs:
         $env:PYTHONPATH = ""
         pip install .[gui]
         echo (Get-Command pypef).Source
-        python -m pytest .\tests -v -m "not main_script_specific"
+        python -m pytest .\tests -v -m "not main_script_specific" --capture=tee-sys --log-cli-level=INFO
 

.gitignore

@@ -9,6 +9,7 @@ Python3127/*
 python-3.12.7-amd64.exe
 run_pypef_gui.bat
 run_pypef_gui.sh
+qt_window.spec
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

build_with_pyinstaller.sh

@@ -1,10 +1,11 @@
 #!/bin/bash
-pip install -r requirements.txt
-pip install -U pyinstaller pyside6
-pip install -e .
+set -e
+pip install pyinstaller
+pip install -e .[gui]
 pyinstaller \
   --console \
   --noconfirm \
+  --paths "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" \
   --collect-data pypef \
   --collect-all pypef \
   --collect-data torch \
@@ -13,5 +14,6 @@ pyinstaller \
   --collect-data torch_geometric \
   --collect-all torch_geometric \
   --hidden-import torch_geometric \
-  gui/PyPEFGUIQtWindow.py
-  #  --add-data=X/:X/. \
+  --hidden-import docopt \
+  --exclude-module PyQt5 \
+  pypef/gui/qt_window.py

pypef/gui/qt_window.py

@@ -7,7 +7,7 @@
 from os import getcwd, cpu_count, chdir
 import logging
 
-from PySide6.QtCore import QObject, QThread, QSize, Qt, QRect, QTimer, Signal, Slot
+from PySide6.QtCore import QObject, QThread, QSize, Qt, QRect, QTimer, Signal, Slot, QMetaObject
 from PySide6.QtWidgets import (
     QApplication, QPushButton, QTextEdit, QVBoxLayout, QWidget, 
     QGridLayout, QLabel, QPlainTextEdit, QSlider, QComboBox, QFileDialog
@@ -137,15 +137,16 @@ def __init__(self, id_: int):
         self.timer = QTimer(self)
         self.timer.setInterval(100)
         self.timer.timeout.connect(self.on_timeout)
-        print(self.__id)
 
         self.sig_abort.connect(self.stop)
 
     def start(self):
         self.timer.start()
 
+    @Slot()
     def stop(self):
         self.abort=True
+        self.timer.stop()
 
     @Slot()
     def on_timeout(self):
@@ -155,7 +156,6 @@ def on_timeout(self):
             self.timer.stop()
 
 
-
 class SecondWindow(QWidget):
    def __init__(self):
       super().__init__()
@@ -721,7 +721,9 @@ def closeEvent(self, event):
         stop InfoWorker and associated threads
         """
         for thread, worker in self.__info_threads:
-                worker.stop()
+                worker.sig_abort.emit()  # stops timer
+                QMetaObject.invokeMethod(worker, "stop", Qt.QueuedConnection)
+                #worker.stop()
                 thread.quit()
                 thread.wait()
         event.accept()

scripts/CLI/run_cli_tests_linux.sh

@@ -188,7 +188,7 @@ $pypef ml -e onehot -m ONEHOT -p 37_ANEH_variants_prediction_set.fasta
 echo
 $pypef ml -e dca -m MLPLMC -p 37_ANEH_variants_prediction_set.fasta --params ANEH_72.6.params --threads $threads
 echo
-$pypef ml -e dca -m MLgremlin -p 37_ANEH_variants_prediction_set.fasta --params GREMLIN
+$pypef ml -e dca -m MLGREMLIN -p 37_ANEH_variants_prediction_set.fasta --params GREMLIN
 echo
 
 $pypef mkps -i 37_ANEH_variants.csv -w Sequence_WT_ANEH.fasta --drecomb --trecomb --qarecomb --qirecomb --ddiverse
@@ -199,7 +199,7 @@ $pypef ml -e onehot -m ONEHOT --pmult --drecomb --trecomb --qarecomb --qirecomb
 echo
 $pypef ml -e dca -m MLPLMC --params ANEH_72.6.params --pmult --drecomb --trecomb --qarecomb --qirecomb --ddiverse --threads $threads
 echo
-$pypef ml -e dca -m MLgremlin --params GREMLIN --pmult --drecomb --trecomb --qarecomb --qirecomb --ddiverse
+$pypef ml -e dca -m MLGREMLIN --params GREMLIN --pmult --drecomb --trecomb --qarecomb --qirecomb --ddiverse
 echo
 
 $pypef ml -e aaidx directevo -m FAUJ880104 -w Sequence_WT_ANEH.fasta --negative
@@ -208,23 +208,23 @@ $pypef ml -e onehot directevo -m ONEHOT -w Sequence_WT_ANEH.fasta --negative
 echo
 $pypef ml -e dca directevo -m MLPLMC -w Sequence_WT_ANEH.fasta --negative --params ANEH_72.6.params
 echo
-$pypef ml -e dca directevo -m MLgremlin -w Sequence_WT_ANEH.fasta --negative --params GREMLIN
+$pypef ml -e dca directevo -m MLGREMLIN -w Sequence_WT_ANEH.fasta --negative --params GREMLIN
 echo
 $pypef ml -e aaidx directevo -m FAUJ880104 -w Sequence_WT_ANEH.fasta --numiter 10 --numtraj 8 --negative
 echo
 $pypef ml -e onehot directevo -m ONEHOT -w Sequence_WT_ANEH.fasta --numiter 10 --numtraj 8 --negative
 echo
 $pypef ml -e dca directevo -m MLPLMC -w Sequence_WT_ANEH.fasta --numiter 10 --numtraj 8 --negative --params ANEH_72.6.params
 echo
-$pypef ml -e dca directevo -m MLgremlin -w Sequence_WT_ANEH.fasta --numiter 10 --numtraj 8 --negative --params GREMLIN
+$pypef ml -e dca directevo -m MLGREMLIN -w Sequence_WT_ANEH.fasta --numiter 10 --numtraj 8 --negative --params GREMLIN
 echo
 $pypef ml -e aaidx directevo -m FAUJ880104 -i 37_ANEH_variants.csv -w Sequence_WT_ANEH.fasta --temp 0.1 --usecsv --csvaa --negative
 echo
 $pypef ml -e onehot directevo -m ONEHOT -i 37_ANEH_variants.csv -w Sequence_WT_ANEH.fasta --temp 0.1 --usecsv --csvaa --negative
 echo
 $pypef ml -e dca directevo -m MLPLMC -i 37_ANEH_variants.csv -w Sequence_WT_ANEH.fasta --temp 0.1 --usecsv --csvaa --negative --params ANEH_72.6.params
 echo
-$pypef ml -e dca directevo -m MLgremlin -i 37_ANEH_variants.csv -w Sequence_WT_ANEH.fasta --temp 0.1 --usecsv --csvaa --negative --params GREMLIN
+$pypef ml -e dca directevo -m MLGREMLIN -i 37_ANEH_variants.csv -w Sequence_WT_ANEH.fasta --temp 0.1 --usecsv --csvaa --negative --params GREMLIN
 echo
 
 $pypef ml -e aaidx -l LS.fasl -t TS.fasl --regressor pls --nofft
@@ -371,7 +371,7 @@ echo
 # ml only TS
 $pypef ml -e dca -m MLPLMC -t TS.fasl --params uref100_avgfp_jhmmer_119_plmc_42.6.params --threads $threads
 echo
-$pypef ml -e dca -m MLgremlin -t TS.fasl --params GREMLIN --threads $threads
+$pypef ml -e dca -m MLGREMLIN -t TS.fasl --params GREMLIN --threads $threads
 echo
 
 echo
@@ -420,7 +420,7 @@ $pypef ml extrapolation -i avGFP_dca_encoded.csv --conc --regressor ridge
 echo
 
 # Direct Evo
-$pypef ml -e dca directevo -m MLgremlin --wt P42212_F64L.fasta --params GREMLIN
+$pypef ml -e dca directevo -m MLGREMLIN --wt P42212_F64L.fasta --params GREMLIN
 echo
 $pypef ml -e dca directevo -m MLPLMC --wt P42212_F64L.fasta --params PLMC
 echo

scripts/ProteinGym_runs/results/dca_esm_and_hybrid_5cv-split_results.csv

@@ -99,3 +99,4 @@ No.,Dataset,N_Variants,N_Max_Muts,Untrained_Performance_DCA,Untrained_Performanc
 98,PTEN_HUMAN_Matreyek_2021,5083,1,5083 variant fitness pairs (below 50 or more than 600)
 99,PTEN_HUMAN_Mighell_2018,7260,1,7260 variant fitness pairs (below 50 or more than 600)
 100,Q2N0S5_9HIV1_Haddox_2018,12729,1,12729 variant fitness pairs (below 50 or more than 600)
+101,Q53Z42_HUMAN_McShan_2019_binding-TAPBPR,3344,1,0.30236928959118303,0.29758327493409265,0.4106333338290412,0.6155205938174899,0.5444802039870617,0.6170146816336404,0.6841040378864747,0.6228855033907258,0.7376342898806972,0.6913379495934746,0.7218016750905504,0.7686186339141997,0.7389457134749116,0.7567534270430136,0.6903353390849041,0.7280497034445114,0.7735694641206315,0.7549957977525813,0.5139437438254881,0.5181436876214243,0.4950673026256684,0.5372292645433243,0.43241860553191147,0.6610097448927186,0.6356562004856172,0.6134093858334889,0.6524652693992385,0.6536614941027378,0.6835604290538351,0.7152345717487829,0.6312263783941386,0.673532765455087,0.626163763305635,0.5172693562317241,0.1946017580527397,0.3734633407764436,0.01692976911480976,0.11444276706135406,0.6458416916777189,0.5087226916123205,0.5269873470447384,0.40650371604050123,0.4986505696835808,0.6884670213733808,0.5342668214178948,0.6272054182572798,0.44182216770593896,0.5223171913551616,32309

tests/gui/test_gui_functions.py

@@ -1,5 +1,3 @@
-
-
 import sys
 import tempfile
 import pytest
@@ -8,18 +6,31 @@
 from pypef import __version__
 
 
-
 @pytest.fixture(scope="session")
 def app():
+    """Create and return a QApplication for all tests in the session."""
     from PySide6.QtWidgets import QApplication
-    return QApplication(sys.argv)
+    app = QApplication.instance()
+    if app is None:
+        app = QApplication(sys.argv)
+    yield app  # No explicit teardown needed for QApplication
 
 
-@pytest.mark.pip_specific
-def test_button_click_changes_label(app):
+@pytest.fixture
+def main_window(app):
     from pypef.gui.qt_window import MainWidget
     window = MainWidget()
     window.show()
+    yield window
+
+    window.close()
+    app.processEvents()
+
+
+#@pytest.mark.skipif(os.environ.get("CI") == "true", reason="Skipping GUI test in CI")
+@pytest.mark.pip_specific
+def test_button_click_changes_label(main_window, app):
+    window = main_window
 
     assert window.version_text.text() == f"PyPEF v. {__version__}"
 
@@ -30,4 +41,3 @@ def test_button_click_changes_label(app):
 
     assert hasattr(window, "working_directory")
     assert window.working_directory == str(tmp_dir)
-