reformatted files with black. moved package data from the setup.py to…

… the MANIFEST.in. Updated readme.

MDANSE/MANIFEST.in

@@ -1,11 +1,11 @@
-include LICENSE
 include LICENCE
+include requirements.txt
 
 recursive-include Extensions/qhull_lib *.h *c *.pxd
+recursive-include Extensions/xtc *.h *c *.pxd
+recursive-include Src/MDANSE/Chemistry *.json
+recursive-include Src/MDANSE/Framework *.json
 
 recursive-include Doc *
 
-include Scripts/*
-
 recursive-include Tests *.py
-

MDANSE/setup.py

@@ -164,12 +164,6 @@ def find_data(
 PACKAGE_INFO = {}
 exec(open("Src/MDANSE/__pkginfo__.py", "r").read(), {}, PACKAGE_INFO)
 
-#################################
-# Package data section
-#################################
-
-# Retrieve all the data related to the MDANSE package.
-PACKAGE_DATA = find_package_data(where="Src", package="MDANSE", show_ignored=False)
 
 #################################
 # User data section
@@ -178,12 +172,6 @@ def find_data(
 DATA_FILES = []
 DATA_FILES.extend(find_data("Doc", exclude=[], prefix="conf_"))
 
-#################################
-# Scripts section
-#################################
-
-SCRIPTS_PATH = "Scripts"
-SCRIPTS = glob.glob(os.path.join(SCRIPTS_PATH, "mdanse*"))
 
 #################################
 # Documentation
@@ -401,11 +389,9 @@ class mdanse_build_api(mdanse_build_doc):
     license=PACKAGE_INFO["__license__"],
     packages=find_packages("Src"),
     package_dir={"": "Src"},
-    package_data=PACKAGE_DATA,
     data_files=DATA_FILES,
     platforms=["Unix", "Windows"],
     ext_modules=EXTENSIONS,
-    scripts=SCRIPTS,
     cmdclass=CMDCLASS,
     # entry_points     = {"console_scripts": []}
     install_requires=[

MDANSE_GUI/MANIFEST.in

@@ -1,13 +1,10 @@
 include LICENSE
-include LICENCE
+include requirements.txt
 
-recursive-include Src/GUI/Resources/Icons *.png
-
-recursive-include Src/PyQtGUI/Icons *.png
+recursive-include Src/MDANSE_GUI/GUI/Resources/Icons *.png
+recursive-include Src/MDANSE_GUI/PyQtGUI/Icons *.png
+recursive-include Src/MDANSE_GUI/PyQtGUI/MolecularViewer/database *.yml
 
 recursive-include Doc *
 
-include Scripts/*
-
 recursive-include Tests *.py
-

MDANSE_GUI/Src/MDANSE_GUI/Scripts/mdanse_elements_database.py

@@ -13,14 +13,19 @@
 #
 # **************************************************************************
 
+
 def main():
-    from MDANSE_GUI.PyQtGUI.ElementsDatabaseEditor import ElementsDatabaseEditor, QApplication
+    from MDANSE_GUI.PyQtGUI.ElementsDatabaseEditor import (
+        ElementsDatabaseEditor,
+        QApplication,
+    )
     import sys
+
     app = QApplication(sys.argv)
     root = ElementsDatabaseEditor()
     root.show()
     app.exec()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

MDANSE_GUI/Src/MDANSE_GUI/Scripts/mdanse_gui.py

@@ -18,6 +18,7 @@
 
 def main():
     from MDANSE_GUI.PyQtGUI.main import startGUI
+
     startGUI(sys.argv)
 
 

MDANSE_GUI/Src/MDANSE_GUI/Scripts/mdanse_periodic_table.py

@@ -13,14 +13,16 @@
 #
 # **************************************************************************
 
+
 def main():
     from MDANSE_GUI.PyQtGUI.PeriodicTableViewer import PeriodicTableViewer, QApplication
     import sys
+
     app = QApplication(sys.argv)
     root = PeriodicTableViewer()
     root.show()
     app.exec()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

MDANSE_GUI/Src/MDANSE_GUI/Scripts/mdanse_plotter.py

@@ -13,12 +13,13 @@
 #
 # **************************************************************************
 
+
 def main():
     from MDANSE.GUI.Apps import PlotterApp
-    
+
     app = PlotterApp()
     app.MainLoop()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

MDANSE_GUI/Src/MDANSE_GUI/Scripts/mdanse_ud_editor.py

@@ -13,13 +13,13 @@
 #
 # **************************************************************************
 
+
 def main():
-
     from MDANSE.GUI.Apps import UserDefinitionViewerApp
 
     app = UserDefinitionViewerApp(None)
     app.MainLoop()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

MDANSE_GUI/Src/MDANSE_GUI/Scripts/mdanse_units_editor.py

@@ -13,13 +13,16 @@
 #
 # **************************************************************************
 
+
 def main():
     from MDANSE_GUI.PyQtGUI.UnitsEditor import UnitsEditor, QApplication
     import sys
+
     app = QApplication(sys.argv)
     root = UnitsEditor()
     root.show()
     app.exec()
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     main()

MDANSE_GUI/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "numpy", "pip", "wheel"]
+requires = ["setuptools", "numpy", "pip", "wheel", "netCDF4"]
 build-backend = "setuptools.build_meta"
 
 [project]

MDANSE_GUI/requirements.txt

@@ -2,4 +2,5 @@ MDANSE
 vtk
 qtpy
 PyYAML
-PyQt6
+PyQt6
+netCDF4

MDANSE_GUI/setup.py

@@ -131,19 +131,6 @@ def find_data(where=".", exclude=EXCLUDE, exclude_directories=EXCLUDE_DIRECTORIE
 PACKAGE_INFO = {}
 exec(open('Src/MDANSE_GUI/__pkginfo__.py','r').read(), {}, PACKAGE_INFO)
 
-#################################
-# Package data section
-#################################
-
-# Retrieve all the data related to the MDANSE package.
-PACKAGE_DATA = find_package_data(where='Src', package='MDANSE_GUI', show_ignored=False)
-
-#################################
-# Scripts section
-#################################
-
-SCRIPTS_PATH = "Scripts"
-SCRIPTS = glob.glob(os.path.join(SCRIPTS_PATH,'mdanse*'))
 
 #################################
 # Documentation
@@ -257,9 +244,7 @@ class mdanse_build_api(mdanse_build_doc):
        license          = PACKAGE_INFO["__license__"],
        packages=find_packages("Src"),
        package_dir={"": "Src"},
-       package_data     = PACKAGE_DATA,
        platforms        = ['Unix','Windows'],
-       scripts          = SCRIPTS,
        cmdclass         = CMDCLASS,
        # entry_points     = {"console_scripts": []}
        install_requires = [pr.requirement for pr in parse_requirements('requirements.txt', session= PipSession())],

README.md

@@ -20,7 +20,7 @@ The current version of MDANSE is currently still at the _alpha_ stage. Once the
 
 ## Quick start
 
-The untested version of MDANSE can be downloaded from GitHub Actions as a Python wheel. There is one wheel for the main code ('MDANSE'), platform depenedent, and another for the GUI ('MDANSE_GUI'). Once downloaded, they can be installed by typing `pip install MDANSE-*.whl`. The GUI script is named *mdanse_gui*, and will be installed in the `bin/` or `Scripts/` directory of your Python virtual environment. Start it by typing `python PATH/TO/mdanse_gui`.
+The untested version of MDANSE can be downloaded from GitHub Actions as a Python wheel. There is one wheel for the main code ('MDANSE'), platform depenedent, and another for the GUI ('MDANSE_GUI'). Once downloaded, they can be installed by typing `pip install MDANSE-*.whl`. The GUI script can be run using the *mdanse_gui* command (*mdanse_gui* on windows).
 
 The typical workflow will look as follows: