Merge pull request #6 from HallLab/5-remove-fbs

5 remove fbs

.gitignore

@@ -89,6 +89,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+Pipfile.lock
 
 # Spyder project settings
 .spyderproject

Pipfile

@@ -0,0 +1,15 @@
+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+flake8 = "*"
+
+[packages]
+clarite = "==1.0.0"
+pyqt5 = "==5.15.0"
+pypiwin32 = {version = "*", sys_platform = "== 'win32'"}
+
+[requires]
+python_version = ">=3.6"

README.md

@@ -6,59 +6,28 @@ A GUI Version of CLARITE
 
 ![alt text][logo]
 
-[logo]: src/main/resources/base/images/clarite_logo.png "CLARITE Logo"
+[logo]: gui/resources/images/clarite_logo.png "CLARITE Logo"
 
 Full documentation on [ReadTheDocs.io](https://clarite-gui.readthedocs.io/en/stable/)
 
-## Install
-
-Requires Python v3.6
-
-1. Download the repository and navigate to the main folder
-2. Create a python venv
-
-        python -m venv venv
-
-3. Activate the environment
-
-    On Mac/Linux:
-
-        source venv/bin/activate
-
-    On Windows:
-
-        call venv\scripts\activate.bat
-
-4. Install the requirements
-
-    On Mac/Linux:
-
-        source src\requirements\base.txt
-
-    On Windows:
-
-        pip install -r src\requirements\windows.txt
-
+*NOTE*: Update resources with `pyrcc -o gui/resources/app_resources.py gui/resources/app_resources.qrc`
 
 ## Running
 
-1. Activate the environment (if not already activated)
-
-    On Mac/Linux:
-
-        source venv/bin/activate
+1. Download or clone this repository and enter the folder
+2. Ensure pipenv is installed
 
-    On Windows:
+    ``pip install pipenv``
 
-        call venv\scripts\activate.bat
+3. Create/update the pipenv
 
-2. Run
+    ``pipenv update``
 
-        fbs run
+4. Run:
 
-## Creating an executable (currently not working)
+    ``pipenv run python main.py``
 
-    python -m fbs freeze
+Executables will be provided for future releases.
 
 ## Citing CLARITE
 

docs/installation.rst

@@ -3,16 +3,16 @@ Installation
 ============
 
 1. Download or clone this repository and enter the folder
-2. Install Requirements
+2. Ensure pipenv is installed
 
-  * Windows:
-     ``python -m pip install -r src/requirements/windows.txt``
-  * Mac:
-     ``python -m pip install -r src/requirements/mac.txt``
-  * Linux:
-     ``python -m pip install -r src/requirements/base.txt``
+    ``pip install pipenv``
 
-3. Run:
-     ``python src\main\python\clarite_gui\main.py``
+3. Create/update the pipenv
 
-Installers will be provided for future releases.
+    ``pipenv update``
+
+4. Run:
+
+    ``pipenv run python main.py``
+
+Executables will be provided for future releases.

gui/__init__.py

@@ -0,0 +1 @@
+from .app_context import AppContext

src/main/python/clarite_gui/main.py → gui/app_context.py

@@ -3,13 +3,13 @@
 
 import pandas as pd
 from PyQt5.QtCore import pyqtSignal, QObject
-from fbs_runtime.application_context.PyQt5 import ApplicationContext, cached_property
+from PyQt5.QtWidgets import QApplication
 
-from main_window import MainWindow
-from models import Dataset
+from .main_window import MainWindow
+from .models import Dataset
 
 
-class AppContext(ApplicationContext):
+class AppContext:
     """
     The application context holds the current data and is passed to all widgets in the app.
     The data in the application context should only be modified via its methods.
@@ -20,9 +20,6 @@ class AppContext(ApplicationContext):
     APPLICATION = "Clarite"
 
     def __init__(self, *args, **kwargs):
-        super(AppContext, self).__init__(*args, **kwargs)
-        self.signals = AppctxSignals()
-
         # Main display widgets that expose functions to update themselves (set to None initially)
         self.dataset_widget = None
         self.command_dock_widget = None
@@ -32,6 +29,12 @@ def __init__(self, *args, **kwargs):
         self.datasets: List[Dataset] = []
         self.current_dataset_idx: Optional[int] = None
 
+        self.signals = AppctxSignals()
+        self.app = QApplication(sys.argv)
+        self.main_window = MainWindow(self)
+
+        self.app.setApplicationName("CLARITE")
+
     def run(self):
         """
         Run the application
@@ -47,10 +50,6 @@ def run(self):
         # self.add_dataset(Dataset("replication_results", "ewas_result", repl_result))
 
         return self.app.exec_()
-
-    @cached_property
-    def main_window(self):
-        return MainWindow(self)
 
     # Slots that update data in the app context
 
@@ -120,9 +119,3 @@ class AppctxSignals(QObject):
     changed_dataset = pyqtSignal(int)  # Idx of dataset that was changed to
     log_info = pyqtSignal(str)
     log_python = pyqtSignal(str)
-
-
-if __name__ == '__main__':
-    appctxt = AppContext()
-    exit_code = appctxt.run()
-    sys.exit(exit_code)

src/main/python/clarite_gui/main_window/main_window_widgets/about_dialog.py → gui/main_window/main_window_widgets/about_dialog.py

@@ -5,6 +5,8 @@
 from PyQt5.QtGui import QIcon
 from PyQt5.QtWidgets import QDialog, QDialogButtonBox, QVBoxLayout, QLabel, QFormLayout, QPushButton, QHBoxLayout
 
+from gui.resources import app_resources
+
 
 class AboutDialog(QDialog):
     """
@@ -41,15 +43,15 @@ def setup_ui(self):
         # Hall Lab Logo Button
         self.button = QPushButton('', self)
         self.button.clicked.connect(lambda: self.open_site("https://www.hall-lab.org"))
-        self.button.setIcon(QIcon(self.appctx.get_resource('images/hall_lab_logo.png')))
+        self.button.setIcon(QIcon(':/images/hall_lab_logo.png'))
         self.button.setIconSize(QSize(60, 60))
         self.button.setFixedSize(64, 64)
         bottom_layout.addWidget(self.button)
 
         # Clarite Logo Button
         self.button = QPushButton('', self)
         self.button.clicked.connect(lambda: self.open_site("https://www.hall-lab.org/clarite-python/"))
-        self.button.setIcon(QIcon(self.appctx.get_resource('images/clarite_logo.png')))
+        self.button.setIcon(QIcon(':/images/clarite_logo.png'))
         self.button.setIconSize(QSize(60, 60))
         self.button.setFixedSize(64, 64)
         bottom_layout.addWidget(self.button)

src/main/python/clarite_gui/main_window/main_window_widgets/command_dock.py → gui/main_window/main_window_widgets/command_dock.py

@@ -1,7 +1,7 @@
 from PyQt5.QtCore import Qt
 from PyQt5.QtWidgets import QDockWidget, QTabWidget
 
-from widgets.commands import LoadButtons, ModifyButtons, DescribeButtons, PlotButtons, AnalyzeButtons
+from gui.widgets.commands import LoadButtons, ModifyButtons, DescribeButtons, PlotButtons, AnalyzeButtons
 
 
 class CommandDockWidget(QDockWidget):

src/main/python/clarite_gui/main_window/main_window_widgets/dataset.py → gui/main_window/main_window_widgets/dataset.py

@@ -2,12 +2,13 @@
 from pathlib import Path
 
 from PyQt5.QtCore import pyqtSlot, Qt, QSettings, QSize
-from PyQt5.QtGui import QFont, QColor, QImage, QPixmap
+from PyQt5.QtGui import QColor, QPixmap
 from PyQt5.QtWidgets import QGroupBox, QHBoxLayout, QVBoxLayout, QComboBox, QLabel, QPushButton, QFileDialog
 
-from main_window.main_window_widgets.dataset_table_view import DatasetTableView
-from models import PandasDFModel
-from widgets.utilities import RunProgress, confirm_click
+from gui.main_window.main_window_widgets.dataset_table_view import DatasetTableView
+from gui.models import PandasDFModel
+from gui.widgets.utilities import RunProgress, confirm_click
+from gui.resources import app_resources
 
 
 class DatasetWidget(QGroupBox):
@@ -54,7 +55,7 @@ def setup_ui(self):
 
         # Placeholder image
         self.data_placeholder_image = QLabel(parent=self)
-        pixmap = QPixmap(self.appctx.get_resource('images/clarite_logo.png'))
+        pixmap = QPixmap(":/images/clarite_logo.png")
         self.data_placeholder_image.setPixmap(pixmap)
         self.data_placeholder_image.setAlignment(Qt.AlignCenter)
         layout.addWidget(self.data_placeholder_image)

src/main/python/clarite_gui/main_window/main_window_widgets/log.py → gui/main_window/main_window_widgets/log.py

@@ -1,7 +1,7 @@
 from PyQt5.QtGui import QTextCursor
 from PyQt5.QtWidgets import QVBoxLayout, QTextEdit, QHBoxLayout, QPushButton, QFileDialog, QWidget
 
-from widgets.utilities import RunProgress
+from gui.widgets.utilities import RunProgress
 
 
 class LogWidget(QWidget):

src/main/python/clarite_gui/main_window/main_window_widgets/preferences_dialog.py → gui/main_window/main_window_widgets/preferences_dialog.py

@@ -2,7 +2,7 @@
 from PyQt5.QtGui import QFont, QColor
 from PyQt5.QtWidgets import QDialog, QDialogButtonBox, QVBoxLayout, QTabWidget, QWidget, QGroupBox, QFormLayout, QLabel, \
     QSpinBox, QHBoxLayout, QPushButton
-from widgets.utilities import ColorPickerWidget, FontPickerWidget
+from gui.widgets.utilities import ColorPickerWidget, FontPickerWidget
 
 
 class PreferencesDialog(QDialog):

src/main/python/clarite_gui/models/df_model.py → gui/models/df_model.py

@@ -1,11 +1,11 @@
 import clarite
-import pandas as pd
+import numpy as np
 from PyQt5 import QtCore
 from PyQt5.QtCore import pyqtSlot, QSettings
 from PyQt5.QtGui import QFont, QColor
 from PyQt5.QtWidgets import QDialog, QFormLayout, QLineEdit, QDialogButtonBox
 
-from widgets.utilities import show_warning
+from gui.widgets.utilities import show_warning
 
 
 class PandasDFModel(QtCore.QAbstractTableModel):
@@ -156,7 +156,7 @@ def data(self, index, role=QtCore.Qt.DisplayRole):
             row_idx = index.row()
             col_idx = index.column()
             value = self.dataset.df.iloc[row_idx, col_idx]
-            if type(value) is pd.np.float64:
+            if type(value) is np.float64:
                 return f"{value:.{self.data_float_precision}E}"
             else:
                 return str(value)