Add build with pyinstaller and remove build with nuitka

Author: niklases

build_with_nuitka.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+pyinstaller \
+  --console \
+  --collect-data torch\
+  --collect-data biotite\
+  --collect-all biotite\
+  --collect-data torch_geometric\
+  --collect-all torch_geometric\
+  --hidden-import torch_geometric\
+  gui/qt_window.py
+  #  --add-data=X/:X/. \

build_with_pyinstaller.sh

@@ -1,17 +1,32 @@
 # GUI created with PyQT/PySide
-import re
+#import re
 import sys
+from io import StringIO 
 import os
 import subprocess
 from PySide6 import QtCore, QtWidgets
 from PySide6.QtCore import QSize
 pypef_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+#sys.path.append(pypef_root)
+from pypef import __version__
 from pypef.main import run_main
 
 
 EXEC_API_OR_CLI = ['api', 'cli'][0]
 
 
+class Capturing(list):
+    """https://stackoverflow.com/questions/16571150/how-to-capture-stdout-output-from-a-python-function-call"""
+    def __enter__(self):
+        self._stdout = sys.stdout
+        sys.stdout = self._stringio = StringIO()
+        return self
+    def __exit__(self, *args):
+        self.extend(self._stringio.getvalue().splitlines())
+        del self._stringio    # free up some memory
+        sys.stdout = self._stdout
+
+
 def capture(command):
     proc = subprocess.Popen(
         command,
@@ -22,8 +37,8 @@ def capture(command):
     return out, err, proc.returncode
 
 
-out, err, exitcode = capture([f'python', f'{pypef_root}/run.py', '--version'])
-version = re.findall(r"[-+]?(?:\d*\.*\d.*\d+)", str(out))[0]
+#out, err, exitcode = capture([f'python', f'{pypef_root}/run.py', '--version'])
+#version = re.findall(r"[-+]?(?:\d*\.*\d.*\d+)", str(out))[0]
 
 button_style = """
 QPushButton {
@@ -71,7 +86,7 @@ def __init__(
 
         # Texts #############################################################################
         layout = QtWidgets.QGridLayout(self)
-        self.version_text = QtWidgets.QLabel(f"PyPEF v. {version}", alignment=QtCore.Qt.AlignRight)
+        self.version_text = QtWidgets.QLabel(f"PyPEF v. {__version__}", alignment=QtCore.Qt.AlignRight)
         self.ncores_text = QtWidgets.QLabel("Single-/multiprocessing")
         self.llm_text = QtWidgets.QLabel("LLM")
         self.regression_model_text =  QtWidgets.QLabel("Regression model")
@@ -266,8 +281,8 @@ def __init__(
         layout.addWidget(self.textedit_out, 8, 0, 1, -1)
 
         self.process = QtCore.QProcess(self)
-        self.process.setProcessChannelMode(QtCore.QProcess.MergedChannels)
-        self.process.readyReadStandardOutput.connect(self.on_readyReadStandardOutput)
+        #self.process.setProcessChannelMode(QtCore.QProcess.MergedChannels)
+        #self.process.readyReadStandardOutput.connect(self.on_readyReadStandardOutput)
         self.process.started.connect(lambda: self.button_help.setEnabled(False))
         self.process.finished.connect(lambda: self.button_help.setEnabled(True))
         self.process.started.connect(lambda: self.button_mklsts.setEnabled(False))
@@ -463,8 +478,20 @@ def exec_pypef_cli(self, cmd):
             self.textedit_out.append("=" * 104 + "\n")
 
     def exec_pypef_api(self, cmd):
-        run_main(argv=cmd)
-        pass
+        self.textedit_out.append(f'Executing command:{cmd}')
+        try:
+            with Capturing() as captured_output:
+                run_main(argv=cmd)
+            print(captured_output)
+            for cap_out_text in captured_output:
+                self.textedit_out.append(cap_out_text)
+        except Exception as e: # anything
+            self.textedit_out.append(f"Provided wrong inputs! Error: {e}")
+        finally:
+            self.process.finished.connect(self.process_finished)
+            if self.c > 0:
+                self.textedit_out.append("=" * 104 + "\n")
+
 
     def process_finished(self):
         self.version_text.setText("Finished...") 

gui/qt_window.py

@@ -0,0 +1,57 @@
+# -*- mode: python ; coding: utf-8 -*-
+from PyInstaller.utils.hooks import collect_data_files
+from PyInstaller.utils.hooks import collect_all
+
+datas = []
+binaries = []
+hiddenimports = ['torch_geometric']
+datas += collect_data_files('torch')
+datas += collect_data_files('biotite')
+datas += collect_data_files('torch_geometric')
+tmp_ret = collect_all('biotite')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('torch_geometric')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+
+
+a = Analysis(
+    ['gui/qt_window.py'],
+    pathex=[],
+    binaries=binaries,
+    datas=datas,
+    hiddenimports=hiddenimports,
+    hookspath=[],
+    hooksconfig={},
+    runtime_hooks=[],
+    excludes=[],
+    noarchive=False,
+    optimize=0,
+)
+pyz = PYZ(a.pure)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    [],
+    exclude_binaries=True,
+    name='qt_window',
+    debug=False,
+    bootloader_ignore_signals=False,
+    strip=False,
+    upx=True,
+    console=True,
+    disable_windowed_traceback=False,
+    argv_emulation=False,
+    target_arch=None,
+    codesign_identity=None,
+    entitlements_file=None,
+)
+coll = COLLECT(
+    exe,
+    a.binaries,
+    a.datas,
+    strip=False,
+    upx=True,
+    upx_exclude=[],
+    name='qt_window',
+)