refactoring menu system from vnm repo to here

.gitattributes

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+# Forcing UNIX LF line endings for text files added to container
+config/*.sh text eol=lf
+config/rc.xml text eol=lf
+config/.bashrc text eol=lf
+config/panel text eol=lf
+menus/lxde-applications.menu text eol=lf
+menus/vnm-applications.menu text eol=lf
+menus/submenus/*.directory text eol=lf
+menus/applications/*.desktop text eol=lf

menus/apps.json

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+{
+    "AFNI": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "afni 20.1.18": {
+                "version": "20.1.18",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh afni 20.1.18 20200702",
+                "comment": "Install afni 20.1.18",
+                "terminal": true
+            }
+        }
+    },
+    "ANTS": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "ants 2.3.1": {
+                "version": "2.3.1",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh ants 2.3.1 20200701",
+                "comment": "Install ants 2.3.1",
+                "terminal": true
+            },
+            "ants 2.3.4": {
+                "version": "2.3.4",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh ants 2.3.4 20200702",
+                "comment": "Install ants 2.3.4",
+                "terminal": true
+            }
+        }
+    },
+    "Convert3D": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "Convert3D 1.0.0": {
+                "version": "1.0.0",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh convert3d 1.0.0 20200702",
+                "comment": "Install Convert3D 1.0.0",
+                "terminal": true
+            }
+        }
+    },
+    "FreeSurfer": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "FreeSurfer 7.1.0": {
+                "version": "7.1.0",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh freesurfer 7.1.0 20200708",
+                "comment": "Install FreeSurfer 7.1.0",
+                "terminal": true
+            }
+        }
+    },
+    "FSL": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "FSL 6.0.1": {
+                "version": "6.0.1",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh fsl 6.0.1 20200702",
+                "comment": "Install fsl 6.0.1",
+                "terminal": true
+            },
+            "FSL 6.0.2": {
+                "version": "6.0.2",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh fsl 6.0.2 20200701",
+                "comment": "Install fsl 6.0.2",
+                "terminal": true
+            },
+            "FSL 6.0.3": {
+                "version": "6.0.3",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh fsl 6.0.3 20200702",
+                "comment": "Install fsl 6.0.3",
+                "terminal": true
+            }
+        }
+    },
+    "ITK snap": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "ITK snap 3.8.0": {
+                "version": "3.8.0",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh itksnap 3.8.0 20200702 itksnap /root/MRI-crop/MRIcrop-orig.gipl",
+                "comment": "Start ITK snap 3.8.0",
+                "terminal": true
+            }
+        }
+    },
+    "MINC": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "MINC 1.9.17": {
+                "version": "1.9.17",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh minc 1.9.17 20200702",
+                "comment": "Start minc 1.9.17",
+                "terminal": true
+            }
+        }
+    },
+    "MRTrix3": {
+        "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+        "apps": {
+            "mrtrix3 3.0.0": {
+                "version": "3.0.0",
+                "icon": "/root/.config/lxpanel/LXDE/icons/vnm.png",
+                "exec": "bash /usr/share/fetch_and_run.sh mrtrix3 3.0.0 20200709",
+                "comment": "Start mrtrix3 3.0.0",
+                "terminal": true
+            }
+        }
+    }
+}

menus/build_menu.py

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+"""Generate the menu items."""
+import configparser
+import json
+import os
+from pathlib import Path
+import re
+from typing import Text
+import xml.etree.ElementTree as et
+from xml.dom import minidom
+
+
+def add_menu(name: Text, icon: Text) -> None:
+    """Add a submenu to 'VNM' menu.
+
+    Parameters
+    ----------
+    name : Text
+        The name of the submenu.
+    icon : Text
+        The path to the submenu icon inside the image (Starting with
+        ``'/root/.config/lxpanel/LXDE/icons/'`` for Xfce).
+    """
+    print(f"Adding submenu for '{name}'")
+    # Generate `.directory` file
+    entry = configparser.ConfigParser()
+    entry.optionxform = str
+    entry["Desktop Entry"] = {
+        "Name": name.capitalize(),
+        "Comment": name.capitalize(),
+        "Icon": icon,
+        "Type": "Directory",
+    }
+    directories_path = "/usr/share/desktop-directories"
+    directory_name = f"vnm-{name.lower().replace(' ', '-')}.directory"
+    with open(Path(f"{directories_path}/{directory_name}"), "w",) as directory_file:
+        entry.write(directory_file, space_around_delimiters=False)
+    # Add entry to `.menu` file
+    menu_path = Path("/etc/xdg/menus/vnm-applications.menu")
+    with open(menu_path, "r") as xml_file:
+        s = xml_file.read()
+    s = re.sub(r"\s+(?=<)", "", s)
+    root = et.fromstring(s)
+    menu_el = root.findall("./Menu")[0]
+    sub_el = et.SubElement(menu_el, "Menu")
+    name_el = et.SubElement(sub_el, "Name")
+    name_el.text = name.capitalize()
+    dir_el = et.SubElement(sub_el, "Directory")
+    dir_el.text = directory_name
+    include_el = et.SubElement(sub_el, "Include")
+    and_el = et.SubElement(include_el, "And")
+    cat_el = et.SubElement(and_el, "Category")
+    cat_el.text = name.replace(" ", "-")
+    xmlstr = minidom.parseString(et.tostring(root)).toprettyxml(indent="\t")
+    with open(menu_path, "w") as f:
+        f.write('<!DOCTYPE Menu PUBLIC "-//freedesktop//DTD Menu 1.0//EN"\n ')
+        f.write('"http://www.freedesktop.org/standards/menu-spec/1.0/menu.dtd">\n\n')
+        f.write(xmlstr[xmlstr.find("?>") + 3 :])
+    os.chmod(menu_path, 0o644)
+
+
+def add_app(
+    name: Text,
+    version: Text,
+    icon: Text,
+    exec: Text,
+    comment: Text,
+    category: Text,
+    terminal: bool = True,
+) -> None:
+    """Add an application to the menu.
+
+    Parameters
+    ----------
+    name : Text
+        The name of the application.
+    version : Text
+        The version of the applciation.
+    icon : Text
+        The path to the icon of the application (Starting with
+        ``'/root/.config/lxpanel/LXDE/icons/'`` for Xfce).
+    exec : Text
+        The command to run when clicking on the application item.
+    comment : Text
+        The tooltip to show when hovering the item.
+    category : Text
+        The category defining the menu in which the application must be added.
+    terminal : bool
+        If set to ``True``, a terminal is opened when launching the application.
+    """
+    entry = configparser.ConfigParser()
+    entry.optionxform = str
+    entry["Desktop Entry"] = {
+        "Name": name.capitalize(),
+        "GenericName": name.capitalize(),
+        "Comment": comment,
+        "Exec": exec,
+        "Icon": icon,
+        "Type": "Application",
+        "Categories": category,
+        "Terminal": str(terminal).lower(),
+    }
+    applications_path = "/usr/share/applications"
+    desktop_path = Path(
+        f"{applications_path}/vnm-{name.lower().replace(' ', '-')}.desktop"
+    )
+    with open(desktop_path, "w",) as desktop_file:
+        entry.write(desktop_file, space_around_delimiters=False)
+    os.chmod(desktop_path, 0o644)
+
+
+if __name__ == "__main__":
+    # Read applications file
+    with open(Path("./apps.json"), "r") as json_file:
+        menu_entries = json.load(json_file)
+
+    for menu_name, menu_data in menu_entries.items():
+        # Add submenu
+        add_menu(menu_name, menu_data["icon"])
+        for app_name, app_data in menu_data.get("apps", {}).items():
+            # Add application
+            add_app(app_name, category=menu_name.replace(" ", "-"), **app_data)