Move to a package

.gitignore

@@ -3,7 +3,7 @@
 irods-basicGUI/logs/*
 irods-iBridgesGui.spec
 *DS_Store
-
+ibridgesgui/_version.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -10,55 +10,67 @@
 
 ## About
 
-The git repository contains a generic *iRODS* graphical user interface and the corresponding command-line interface clients.  The GUI and CLI work with any *iRODS* instance.  However, for user and data security we depend on some *iRODS* event hooks that need to be installed on the *iRODS* server.  Please refer to the documentation below.
+The git repository contains a generic *iRODS* graphical user interface.  The iRODS functioality is based on [ibridges](https://github.com/UtrechtUniversity/iBridges) and works with any *iRODS* instance.  
+
+
+
+## Highlights
+
+- Works on Windows, Mac OS and Linux
+- Runs on Python 3.9 or higher.
+- Supported iRODS server versions: 4.2.11 or higher and 4.3.0 or higher.
+- **Upload** and **Download** your data.
+- Manipulate the **metadata** on the iRODS server.
+- **Synchronize** your data between your local computer and the iRODS server.
+- **Search** through all metadata for your dataset or collection.
+- Safe default options when working with your data.
+
+## Installation
+- As python package
+
+  ```bash
+  pip install ibridges
+  pip install git+https://github.com/chStaiger/iBridges-Gui.git@develop
+  ```
+- Locally from code (for developers)
+
+  ```bash
+  git clone git@github.com:chStaiger/iBridges-Gui.git
+  cd iBridges-Gui
+  pip install .
+  ```
+
+## Start the GUI
+- From a pip python package
+
+  ```bash
+  ibridges-gui
+  ```
+- From code (for developers)
+
+  ```bash
+  python ibridgesgui/__main__.py
+  ```
+
+
 
 ## Authors
+**Christine Staiger (Maintainer) [ORCID](https://orcid.org/0000-0002-6754-7647)**
 
-Tim van Daalen, Christine Staiger
+- *Wageningen University & Research* 2021 - 2022
+- *Utrecht University* 2022
 
-Wageningen University & Research 2021
+**Tim van Daalen**, *Wageningen University & Research* 2021
 
-## Contributors
-
-J.P. Mc Farland
-
-University of Groningen, Center for Information Technology, 2022
-
-## Dependencies
-
-### Supported iRODS versions
-
-- 4.2.11, 4.2.12
-- 4.3.0
-
-### Python
+**Maarten Schermer (Maintainer) [ORCID](https://orcid.org/my-orcid?orcid=0000-0001-6770-3155)**, *Utrecht University* 2023
 
-- Python 3 (>= 3.9)
-  - Tested with python versions 3.9 and 3.10 on Windows, Ubuntu20.22 and MacOs
-- pip-22.2.2
-- Python packages (see install via `requirements.txt` below)
+**Raoul Schram (Maintainer) [ORCID](https://orcid.org/my-orcid?orcid=0000-0001-6616-230X)**. 
+*Utrecht University* 2023
 
-Install dependencies with, for example:
-
-```sh
-python3.10 -m pip install -r requirements.txt
-```
-### icommands (optional)
-If the icommands are installed, the users can choose them as backend for up and downloads.
-
-## Usage
-```
-export PYTHON_IRODSCLIENT_DEFAULT_XML=QUASI_XML
-./iBridges.py
-```
-
-
-
-Please consult the documentation for more information about the configuration: 
-
+## Contributors
 
-<p align="center">
-    <a href="https://chstaiger.github.io/iBridges-Gui/docs/getting-started.html#configuration"><strong> iBridges Configuration »</strong></a> .
+**J.P. Mc Farland**,
+*University of Groningen, Center for Information Technology*, 2022
 
 ## Contributing
 ### Code

gui/IrodsExampleTab.py → ibridgesgui/IrodsExampleTab.py

@@ -1,15 +1,17 @@
 import logging
 import sys
 
+import meta
 import PyQt6.QtCore
 import PyQt6.QtGui
 import PyQt6.QtWidgets
 import PyQt6.uic
-
-import gui
-import meta
 import utils
-from gui.irodsTreeView import IrodsModel
+
+import ibridgesgui as gui
+from ibridgesgui.gui_utils import UI_FILE_DIR
+from ibridgesgui.irodsTreeView import IrodsModel
+
 
 class IrodsExampleTab(PyQt6.QtWidgets.QWidget,
                    gui.ui_files.ExampleTab.Ui_ExampleTab):
@@ -19,7 +21,7 @@ def __init__(self):
         if getattr(sys, 'frozen', False):
             super().setupUi(self)
         else:
-            PyQt6.uic.loadUi("gui/ui_files/ExampleTab.ui", self)
+            PyQt6.uic.loadUi(UI_FILE_DIR / "ExampleTab.ui", self)
         self.error_label.setText("Whooohoo")
 
         self.ienv_dict = self.context.irods_environment.config

gui/IrodsInfo.py → ibridgesgui/IrodsInfo.py

@@ -6,10 +6,11 @@
 import PyQt6
 import PyQt6.QtWidgets
 import PyQt6.uic
-
 from ibridges.resources import Resources
-import gui
-from gui.gui_utils import populate_table
+
+import ibridgesgui as gui
+from ibridgesgui.gui_utils import UI_FILE_DIR, populate_table
+
 
 class IrodsInfo(PyQt6.QtWidgets.QWidget,
                 gui.ui_files.tabInfo.Ui_tabInfo):
@@ -22,7 +23,7 @@ def __init__(self, session):
         if getattr(sys, 'frozen', False):
             super().setupUi(self)
         else:
-            PyQt6.uic.loadUi("gui/ui_files/tabInfo.ui", self)
+            PyQt6.uic.loadUi(UI_FILE_DIR / "tabInfo.ui", self)
         self.session = session
 
         self.refreshButton.clicked.connect(self.refresh_info)

gui/IrodsLogin.py → ibridgesgui/IrodsLogin.py

@@ -3,12 +3,14 @@
 import sys
 from pathlib import Path
 
+from ibridges import Session
+from ibridges.session import LoginError, PasswordError
 from PyQt6.QtWidgets import QDialog, QLineEdit
 from PyQt6.uic import loadUi
 
-from gui.ui_files.irodsLogin import Ui_irodsLogin
-from ibridges import Session
-from ibridges.session import LoginError, PasswordError
+from ibridgesgui.gui_utils import UI_FILE_DIR
+from ibridgesgui.ui_files.irodsLogin import Ui_irodsLogin
+
 
 class IrodsLogin(QDialog, Ui_irodsLogin):
     """Definition and initialization of the iRODS login window.
@@ -20,7 +22,7 @@ def __init__(self, session_dict):
         if getattr(sys, 'frozen', False):
             super().setupUi(self)
         else:
-            loadUi("gui/ui_files/irodsLogin.ui", self)
+            loadUi(UI_FILE_DIR / "irodsLogin.ui", self)
 
         self.session_dict = session_dict
         self.irods_path = Path('~', '.irods').expanduser()

iBridges.py → ibridgesgui/__main__.py

@@ -2,15 +2,16 @@
 """iBridges GUI startup script."""
 import os
 import sys
-import setproctitle
 
 import PyQt6.QtWidgets
 import PyQt6.uic
+import setproctitle
 
-from gui import ui_files
-from gui.info import Info
-from gui.login import Login
-from gui.browser import Browser
+from ibridgesgui import ui_files
+from ibridgesgui.browser import Browser
+from ibridgesgui.gui_utils import UI_FILE_DIR
+from ibridgesgui.info import Info
+from ibridgesgui.login import Login
 
 # Global constants
 THIS_APPLICATION = 'iBridges-GUI'
@@ -30,7 +31,7 @@ def __init__(self, widget):
         if getattr(sys, 'frozen', False):
             super().setupUi(self)
         else:
-            PyQt6.uic.loadUi('gui/ui_files/MainMenu.ui', self)
+            PyQt6.uic.loadUi(UI_FILE_DIR/'MainMenu.ui', self)
 
         self.ui_tabs_lookup = {
             'tabBrowser': self.init_browser_tab,
@@ -100,9 +101,7 @@ def init_browser_tab(self):
         self.tabWidget.addTab(self.irods_browser, "Browser")
 
 def main():
-    """Main function
-
-    """
+    """Main function"""
     # Initialize logger first because Context may want to log as well.
     application_name = THIS_APPLICATION
     setproctitle.setproctitle(application_name)

gui/browser.py → ibridgesgui/browser.py

@@ -7,19 +7,24 @@
 import PyQt6.QtGui
 import PyQt6.QtWidgets
 import PyQt6.uic
-
-from ibridges import get_collection, get_dataobject
-from ibridges import upload, download
-from ibridges import IrodsPath
+from ibridges import IrodsPath, download, get_collection, get_dataobject, upload
 from ibridges.data_operations import obj_replicas
 from ibridges.meta import MetaData
 from ibridges.permissions import Permissions
 
-import gui.popup_widgets
-from gui.gui_utils import populate_table, get_irods_item, get_coll_dict, get_downloads_dir
+import ibridgesgui as gui
+import ibridgesgui.popup_widgets
+from ibridgesgui.gui_utils import (
+    UI_FILE_DIR,
+    get_coll_dict,
+    get_downloads_dir,
+    get_irods_item,
+    populate_table,
+)
+
 
 class Browser(PyQt6.QtWidgets.QWidget,
-                   gui.ui_files.tabBrowser.Ui_tabBrowser):
+              gui.ui_files.tabBrowser.Ui_tabBrowser):
     """Browser view for iRODS session.
 
     """
@@ -32,7 +37,7 @@ def __init__(self, session):
         if getattr(sys, 'frozen', False):
             super().setupUi(self)
         else:
-            PyQt6.uic.loadUi("gui/ui_files/tabBrowser.ui", self)
+            PyQt6.uic.loadUi(UI_FILE_DIR / "tabBrowser.ui", self)
 
         self.session = session
         self.viewTabs.setCurrentIndex(0)

gui/checkableFsTree.py → ibridgesgui/checkableFsTree.py

@@ -1,10 +1,12 @@
-from PyQt6.QtWidgets import QFileIconProvider, QMessageBox
-from PyQt6.QtCore import QFile, Qt, QDir
-from PyQt6.QtGui import QFileSystemModel, QStandardItemModel, QStandardItem
-from sys import platform
-from time import sleep
 import logging
 import os
+from sys import platform
+from time import sleep
+
+from PyQt6.QtCore import QDir, QFile, Qt
+from PyQt6.QtGui import QFileSystemModel, QStandardItem, QStandardItemModel
+from PyQt6.QtWidgets import QFileIconProvider, QMessageBox
+
 
 # a class to put checkbox on the folders and record which ones are checked.
 class checkableFsTreeModel(QFileSystemModel):

gui/gui_utils.py → ibridgesgui/gui_utils.py

@@ -1,17 +1,21 @@
 """Handy and reusable functions for the GUI"""
-import PyQt6
-import irods
 import pathlib
+from importlib.resources import files
 
+import irods
+import PyQt6
 from ibridges import get_collection, get_dataobject
 
+UI_FILE_DIR = files(__package__) / "ui_files"
+
+
 def populate_table(tableWidget, rows, data_by_row):
 
     tableWidget.setRowCount(rows)
     for row, data in enumerate(data_by_row):
         for col, item in enumerate(data):
             tableWidget.setItem(row, col, PyQt6.QtWidgets.QTableWidgetItem(str(item)))
-    tableWidget.resizeColumnsToContents()    
+    tableWidget.resizeColumnsToContents()
 
 def get_irods_item(irods_path):
     try:

gui/info.py → ibridgesgui/info.py

@@ -6,10 +6,11 @@
 import PyQt6
 import PyQt6.QtWidgets
 import PyQt6.uic
-
 from ibridges.resources import Resources
-import gui
-from gui.gui_utils import populate_table
+
+import ibridgesgui as gui
+from ibridgesgui.gui_utils import populate_table, UI_FILE_DIR
+
 
 class Info(PyQt6.QtWidgets.QWidget, gui.ui_files.tabInfo.Ui_tabInfo):
     """Set iRODS information in the GUI"""
@@ -19,7 +20,7 @@ def __init__(self, session):
         if getattr(sys, 'frozen', False):
             super().setupUi(self)
         else:
-            PyQt6.uic.loadUi("gui/ui_files/tabInfo.ui", self)
+            PyQt6.uic.loadUi(UI_FILE_DIR / "tabInfo.ui", self)
         self.session = session
 
         self.refreshButton.clicked.connect(self.refresh_info)

gui/irodsSearch.py → ibridgesgui/irodsSearch.py

@@ -5,12 +5,13 @@
 import os
 import sys
 
-from PyQt6 import QtWidgets, QtGui, QtCore
+import utils
+from PyQt6 import QtCore, QtGui, QtWidgets
 from PyQt6.QtWidgets import QDialog, QMessageBox
 from PyQt6.uic import loadUi
 
-from gui.ui_files.searchDialog import Ui_searchDialog
-import utils
+from ibridgesgui.gui_utils import UI_FILE_DIR
+from ibridgesgui.ui_files.searchDialog import Ui_searchDialog
 
 
 class irodsSearch(QDialog, Ui_searchDialog):
@@ -32,7 +33,7 @@ def __init__(self, collTable):
         if getattr(sys, 'frozen', False):
             super().setupUi(self)
         else:
-            loadUi("gui/ui_files/searchDialog.ui", self)
+            loadUi(UI_FILE_DIR / "searchDialog.ui", self)
 
         self.conn = self.context.irods_connector
 

gui/irodsTreeView.py → ibridgesgui/irodsTreeView.py

@@ -13,7 +13,6 @@
 import PyQt6.QtCore
 import PyQt6.QtGui
 import PyQt6.QtWidgets
-
 import utils
 
 ACCESS_NAMES = [