use json mechanism

code/plugins/construct_plugin_json.py

@@ -0,0 +1,17 @@
+import json
+ordering = ['ICLabel', 'dipfit', 'EEG-BIDS', 'roiconnect', 'amica', 'cleanline', 'clean_rawdata', 'SIFT', 'zapline-plus', 'eegstats', 'trimOutlier', 'fMRIb', 'imat', 'nwbio', 'NIMA', 'PACT', 'NFT', 'PACTools', 'ARfitStudio', 'PowPowCAT', 'relica', 'std_dipoleDensity', 'viewprops', 'firfilt', 'groupSIFT', 'get_chanlocs', 'nsgportal']
+naming = ['ICLabel', 'dipfit', 'EEG-BIDS', 'roiconnect', 'amica', 'cleanline', 'clean_rawdata', 'SIFT', 'zapline-plus', 'eegstats', 'trimOutlier', 'fMRIb', 'imat', 'nwbio', 'NIMA', 'PACT', 'NFT', 'PACTools', 'ARfitStudio', 'PowPowCAT', 'relica', 'std_dipoleDensity', 'viewprops', 'firfilt', 'groupSIFT', 'get_chanlocs', 'nsgportal']
+wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'EEG-BIDS', 'nsgportal', 'clean_rawdata', 'amica', 'LIMO']
+readme_plugins = list(set(ordering) - set(wiki_plugins))
+
+plugin_json = []
+for plugin in ordering:
+     ptype = 'wiki' if plugin in wiki_plugins else 'readme'
+     link = f'https://github.com/sccn/{plugin}'
+     plugin_json.append({'plugin': plugin, 
+                         'name': naming[ordering.index(plugin)],
+                         'type': ptype, 
+                         'link': link})
+
+with open('plugins.json', 'w') as out:
+    json.dump(plugin_json, out, indent=2)

code/plugins/plugins.json

@@ -0,0 +1,164 @@
+[
+  {
+    "plugin": "ICLabel",
+    "name": "ICLabel",
+    "type": "readme",
+    "link": "https://github.com/sccn/ICLabel"
+  },
+  {
+    "plugin": "dipfit",
+    "name": "dipfit",
+    "type": "readme",
+    "link": "https://github.com/sccn/dipfit"
+  },
+  {
+    "plugin": "EEG-BIDS",
+    "name": "EEG-BIDS",
+    "type": "wiki",
+    "link": "https://github.com/sccn/EEG-BIDS"
+  },
+  {
+    "plugin": "roiconnect",
+    "name": "roiconnect",
+    "type": "readme",
+    "link": "https://github.com/sccn/roiconnect"
+  },
+  {
+    "plugin": "amica",
+    "name": "amica",
+    "type": "wiki",
+    "link": "https://github.com/sccn/amica"
+  },
+  {
+    "plugin": "cleanline",
+    "name": "cleanline",
+    "type": "readme",
+    "link": "https://github.com/sccn/cleanline"
+  },
+  {
+    "plugin": "clean_rawdata",
+    "name": "clean_rawdata",
+    "type": "wiki",
+    "link": "https://github.com/sccn/clean_rawdata"
+  },
+  {
+    "plugin": "SIFT",
+    "name": "SIFT",
+    "type": "wiki",
+    "link": "https://github.com/sccn/SIFT"
+  },
+  {
+    "plugin": "zapline-plus",
+    "name": "zapline-plus",
+    "type": "readme",
+    "link": "https://github.com/sccn/zapline-plus"
+  },
+  {
+    "plugin": "eegstats",
+    "name": "eegstats",
+    "type": "readme",
+    "link": "https://github.com/sccn/eegstats"
+  },
+  {
+    "plugin": "trimOutlier",
+    "name": "trimOutlier",
+    "type": "readme",
+    "link": "https://github.com/sccn/trimOutlier"
+  },
+  {
+    "plugin": "fMRIb",
+    "name": "fMRIb",
+    "type": "readme",
+    "link": "https://github.com/sccn/fMRIb"
+  },
+  {
+    "plugin": "imat",
+    "name": "imat",
+    "type": "readme",
+    "link": "https://github.com/sccn/imat"
+  },
+  {
+    "plugin": "nwbio",
+    "name": "nwbio",
+    "type": "readme",
+    "link": "https://github.com/sccn/nwbio"
+  },
+  {
+    "plugin": "NIMA",
+    "name": "NIMA",
+    "type": "readme",
+    "link": "https://github.com/sccn/NIMA"
+  },
+  {
+    "plugin": "PACT",
+    "name": "PACT",
+    "type": "readme",
+    "link": "https://github.com/sccn/PACT"
+  },
+  {
+    "plugin": "NFT",
+    "name": "NFT",
+    "type": "wiki",
+    "link": "https://github.com/sccn/NFT"
+  },
+  {
+    "plugin": "PACTools",
+    "name": "PACTools",
+    "type": "readme",
+    "link": "https://github.com/sccn/PACTools"
+  },
+  {
+    "plugin": "ARfitStudio",
+    "name": "ARfitStudio",
+    "type": "readme",
+    "link": "https://github.com/sccn/ARfitStudio"
+  },
+  {
+    "plugin": "PowPowCAT",
+    "name": "PowPowCAT",
+    "type": "readme",
+    "link": "https://github.com/sccn/PowPowCAT"
+  },
+  {
+    "plugin": "relica",
+    "name": "relica",
+    "type": "readme",
+    "link": "https://github.com/sccn/relica"
+  },
+  {
+    "plugin": "std_dipoleDensity",
+    "name": "std_dipoleDensity",
+    "type": "readme",
+    "link": "https://github.com/sccn/std_dipoleDensity"
+  },
+  {
+    "plugin": "viewprops",
+    "name": "viewprops",
+    "type": "readme",
+    "link": "https://github.com/sccn/viewprops"
+  },
+  {
+    "plugin": "firfilt",
+    "name": "firfilt",
+    "type": "readme",
+    "link": "https://github.com/sccn/firfilt"
+  },
+  {
+    "plugin": "groupSIFT",
+    "name": "groupSIFT",
+    "type": "readme",
+    "link": "https://github.com/sccn/groupSIFT"
+  },
+  {
+    "plugin": "get_chanlocs",
+    "name": "get_chanlocs",
+    "type": "wiki",
+    "link": "https://github.com/sccn/get_chanlocs"
+  },
+  {
+    "plugin": "nsgportal",
+    "name": "nsgportal",
+    "type": "wiki",
+    "link": "https://github.com/sccn/nsgportal"
+  }
+]

code/plugins/reformat_plugin.py

@@ -12,13 +12,13 @@ def reformat_wiki_pages(filepath, filename, parent, output_file, wiki_input_dir=
 grand_parent: Plugins
 '''.format(filename=filename, parent=parent)
 
-    if parent == "nsgportal":
+    if parent in ["nsgportal", "LIMO"]:
         pages = []
         # load _Sidebar.md and extract all links from markdown file
         with open(os.path.join(wiki_input_dir, '_Sidebar.md')) as f:
             lines = f.readlines()
             for line in lines:
-                if line.startswith('*'):
+                if '(' in line:
                     # extract text between square brackets
                     page = line[line.find('(')+1:line.find(')')]
                     pages.append(page)

code/plugins/update_plugins.py

@@ -1,14 +1,15 @@
 import os
 import subprocess
 import sys
+import json
 
 def run_command(command):
     result = subprocess.run(command, shell=True, capture_output=False, text=True)
     if result.returncode != 0:
         print(f"Command failed: {command}\nError: {result.stderr}")
     return result
 
-def update_repo(repo, order, plugin_type='readme'):
+def update_repo(repo, order, plugin_type='readme', plugin_link="https://github.com/sccn"):
     print(f"Updating {repo}...")
     current_dir = os.getcwd()
     repo_path = os.path.join(current_dir, 'github', repo)
@@ -17,15 +18,15 @@ def update_repo(repo, order, plugin_type='readme'):
         os.chdir(repo_path)
         run_command('git pull')
     else:
-        run_command(f'git clone https://github.com/sccn/{repo}.git {repo_path}')
+        run_command(f'git clone {plugin_link}.git {repo_path}')
 
     if plugin_type == "wiki":
         wiki_repo_path = f"{repo_path}.wiki"
         if os.path.exists(wiki_repo_path):
             os.chdir(wiki_repo_path)
             run_command('git pull')
         else:
-            run_command(f'git clone https://github.com/sccn/{repo}.wiki.git {wiki_repo_path}')
+            run_command(f'git clone {plugin_link}.wiki.git {wiki_repo_path}')
 
     os.chdir(current_dir)
     script = 'reformat_plugin.py'
@@ -36,28 +37,26 @@ def update_repo(repo, order, plugin_type='readme'):
     # if 'github' not in current directory, create it
     if not os.path.exists('github'):
         os.makedirs('github')
-    wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'EEG-BIDS', 'nsgportal', 'clean_rawdata', 'amica']
-    readme_plugins = ['ARfitStudio', 'roiconnect', 'trimOutlier', 'PACT', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
-    ordering = ['ICLabel', 'dipfit', 'EEG-BIDS', 'roiconnect', 'amica', 'cleanline', 'clean_rawdata', 'SIFT', 'zapline-plus', 'eegstats', 'trimOutlier', 'fMRIb', 'imat', 'nwbio', 'NIMA', 'PACT', 'NFT', 'PACTools', 'ARfitStudio', 'PowPowCAT', 'relica', 'std_dipoleDensity', 'viewprops', 'firfilt', 'groupSIFT', 'get_chanlocs', 'nsgportal']
+
+    if not os.path.exists('plugins.json'):
+        print('Error: plugins.json not found.')
+        sys.exit(1)
+    plugin_info = json.load(open('plugins.json'))
+    plugins = [plugin['plugin'] for plugin in plugin_info]
+    # wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'EEG-BIDS', 'nsgportal', 'clean_rawdata', 'amica', 'LIMO']
+    # readme_plugins = ['ARfitStudio', 'roiconnect', 'trimOutlier', 'PACT', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
+    # ordering = ['ICLabel', 'dipfit', 'EEG-BIDS', 'roiconnect', 'amica', 'cleanline', 'clean_rawdata', 'SIFT', 'zapline-plus', 'eegstats', 'trimOutlier', 'fMRIb', 'imat', 'nwbio', 'NIMA', 'PACT', 'NFT', 'PACTools', 'ARfitStudio', 'PowPowCAT', 'relica', 'std_dipoleDensity', 'viewprops', 'firfilt', 'groupSIFT', 'get_chanlocs', 'nsgportal']
 
     if len(sys.argv) == 1:
-        order = 1
-        for plugin in wiki_plugins:
-            update_repo(plugin, order, 'wiki')
-            order += 1
-        for plugin in readme_plugins:
-            update_repo(plugin, order, "readme")
-            order += 1
+        for plugin in plugin_info:
+            update_repo(plugin['plugin'], plugins.index(plugin['plugin']), plugin['type'], plugin['link'])
     elif len(sys.argv) == 2:
         plugin_name = sys.argv[1]
-        if plugin_name not in wiki_plugins and plugin_name not in readme_plugins:
+        if plugin_name not in plugins:
             print(f"Plugin {plugin_name} not found.")
             sys.exit(1)
-
-        plugin_type = 'wiki' if plugin_name in wiki_plugins else 'readme'
-        plugin_order = ordering.index(plugin_name) + 1
-
-        update_repo(plugin_name, plugin_order, plugin_type)
+        plugin = plugin_info[plugins.index(plugin_name)]
+        update_repo(plugin['plugin'], plugins.index(plugin['plugin']), plugin['type'], plugin['link'])
     else:
         print('Usage: python update_plugins.py <plugin_name>')
         sys.exit(1)

plugins/ARfitStudio/index.md

@@ -4,7 +4,7 @@ title: ARfitStudio
 long_title: ARfitStudio
 parent: Plugins
 has_children: true
-nav_order: 8
+nav_order: 18
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/ARfitStudio).
 

plugins/EEG-BIDS/index.md

@@ -4,7 +4,7 @@ title: EEG-BIDS
 long_title: EEG-BIDS
 parent: Plugins
 has_children: true
-nav_order: 4
+nav_order: 2
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/EEG-BIDS).
 

plugins/ICLabel/index.md

@@ -4,7 +4,7 @@ title: ICLabel
 long_title: ICLabel
 parent: Plugins
 has_children: true
-nav_order: 14
+nav_order: 0
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/ICLabel).
 

plugins/NFT/index.md

@@ -4,7 +4,7 @@ title: NFT
 long_title: NFT
 parent: Plugins
 has_children: true
-nav_order: 3
+nav_order: 16
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/NFT).
 

plugins/NIMA/index.md

@@ -4,7 +4,7 @@ title: NIMA
 long_title: NIMA
 parent: Plugins
 has_children: true
-nav_order: 26
+nav_order: 14
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/NIMA).
 

plugins/PACT/index.md

@@ -4,7 +4,7 @@ title: PACT
 long_title: PACT
 parent: Plugins
 has_children: true
-nav_order: 11
+nav_order: 15
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/PACT).
 

plugins/PACTools/index.md

@@ -4,7 +4,7 @@ title: PACTools
 long_title: PACTools
 parent: Plugins
 has_children: true
-nav_order: 18
+nav_order: 17
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/PACTools).
 

plugins/PowPowCAT/index.md

@@ -4,7 +4,7 @@ title: PowPowCAT
 long_title: PowPowCAT
 parent: Plugins
 has_children: true
-nav_order: 17
+nav_order: 19
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/PowPowCAT).
 

plugins/SIFT/index.md

@@ -4,7 +4,7 @@ title: SIFT
 long_title: SIFT
 parent: Plugins
 has_children: true
-nav_order: 1
+nav_order: 7
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/SIFT).
 

plugins/amica/index.md

@@ -4,7 +4,7 @@ title: amica
 long_title: amica
 parent: Plugins
 has_children: true
-nav_order: 7
+nav_order: 4
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/amica).
 

plugins/cleanline/index.md

@@ -4,7 +4,7 @@ title: cleanline
 long_title: cleanline
 parent: Plugins
 has_children: true
-nav_order: 25
+nav_order: 5
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/cleanline).
 

plugins/dipfit/index.md

@@ -4,7 +4,7 @@ title: dipfit
 long_title: dipfit
 parent: Plugins
 has_children: true
-nav_order: 15
+nav_order: 1
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/dipfit).
 

plugins/eegstats/index.md

@@ -4,7 +4,7 @@ title: eegstats
 long_title: eegstats
 parent: Plugins
 has_children: true
-nav_order: 16
+nav_order: 9
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/eegstats).